diff options
102 files changed, 3886 insertions, 8225 deletions
diff --git a/.Rbuildignore b/.Rbuildignore index 4159cc9..99c6d74 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,12 +1,12 @@ ^pfm_.*.tar.gz ^pfm_.*.zip +^pfm.Rcheck$ ^GNUmakefile$ ^README.html$ -^build.log$ -^test.log$ +^log ^test.R$ +^pesticide.txt$ ^inst/extdata/Tabelle\ der\ Abdrifteckwerte.xls$ -^inst/extdata/FOCUS_Step_12_scenarios.txt$ ^_pkgdown.yml$ ^\.travis\.yml$ ^docs$ diff --git a/ChangeLog b/ChangeLog deleted file mode 100644 index 0ad0374..0000000 --- a/ChangeLog +++ /dev/null @@ -1,1561 +0,0 @@ -commit df4034c64aa3590c3911dca88b066332dc8e4df1 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-11 14:35:37 +0100 - - Simplify travis config - -commit f4e22fc28fa0b05b05c8a1277333777635802e86 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-11 13:46:24 +0100 - - Try to simplify drat configuration - -commit 6bc40dbd4e7c76179009a501ae168f0fa73f2be2 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-11 12:12:09 +0100 - - Disable bspm to make install from drat work - -commit 96b6f8954d4eb9ec5b8ee9209074d21fdd67f966 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-11 12:04:15 +0100 - - Fix last commit - -commit c9e9f1312e7b73c8596d2d01324fcb67c000f3e9 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-11 12:00:39 +0100 - - Install drat to use it... - -commit b0a7a94ac0a7070e8612e443b4aa485beb07b85d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-11 11:57:20 +0100 - - Another attempt to make drat work on travis - -commit 854cc695a1f64a9b37957fdcd81c1ce23a6a2d69 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-11 11:52:53 +0100 - - Try to make drat work - -commit c463f9fb197f70f97831b3648bc398be8ff9ae7d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-11 11:41:40 +0100 - - mkin was not pulled from the drat repo - -commit f3ba961b6be63d3995cccea2968d7b2fb907ca16 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-11 11:35:27 +0100 - - Use drat instead of install_github - -commit 510416bc07eb7b3197c20d687f6c51a032cfbfec -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-11 11:12:59 +0100 - - Forgot to commit .travis.yml ... - -commit f21a53421dc481604c681c2be8438c8a8b5db23d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-11 10:58:46 +0100 - - mkin and chents from github for check on travis - -commit e63dbdf1fdae0abc7246f721357504798309033d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-11 10:52:07 +0100 - - Don't force suggested packages - -commit 60a217ecc9a035ab956bd4229da6ad4c654e7d6e -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-11 10:37:13 +0100 - - Remove Remotes: field from DESCRIPTION - - It causes trouble with remotes::install_deps() on travis, see the - various previous build logs. - -commit 3ef243d18b7972eb8cb4a561ac07d93b46df13a5 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-11 10:06:39 +0100 - - Fix call to download.file for debugging - -commit 9f977cb5d9657d0066598cda38908282dadae0c4 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-11 10:02:57 +0100 - - Try to debug the failure in remotes::install_deps - -commit 6681356b8abab27f0735341ed6d3a44e1374e2e5 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-11 09:00:41 +0100 - - Typo, remove PELMO related suggestions - - PELMO related functions are not used in pfm, so apart from advertising, - these suggestions did not do anything. - -commit 3e82035d2753d031401f80833de8939740491bd0 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-10 17:17:03 +0100 - - Revert standalone option for remotes on travis - -commit 9f28f36b00c156ff9c78790302c6fc74e0195651 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-10 16:48:27 +0100 - - Yet another attempt on remotes on travis - -commit 4f315619d56a191a80d2223913ee976d96ae5f97 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-10 16:43:39 +0100 - - Another attempt to make remotes work on travis - -commit 8d03f6ae52e6c45e3da93e41b15eb5f853ab6d17 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-10 16:35:33 +0100 - - Try to make remotes work - -commit e46ee27b218dde8ebb948e8b3b28e9cd8250bc70 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-10 16:27:12 +0100 - - Skip BSPM, it's the default - -commit f41d1759b890613895879f36e69e9928dd517f0e -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-10 15:49:36 +0100 - - Only install dependencies, as chents fails to install - -commit 7a54d9b65fc55e28411126b97c542fb4c180c0a7 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-10 15:43:43 +0100 - - Use Dirks run.sh on travis - -commit a0364c2561dda4c4b67e7e3b6830719b4ed60916 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2022-11-10 12:17:34 +0100 - - set_nd_nq is now in mkin, fix Steps12 bug - - If a scenario with a slash "/" was selected in PEC_sw_focus(), - the Step 2 file generated giving an error (path not found) in the - Steps12 calculator, because the scenario name is part of the "compound" - name in this implementation, in order to show it in the list that the - calculator presents. - -commit aa0c59c7a3ede267730fe85f9e27b1814f9e897a -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2021-11-19 00:18:41 +0100 - - Update static docs - -commit f4e35b0bf9c4de0b5c6235f5cf9e284faf40569f -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2021-11-19 00:17:33 +0100 - - Update docs and logs - -commit 6e3917d814500d5af43702b4d4be1e44cefc00d4 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2021-11-18 11:22:44 +0100 - - Update README after changing default branch to main - -commit e0029129aec8b92d58aea8552006002c5fe409f5 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2021-02-10 09:29:33 +0100 - - Treat Kfoc = 0 like Exposit in runoff calcs - -commit c97a4f5a9fe30ffc3321681a97eea167cfc427b5 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2020-07-23 12:22:25 +0200 - - PEC_sw_drift: Rautmann formula (1 app, Ackerbau) - - This makes it possible to calculate drift PECsw for other distances than - present in the JKI data or the Rautmann paper. - -commit 90fa42c86596c85168931148bf8d5fa014fa7794 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2020-07-23 10:51:39 +0200 - - Update docs, use R6 support of roxygen - -commit df70d80d9ef13b69e58de6f47b9041b6a021025e -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2020-07-21 15:50:21 +0200 - - Clean test.log after testing - -commit 512cd50874b060d50a14d28df88018ac144cf6d3 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2020-07-07 12:36:56 +0200 - - Remove copyright headers, update TOXSWA_cwa test - - - The window column of the windows component of a TOXSWA_cwa object is not - a factor any more, but a character vector. - - testthat::expect_equal_to_reference is replaced by - testthat::expect_known_output, so we can have git diff show what has - changed - -commit 58c6214f459b28b899794f32a60836aef97ac01b -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2020-07-07 11:27:44 +0200 - - Adapt pfm_degradation to current mkin - - use_of_ff = "max" is now the default - -commit e3bc264df69f892e9ad990be22d3ec1b22041daa -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2020-06-17 13:37:59 +0200 - - TSCF estimation equations, update docs - - Briggs et al. (1982) and Dettenmaier et al. (2009) - -commit e505ecc4aba0f6719fd772faa2655dd824a6930d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2020-04-17 09:51:33 +0200 - - Skip testing on R-devel - - it currently fails with - - ✖ | 6 1 | Read and analyse TOXSWA cwa files [6.4 s] - ──────────────────────────────────────────────────────────────────────────────────────────────────── - test_TOXSWA.R:68: failure: Getting events and moving window analysis works - H_sw_R1_stream$windows has changed from known value recorded in 'H_sw_R1_stream_windows.rds'. - Component "window": Modes: character, numeric - Component "window": Attributes: < target is NULL, current is list > - Component "window": target is character, current is factor - -commit d81550d0cccae824cc748de48e7fd50ea8d8033a -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2020-04-16 18:02:18 +0200 - - Make na.rm = FALSE the default for geomean() - - This makes more sense and is in line with mean() from base R. Adapt - tests and update docs. - -commit 4bc95b3e4aae22e4052e0a4c905a9227c909e2cd -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2020-02-19 07:49:08 +0100 - - Check in last build log - -commit 00e177fdf6929058fd26c3086ae159462ae0a456 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-10-23 16:18:24 +0200 - - Fix static docs for set_nd_nq - -commit a23fdf1152744341bd73f22f9b86951987125e6d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-10-23 16:15:38 +0200 - - Updated ChangeLog and DESCRIPTION - -commit 020bce41dd821b5949f824eaa3a2998584a14585 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-10-15 11:27:59 +0200 - - Residue processing for depth profiles over time - -commit a2ca8be6f5593f0afd833ea73b62149055ee84f9 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-10-10 14:56:35 +0200 - - Do not mess with zero values at time zero - -commit a071d46f698397a6c8247e19eceb0fcd5f139056 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-10-10 12:25:42 +0200 - - Fix set_nd for metabolites, handle zero at time zero - -commit a5503d3e26408f7308a7bf4da617205b93d17422 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-10-10 09:21:46 +0200 - - Fix documentation for set_nd - -commit a5e458ecb33ae87e46b2237174a194f6252a97cf -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-10-10 08:53:30 +0200 - - Finish documentation of set_nd and test it - -commit 63df3871a442de4bf47e4d9de1449e7f6ed65b2f -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-10-09 19:17:07 +0200 - - Function to set non-detects in residue series - -commit 9f848a9518aabf162723271bafba244221ee83ed -Author: Johannes Ranke <johannes.ranke@jrwb.de> -Date: 2019-09-27 12:55:03 +0200 - - Built windows binary for drat - -commit 435e07a6f7fd2599d783fd306ee6d9e08acc0c6b -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-09-27 10:00:15 +0200 - - Fix for UK drainage, some EFSA interception and washoff - - - PEC_sw_drainage_UK() gave results that were a little bit too high - for the substances with the highest Koc (>4000), as I used 0.01% instead - of 0.008% for them. This must have come from an old vesion of the UK - data requirements handbook, at least I do not have another explanation - - - Add EFSA interception (from 2014 DegT50 guidance) and tier 1 - crop wash-off factors (from 2017 PEC soil guidance) for some major - arable crops - - - Update docs - -commit 803fe13e505960fddccdbd4dcb524715f5eb068d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-09-18 18:18:40 +0200 - - Add url: tag to _pkgdown.yml, typo, update docs - -commit 8deaa29a659630a40e8b11df1fa3ebbbd9ca9e68 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-07-01 08:04:40 +0200 - - Typo - -commit 37a1513d73201dbacc71af3c33a2a2a4e798583c -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-06-12 18:15:46 +0200 - - Update of static docs - -commit 5c9dd5c269acc4a6e6e32a7e599afb8f98d8ca36 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-06-12 18:14:46 +0200 - - Documentation fix - -commit 069824057caf8e57507852b858a7ecfd8e13e49a -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-05-14 12:41:16 +0200 - - Version bump and doc update - -commit 41f3c867008c24b69a9bb0e5c7c084969d46bebd -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-05-14 12:33:21 +0200 - - Add Exposit version 3.01a2 for runoff calculations - - At the request of Muris Korkaric (Agroscope). This is for 3 m buffer - only and provides consistency with earlier calculations - -commit 7b11b5d0da29447df026002af3ae5283510fdae9 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-04-29 13:03:00 +0200 - - Additional runoff data used by Agroscope - -commit 67cd9e04caaf18a40231262c9033fb24e8bb2a66 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-04-26 13:45:44 +0200 - - Formatting improvement for the online docs - -commit 45f540ef19fd2a2a80e3f3f72950933ed6396f0c -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-04-26 13:33:27 +0200 - - Another take on completing the drift data - - The R script I used yesterday got lost because I used the .Rd file - that got overwritten by roxygen later. - -commit 451b332c8888bac8279340b086abb3b714ac3ae1 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-04-25 11:50:35 +0200 - - Add more drift data, especially 3 m field crop data - - To support Agroscope in doing lots of PEC calculations for Switzerland - -commit 3bb842b93107dd6207610de1fe5b44be66779e4d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-04-25 10:25:56 +0200 - - Remove leftover docs from earlier version - - Docs now live in docs/ - -commit 77f63efa62b6530fbe2accdacc866e34626fe4e3 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-02-21 16:01:38 +0100 - - Update docs - -commit 5086e2b87eaec90a02b4744d1321c6949d0b8982 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-02-21 15:59:22 +0100 - - Use codecov - -commit e21ec96873bf60072414369bc96e4c076a450235 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-02-19 17:13:55 +0100 - - Add grImport to Suggests: - - Because chent which in turn suggests grImport is loaded from github - which obviously does not pull grImport - -commit 4e99ae029638a3720eba97b28bd7de3129a727ce -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-02-19 15:22:26 +0100 - - Update README.html - -commit 31eca93dadf58d47b3f3dd7aa485f89023090440 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-02-19 14:54:26 +0100 - - Add Remotes: field for travis - -commit 70b85fd2a11da1e20cd4978c717540021af34be8 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-02-19 14:35:15 +0100 - - Test on Travis - -commit 17755babc3a517f4c7cec1c04e3e1f32b7ffb5d9 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-02-19 14:27:03 +0100 - - Add another test for Exposit drainage - - to test overriding the mobility group derived from Koc - -commit 138638976f792684483520fe7837ded0a27938e4 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-02-19 12:35:19 +0100 - - Stop endless appending to pesticide.txt example - -commit 72c56f4246966c1bea627f601cf3cc457734f023 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-02-19 12:27:00 +0100 - - Add German drainage calculations using Exposit 3.02 - -commit e5a077e28153f6494c99d6945b8b1bd239464609 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-02-08 15:25:19 +0100 - - Make SSLRC and PEC drainage UK accept NA for Koc - -commit b935273d651301b271e0cb66bf36c2bbc1d15b32 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-01-31 01:40:24 +0100 - - Separate out PELMO utilities into rPELMO - -commit 1611dd58df6b2b2e6ad01af6573664da8ce8b6b9 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2019-01-30 23:58:55 +0100 - - Convenience function for metabolite PEC soil - -commit eab95c62479d732cbd531ad67ea458d2744af420 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-09-27 18:58:32 +0200 - - Create valid Step 1 files with fewer arguments - -commit 8452daa2015aa645dcc1eca3ec2bba5726603e4e -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-09-22 09:54:59 +0200 - - Add test and update docs - -commit ff7e67a4d3415419dd3f712ef1af7467ebf65508 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-09-21 19:39:44 +0200 - - Support FOMC in PEC_soil - -commit 03c3035ca01c66b6a1352f7e509753fe2d057af2 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-07-11 03:41:43 +0200 - - Improve PELMO tests - -commit 22b36c824fe5e1561868a649216fe079c6fbfb85 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-07-10 18:06:29 +0200 - - Update static docs - -commit cb3695dd434b3a3273217fb22c5ffb86065ae96d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-07-10 17:57:33 +0200 - - EFSA PEC soil guidance from 2017 - - - Implement the new guidance as well as possible - - Maintenance work addressing CRAN checks - -commit c4c3ca282c6aadca82e392692ae4100fec1dd834 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-07-10 16:46:47 +0200 - - .out file from TOXSWA 5.5.3 for testing - -commit a736ecc357889107b6e93f14cdf0c1ea4587817f -Author: Johannes Ranke <johannes.ranke@jrwb.de> -Date: 2018-07-10 16:08:52 +0200 - - Adapt path to package on windows - -commit 8989a484b9b2d23463c95e0a3927e307ec0a5e64 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-07-04 10:59:47 +0200 - - Some documentation updates - - Document that TOXSWA 5.5.3 is supported in the help files - -commit 6ca8bdb8636141fac592688a6794ae092f0bc85a -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-06-20 14:58:44 +0200 - - Advertise drat repo - -commit 6acfd0dfb2670e3eeab6144c90586f28105583a8 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-06-20 14:53:02 +0200 - - Update static docs - -commit cac29c8c1cc0f6004ef0cd63229cfb993a24496c -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-06-11 16:27:22 +0200 - - Adapt to TOXSWA 5.5.3 - -commit bd15236d5dedb4067bd29e58e655c5352aca1db4 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-06-08 16:20:40 +0200 - - Enable PEC porewater for the default scenario - - The default scenario uses soil parameters from the REACH guidance R.16, - Table R.16-9. - -commit ec2052d68950745380c2724757b3ba8b116605fc -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-06-08 14:54:40 +0200 - - Add actual/twa calcs for FOMC, typo - -commit edc3462fb4fa9f0eb604fc18ec62bb48997b5627 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-06-08 14:53:58 +0200 - - Pending stuff from the doc update - -commit 197606de234a936751ac3c1db2e4feb3fa117a92 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-06-06 02:48:44 +0200 - - Rebuild docs with pkgdown 1.1.0 - -commit 282820693c62b958e12104f4bb6229c04803f098 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-03-01 10:32:08 +0100 - - Add a README.html for cgit.jrwb.de - -commit 6d8de73e68f2c0349e618af35ce4a8f095ca0ed5 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-03-01 10:10:08 +0100 - - Rebuild static docs using current pkdown - - Process PELMO runs in example using 15 (hyperthreading) cores and show - processor info. - -commit ffeec05d913f2e987da362c05df2afc2a8a23965 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-01-29 10:11:27 +0100 - - Documentation fixes and updates - -commit 8423df9693c5cd2f2d36ee3131c7b6fcefa4d0ca -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-01-29 10:11:27 +0100 - - Documentation fixes and updates - -commit b9ce44748f2795ae1f35fe5a510e88635f247a7f -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2018-01-29 09:22:42 +0100 - - Correction of return value documentation for PEC_sw_exposit_runoff - - Rebuild pkgdown documentation - -commit 87d63e649da5e12409c50cb06d3d2a01e9880759 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-12-15 17:25:21 +0100 - - Improve handling of µ in y axis for plot.TOXSWA_cwa - -commit 4944d7ade227f1dd54c94b6a02c3c849dc1fb8ab -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-12-14 10:19:43 +0100 - - Update copyright date - -commit 0e1d517d4d6351f2d43ab8636363e73d8b8cf677 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-11-04 11:48:08 +0100 - - Option to thin low TOXSWA PECsw data for plotting - - to reduce the file size of plots e.g. as PDF files - -commit eb4465035dd44907eae3ea0340221316b7cfca12 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-11-03 11:18:10 +0100 - - Also return runoff percentages - -commit 06b528f0c19ca9f7a311612c0e9ae80c0d0c1d3f -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-10-27 18:15:29 +0200 - - Exposit runoff calculations for surface water - -commit 2cd464455a22791c0450ada45a0e0128c637fade -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-10-23 15:19:03 +0200 - - Typos, rebuild static docs - -commit 6f6575701d9b028af4b3b1b4b61c36d4989e2812 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-10-10 14:03:20 +0200 - - Add ORCID - -commit a33f1bbbf6f6121e8ad40284690a463733a00bc2 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-10-09 08:48:39 +0200 - - Write Step 2 input files on windows - -commit 311c4fbcc51ad727551da41569d64e6bc290c2b2 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-10-06 09:30:21 +0200 - - Update docs, small bugfix - -commit 72d7358581bca88af8c507b6c80791100aaafafc -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-08-24 10:30:11 +0200 - - Build for windows using roxygen from master - - Now that roxygen can handle UTF8 characters in function - arguments thanks to Hadley Wickham and Jim Hester - -commit a8a2a9d57f40ec7a4fc70df3dc470d88cd10c525 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-07-24 16:31:07 +0200 - - Improve Makefile - -commit 89fc0926722fbfd6420297194c8b18f5b8a9447d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-07-24 16:26:51 +0200 - - Version bump as I had 0.4.3 in my drat already - -commit 762880a78620e50814351248c02d012a7b030fb8 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-07-24 16:23:22 +0200 - - Avoid warning about possibly mis-spelled word - -commit a2e24495c01f837474b69263a9861a89050cbfd1 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-07-21 11:15:41 +0200 - - New Option for Step 1, fix example, update docs - - Also add the reference file for testing Step12 input file generation - -commit dffa31a5ad5026d4d67327da622f45c00be40584 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-06-22 08:23:13 +0200 - - Add scenario, region and season to run name - -commit 0607a619d92d582ba40f9c0c3b32a1d0a8791655 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-06-20 16:40:21 +0200 - - Possibility to turn off formation in water - - This makes it possible to compare the Step 1 output with earlier - versions of the Steps 12 tool. - -commit 0d60c88ba7e0693a832056ea3db5cc0eaf3b0819 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-06-20 14:16:14 +0200 - - Fix line endings and allow all interception classes - -commit dc1e49c8bb27cac81268719055bc4336843c0506 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-06-20 06:16:19 +0200 - - Keep dos format for pesticide.txt test data - -commit fd40f74907e89077bd81af5d779ae93e1434d8c6 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-06-20 06:11:12 +0200 - - Now the errors in PELMO output are gone - not reproducible - -commit 88044fd98c5b95d3f3f9bbef7416af66552189c1 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-06-20 06:04:14 +0200 - - Tests for Step 1 and 2 (input file only) pass, PELMO fails - - There are spurious errors in the output PELMO generates. Two examples - are in the test.log - -commit 34d4915297faf6236479f0e6474f8aa6b8d4b416 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-06-20 04:30:52 +0200 - - Fix generation of input files - - - Write header only if not appending - - Write max_soil and max_ws for metabolites - - Formatting - -commit 7233eed00b799e08c31ae971f997b4b3c14eaea2 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-06-19 20:10:21 +0200 - - Single line of generated Step12 input file partially validated - -commit c9bcd8e68db61515080ff377c6a04fa807337258 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-06-17 16:36:13 +0200 - - Start with the generation of an input file - -commit e6f968cf97ed6ca9268e6098d86ba63ff2c6d2b0 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-05-24 16:07:35 +0200 - - Fix for the sawtooth function for repeated applications - - For n > 2, the second application was made at 2 * i instead of i. - -commit 4835e20d1d08203657ab616600286ad9dfd71344 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-05-24 15:46:44 +0200 - - Re-enable PELMO examples and tests - - - Add .gitattributes to make sure CRLF line endings are kept for PELMO - .psm files - - Update static docs - -commit 539ea37b45ddc41b36dd199f06ffe5936ab13f21 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-05-17 12:23:38 +0200 - - Documentation fix - -commit 62bffd4873bc53fa9cd81336efa716b220c83e0a -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-05-17 09:36:22 +0200 - - Simplify tests where possible - -commit d60bb9c0b52c8e0452bfbe507e60d5f651589cc8 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-05-16 18:57:16 +0200 - - Update static documentation - -commit 14fa47b1ea1651fc2cb7bbf0086741a8004d35ee -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-05-16 18:54:34 +0200 - - Remove external data also from git as their licence is unclear - -commit 608c4f89a2656f67ba915aab17633d41acc789a7 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-05-16 18:44:22 +0200 - - Add build and test logs to the git repo - -commit 3e26a8ab76a434c3465ea1db1b4a2a2ff3ea8ec8 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-05-16 18:40:25 +0200 - - Add TWA concentrations for days > 1, fix link - - Now we have seven test calculations for the Step 1 calculator, all - perfectly passing. This provides confidence that this is a - correct reimplementation of the Step 1 part of the Step 1/2 calculator. - -commit 36036b5901223591e7e21e8b73d8cd1fb034f4cb -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-05-16 15:43:50 +0200 - - Finish the Step 1 calculator including tests - - Some cleaning up. PELMO facilities do not currently work at my end, - as I have no working wine installation on this computer - -commit d042f8f06b313e8595087587455daac73d84f17b -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-05-15 20:01:28 +0200 - - Start of an Steps 1/2 calculator in R - -commit b052bf8d1e090e07bf0853f0aa8b895db8f41a2a -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-03-29 19:24:37 +0200 - - Make it possible to use expressions in axis labels - -commit d69fda8d8f854b735394ecdaec9d59fb18c42b00 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-03-28 10:09:45 +0200 - - Update Changelog - -commit 90e5ff0a9fdadd65e179c04c7d43b4db6e301984 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-03-06 17:59:16 +0100 - - Move static docs to pkdown.jrwb.de, update them - -commit 68e36eb0a5f1b611588d47f77e0ef7c3d9ba0beb -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-03-01 11:37:31 +0100 - - The package is not in subdir `pkg` any more - -commit f67ea0c4aeb68631e9f93c95e86c14364718477a -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-31 07:33:21 +0100 - - Small documentation fix - -commit 4e696997516543e29119e94d67283f513be4484d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-30 18:08:50 +0100 - - Regenerate static documentation - -commit 03bda75d343402dad99df2aad55611e11279b833 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-30 18:04:53 +0100 - - Correct psm file in the example with metabolites - -commit 39d202b0a0f833c756bc98fb4961483de1b15353 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-30 16:14:15 +0100 - - Ignore windows binary builds in git and in R package - -commit e6bb9654679f43af6958d6e28cb5206abb91d574 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-30 16:10:30 +0100 - - Test reproducing the FOCUS Summary information - - generated from the FOCUS PELMO GUI, as copied into the text files - in the testdata directory. - -commit 80b451ddb4e749041c2b216603274a012dc83d59 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-30 14:28:23 +0100 - - PELMO summary files for testing - -commit 826cf9a2687ff1d7ca5b568882f5686f76f82074 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-30 14:11:34 +0100 - - Use relative tolerance of 1e-6 for flux test - - to pass test also for more extreme situations as in the current test data. - -commit eea72720956dc8358fac98b29c9a627a9363cbd2 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-30 13:12:24 +0100 - - Better documentation of PELMO_runs(). - -commit d78d2effd517ab3c27412ae6f4ae701c456ae590 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-30 12:46:57 +0100 - - pfm for windows in my drat - -commit eaf3b558747ff8228e87ded727a6c0e91a6579f8 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-30 12:01:14 +0100 - - More extreme parameters for metabolites for testing - -commit a6c13f70f6c6669a8088827a602ac475fdf9b624 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-29 16:58:53 +0100 - - Setting up PELMO runs, execution and evaluation - - It all works! - -commit bc97a35a32c4f47e29364488a3601f94c6e68d45 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-27 18:33:45 +0100 - - Really use all scenarios in test data - - Maize, that was used in the last commit, is not parameterised for - Jokioinen - -commit a4081ddfea726283874968c0b62a7f46e4fd1232 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-27 18:23:35 +0100 - - Use all scenarios in the test data - -commit 3c82d26206e2f2e74600acd71a49c70eaed555c4 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-27 08:17:08 +0100 - - Also test run with metabolites - -commit 8fd050e57b7babfbdb1ccfabb468a0398396d466 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-27 07:54:53 +0100 - - Include a run with metabolites in PELMO test data - -commit b38055278d4a801598ece9d2c93716a9bf67134a -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-27 01:00:07 +0100 - - Set up FOCUS PELMO runs and run them in parallel - - - This works on Linux using wine - - PELMO runs (including pelmo.inp files) are correctly generated - - The PLM files for FOCUS Pesticide_D in the test data archive are - correctly reproduced - - The data files (including FOCUS groundwater scenario data) are now - created and documented in R files - -commit 40c2f387775a168df1be699813807586cf098648 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-26 10:30:32 +0100 - - Improved test data with 'irrigation' - -commit 228ab628b407af4812a48f20693a9a3a6bba8af4 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-25 16:45:24 +0100 - - More variable selection of test data - -commit bf6634b7d9a5033a217f04060f77e0c7d5b3046a -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-25 15:27:05 +0100 - - Use tar.bz2 to correctly transfer file names - -commit 476d556cb6a490b138e47d487dd732f298aa6c3d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-25 14:29:41 +0100 - - Add FOCUS PELMO 5.5.3 output for dummy pesticide D - -commit 9f16be247e851c948edb30ac756550d89ba0af52 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-19 11:44:22 +0100 - - Another correction of the docs - -commit 2ab822d51c4c7e29d62076336d7a3f02a46e41a5 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-19 11:41:19 +0100 - - Corrections in the documentation - -commit 46883a0c3a3c00127a563a7befa0af440573baaa -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-19 11:22:08 +0100 - - Correct default y axis label for plot.one_box - -commit 3947731a5a8c3598271b26f5201dea4bcb13ef6d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-19 10:47:09 +0100 - - Fix one_box for ini = 1, use in sawtooth examples - -commit dd30f0d0ff1d8d0cc46aaef6e0917c51fe798f52 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-19 10:36:19 +0100 - - Move mkin::twa to pfm::max_twa.mkinfit - - - Add max_twa.mkinfit() recently introduced to mkin as mkin::twa() but - never released with it - - Add a test to check max_twa.one_box() against analytical solutions in - max_twa.mkinfit(). - - Clean up R CMD check - - Update docs - -commit 3ead7acba845b4f2552f555dfb29da889ed0cda8 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-19 09:42:21 +0100 - - Make max_twa() a bit safer - -commit 74ed85b07f09ea99476208749cd274a476ba4536 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-19 09:27:36 +0100 - - Documentation updates - -commit a6d61c06d573574cf574ed893cc13808a9e8b785 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-19 09:20:22 +0100 - - Fix order of arguments to one_box, correct docs - -commit b8ac1393b9e1bef8c48b26b790cf5759ccd69fed -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-19 09:10:37 +0100 - - Predict parent decline without fitting for non-SFO models - -commit 3d4f6f8c582c19c38587ead305a1229ff069da63 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-19 08:24:44 +0100 - - Switch sawtooth plotting example to FOMC - - as this it is claimed in the README that an mkinfit prediction is used. - - Add another seealso link - - Delete trailing whitespace - -commit 9b5faa8b8475bdd7624c58b07d45d28d42a47a2e -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-18 23:02:14 +0100 - - Point to the github.io documentation site - -commit cff68edc1ac113ac9e159dfdf7cfcbb6721ff2a7 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-18 22:58:51 +0100 - - Make README.md simple, and point to the reference - -commit a76221d87485029444c8e684022ca606a0c7e68d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-18 22:41:01 +0100 - - Update static docs using pkgdown - - - Add _pkgdown.yml for a structured function/data reference - - Make seealso links active - - Make mkinfit calls quiet - - Use pkgdown branch from pull request hadley/pkgdown#229 to have topics - ordered - -commit a1d9f93138c2cfed92a683e37e72c737d52b7ad7 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2017-01-18 19:58:13 +0100 - - One box time series and twa values - - - one_box() creates decline time series from mkinfit objects or simply - from a half-life - - sawtooth() generates sawtooth curves for arbitrary application - patterns and decline models - - twa() calculates moving window averages - - max_twa() gives their maxima and - - plot.one_box() can plot series generated by one_box() or sawtooth(), - optionally adding a greay rectangle to illustrate the maximum moving - window time weighted average - -commit bba2cf3a70849ba86f37520d3e909cf1c706f416 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-12-22 11:06:57 +0100 - - Fix reading in times from .out files - - The code from the previous commit was broken. Also, the time - zone for the times that are read is now wet to 'UTC', in order to - avoid setting different time zones due to daylight savings, which - introduces artificial one-hour offsets on changeover days. - -commit 0af7c7b8c34067fc4756929925239c329b28ed32 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-12-14 18:26:14 +0100 - - Changelog update and roxygen run - -commit 5a04ad3061c1484b45703e44149f49ec97cfbf15 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-12-14 16:52:14 +0100 - - Set time correctly for 00:00 hours in .out file - - For ConLiqWatLayCur_xxxxx entries which are output at 00:00 (midnight), - no time is listed in the .out file for this time. This commit introduces - a workaround, setting the time to 00:00 when there is no time - information. - -commit e51e063564bffcb75dbb6ab7a364704c8d8e992e -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-12-12 21:24:24 +0100 - - Fix reading .out for acronyms containing numbers - -commit 9124e0f7d673c65584c1b2f838a3b944ea89c31d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-10-13 17:49:18 +0200 - - Add drat target, remove unmaintained usage hints - -commit 12a31f4c130c551f82232d9ef7dfb608bd52c53f -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-09-27 23:00:48 +0200 - - Reorganise repository using standard package layout - -commit 0d958ab6f84b569b5437f231c56004890c4ae23b -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-09-27 17:50:34 +0200 - - Make the chents package optional - -commit 399383adcdb37c4a3e32f1a2133a2fa3663618d0 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-09-23 18:23:00 +0200 - - Keep the graph for the markdown file - - The markdown file is not self-contained as the html file... - -commit 9fb69b042924045df90119e47ad4dc666dbc8b4d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-09-23 18:16:51 +0200 - - Slightly update the README - -commit 2f618da8cfbeb0379f4d38af6f608a69c6d54bd5 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-07-30 11:29:09 +0200 - - Update static documentation - -commit 3b8730a58f7846b5261922ec90e582e0158a54c7 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-07-30 11:09:47 +0200 - - Add 'methods' to dependecies - -commit 3260b0e875b7af24f2aef7bc2464418525a192df -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-07-30 11:08:05 +0200 - - Fix the TOXSWA reading test - - Since a recent commit we are reading the concentrations at the end - of each hour, so the test needed to be updated accordingly - -commit b8f953d04e4094c79b4f860d99f3c1466ed3ad6a -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-07-30 11:06:53 +0200 - - Import 'is' from methods - -commit 1ceb226d999d56276c9e361f359368287a0749c4 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-07-30 10:42:48 +0200 - - Read cwas from .out files with metabolites - - TOXSWA 4 stores the detailed output for SWASH runs with metabolites - in its .out files. With this commit it is possible to read in - .out files from such runs with metabolites. Default is to read in - the concentrations for the parent, a newly gained "substance" argument - makes it possible to specify the metabolite for which the data should - be read. - -commit d6b230cd1b415a112009227bc9e0ff50316c42f7 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-07-15 15:05:22 +0200 - - Fix calculation of t_firstjan - - There is an inconsistency in (some?) output files, so the first - datetime needs to be fixed before reading it into a data frame - -commit b45c9bfae9e5578dd455ed417363b4996cffd46a -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-06-08 08:36:48 +0200 - - Clean up remainders of NL drift calculation function - -commit 234a20018fe9fe9824bcfaae2c391e59d09f9871 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-06-08 08:29:39 +0200 - - Use the concentration at the end of the hour - - This is also what TOXSWA presents in the summary files - -commit 4284c57c7d53a9aef0c917a050ccf2ab779cfce3 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-06-08 08:29:39 +0200 - - Use the concentration at the end of the hour - - This is also what TOXSWA presents in the summary files - -commit 057d53d0faed7b297bbb99de8cd4bf3e3e448538 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-03-10 05:28:03 +0100 - - Merge the NL drift calculations based on percentages into PEC_sw_drift - -commit 527d927371083e784ad583a6b3c7465c49a53cdc -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-03-10 05:17:45 +0100 - - Add NL specific drift calculations - -commit 1ab6d4c9f186fb7ea9bb8b968e47a9f1eab64583 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-03-02 17:51:21 +0100 - - Fix the name of the Chateadun scenario - -commit d14923ae1ac023c8f8f5ae8b5c0884f4247f764b -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2016-02-04 18:06:15 +0100 - - Test reading .out files and close connections - -commit 98a706373107188496a1df295697e739e51d6b06 -Author: Johannes Ranke <johannes.ranke@jrwb.de> -Date: 2016-02-04 17:45:02 +0100 - - Improve reading spead for new TOXSWA format - -commit 057ba40426d49e09c06db26fb7d4072741b4cb8d -Author: Johannes Ranke <johannes.ranke@jrwb.de> -Date: 2016-02-04 12:21:02 +0100 - - Read cwa data from TOXSWA 4.4.2 .out files - -commit e7f8a0e82b24d28b74681dafc97f1cf8a4662b51 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-12-27 12:30:20 +0100 - - Fix rounding of endpoint retrieval functions - -commit f9373e361dde232b08fe7431e85bf367a1cfc269 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-12-27 12:29:37 +0100 - - Another useless variant to avoid warnings in staticdoc plots - -commit 3a579d87820ccbec514f1be5eb090e874fd87eec -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-12-22 19:32:54 +0100 - - EFSA 2015 tier 1 PEC soil, clean up, add static docs - -commit 9851a97ec915ddbfc8357f1a7e2cabae56c89f7d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-12-18 14:45:24 +0100 - - Documentation fixes, chents is currently a hard dependency - -commit 6b4e342b240baaf18150360986d15895fc80a937 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-10-15 14:41:26 +0200 - - Add endpoint and GUS functions, roxygenize - -commit c43b4947007b3c26bc56260499af51c41b8cd702 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-10-01 14:42:14 +0200 - - Add some soil data for FOCUS groundwater scenarios - -commit 697e0554bf89a63f23b9ab5548e31f218bc483e9 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-09-11 10:07:53 +0200 - - Added PEC soil for products as defined in chents v0.1-2 - -commit 634d4a0a93882a3b2d3961abbdd33694fd93dcc6 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-09-10 16:18:17 +0200 - - Add PEC soil for product with serveral ais - -commit 1ec3ee4a03d4e47fdd3be1bcbe754e478353410b -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-08-22 12:10:06 +0200 - - Updates of DESCRIPTION and NAMESPACE - -commit 51aa1a77c9b9b9a6becdb2a5a85213946719b051 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-08-22 12:06:37 +0200 - - Add README.html for cgit on jrwb.de - -commit 83c8575e2abde12208584b9c80935d4a873689fd -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-08-22 12:01:57 +0200 - - Small documentation updates - -commit 5038ba57fef6cc386566ec30f3d5dd67e62decff -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-08-21 15:10:42 +0200 - - Adapt the description to R CMD check requirements - -commit 4477e69b46e88c196f354463190753650157ea0d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-08-21 15:01:10 +0200 - - Updates to pass checks and tests - -commit ad4cd5d9a1f8c3976d08048a441129b1fb49a62b -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-07-02 16:05:59 +0200 - - Changes to pass R CMD check --as-cran, roxygen run - -commit fef0bb7fe916f91dcff089c17aa3290c0ea1ab1f -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-06-12 02:19:38 +0200 - - Add sediment PEC calculations using the percentage method - -commit 5b32c30549bfa3cb42ffde7e13f75608b98c79c2 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-06-12 02:19:01 +0200 - - Make UK drainage with non-SFO soil degradation work - -commit 9b8e5cb80ba4a89578d979bee134f8342ca0a527 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-06-11 17:38:01 +0200 - - Now we pass R CMD check - -commit dd803b191062925eda830543236836e7822fd884 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-06-11 16:57:43 +0200 - - Add UK tier 1 drainage PEC calculations - -commit 09cf970942706cfab43753d298b42e8d85216d80 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-06-11 15:25:22 +0200 - - Now there is enough content to warrant 0.2-x - -commit 3aa5fb86772c28402047c7ebd07841061dbcdbba -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-06-11 15:23:22 +0200 - - Add facilities to calculate decline curves - -commit d3daa7b73fa5d0508ff51a843247d126c2a11691 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-06-11 13:17:13 +0200 - - Generate README.md with current pfm version - -commit cb0d72e2c2d431bd32ffb129b62ea1a522cbdfeb -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-06-11 13:09:10 +0200 - - Rename PEC_sw_drift() to PEC_sw_drift_ini() - -commit ea9b75183bcf41fcdd6f61ec6060e94c4bc321a2 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-06-11 12:13:47 +0200 - - Add simple drift PEC ini calculations - - These are tested for field crops with the CRD spreadsheet - -commit cbba81d73faa83c63a33afc61be5efc1964925bb -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-06-11 12:12:40 +0200 - - Use devtools for roxygenizing, improve logging - -commit 6e4a152925011528c21937f12bc53042a53f72de -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-06-11 10:13:18 +0200 - - JKI drift percentage data for field crops and pome/stone fruit - -commit 53099978c971ee8e5c94e67bf972f51629d67fd3 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-06-11 10:04:22 +0200 - - and the incomplete documentation - -commit 372ab2f2f59f0baaee759ce966a705f9f754cf6d -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-06-11 10:03:32 +0200 - - Intermediate stage for pfm_chent - -commit 586b248f5d249f4ebaad2175c9f78fcae8646636 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-06-11 09:54:57 +0200 - - Formatting - -commit fd1609aafd2f40266c1e29d8dfdf5e08e8838d35 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-05-24 03:52:28 +0200 - - Start of a pfm_chent data object - -commit e2b1d510e921f7721647b0df6602c2618937c1da -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-05-08 08:47:11 +0200 - - Update the Figure in the README - -commit 8021c7cb9aac06e961227a3c0e0b013ec2d2d501 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-05-07 16:15:23 +0200 - - Bugfix: Reset maximum event concentration for each event - -commit 508d883f7689d617d15915dbd26a27f1613bb857 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-05-07 12:04:28 +0200 - - Make quarterly labels for plot.TOXSWA_cwa - -commit c6e57ab29170266b3038b01c54bf161ab361d440 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-04-24 02:22:21 +0200 - - Do not test the path to the zip file - -commit 7d2096855edcc196629c1c7a9983a56ec6addd1e -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-04-24 02:21:04 +0200 - - Add a geometric mean function - -commit bcfe0af7970efe36c3aa661e89953fbe3689c310 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-04-24 02:20:21 +0200 - - Clean the Makefile a bit - -commit 768a043848dd84b9e699916657d0a23b2f3b9e83 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-04-22 13:48:42 +0200 - - Fix header formatting - -commit 04502ca0c658a6c929debd61aee87be8c7eceb04 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-04-22 13:46:32 +0200 - - Update markdown version of README - -commit ec79637749d300ab4ca170805c673905e52d67dd -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-04-22 13:42:10 +0200 - - Add simplest PEC soil calcs, use testthat - -commit 8ffbc49b3f01deac6f9e83aaa6d318d4e2f8552b -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-01-23 16:44:04 +0100 - - Add option to plot relative to maximum - -commit 8975dc148d0a6f222174980eb60314054be9b6cf -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-01-13 14:54:58 +0100 - - Fix warning in README - -commit 891af5d0f1ee8d45cd4403af43293463d23ba96b -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-01-13 14:05:31 +0100 - - README.rmd with example, fix reading unzipped files - -commit 4d74570f1ca4a94d894c6c5169684a8246d0a51c -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-01-13 12:58:26 +0100 - - Correctly initialize R6 fields, read from zip files - -commit ee070c11f7c7faff2f573d27cf32aafab78971a8 -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2015-01-07 23:56:54 +0100 - - Pass ... parameters to added cwa lines - -commit 92d97ba99d7b90d95a67796cb5e68f28f752b70b -Author: Johannes Ranke <jranke@uni-bremen.de> -Date: 2014-12-17 21:39:42 +0100 - - Initial commit: R6 class for TOXSWA cwa files diff --git a/DESCRIPTION b/DESCRIPTION index 8d11e33..ab6d2ce 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling -Version: 0.6.0 -Date: 2023-11-11 +Version: 0.6.1 +Date: 2024-01-31 Authors@R: person("Johannes Ranke", email = "johannes.ranke@agroscope.admin.ch", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4371-6538")) @@ -10,6 +10,7 @@ Description: Utilities for simple calculations of predicted environmental concentrations ('PEC' values) and for dealing with data from some FOCUS pesticide fate modelling software packages. Depends: + R (>= 3.5.0), R6, mkin (>= 1.2) Imports: @@ -21,10 +22,12 @@ Suggests: chents, grImport, magrittr, - covr + covr, + here, + waldo License: GPL -LazyLoad: yes -LazyData: yes +LazyLoad: true +LazyData: true Encoding: UTF-8 URL: https://pkgdown.jrwb.de/pfm RoxygenNote: 7.2.3 diff --git a/GNUmakefile b/GNUmakefile index fae80e3..b987f41 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -2,80 +2,51 @@ PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION) PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION) TGZ := $(PKGNAME)_$(PKGVERS).tar.gz WINBIN := $(PKGNAME)_$(PKGVERS).zip -R_HOME ?= $(shell R RHOME) -DATE := $(shell date +%Y-%m-%d) +RBIN ?= $(shell dirname "`which R`") -.PHONEY: usage check clean +.PHONEY: check pkgfiles = \ .Rbuildignore \ - ChangeLog \ DESCRIPTION \ data/* \ - docs/* \ - docs/reference/* \ + GNUmakefile \ + inst/data_generation/* \ inst/testdata/* \ README.html \ R/* \ tests/testthat.R \ tests/testthat/* -clean: - @echo "Cleaning up..." - rm -fR pfm.Rcheck - @echo "DONE." +all: build -roxygen: - @echo "Roxygenizing package..." - "$(R_HOME)/bin/Rscript" -e 'devtools::document()' - @echo "DONE." +roxy: + Rscript -e "roxygen2::roxygenize(roclets = c('rd', 'collate', 'namespace'))" README.html: README.md - "$(R_HOME)/bin/Rscript" -e "rmarkdown::render('README.md', output_format = 'html_document', output_options = list(mathjax = NULL))" - -pd: roxygen - @echo "Building static documentation..." - # suppressWarnings to get rid of mbcsToSbcs warnings when plotting the 'µ' character - "$(R_HOME)/bin/Rscript" -e 'suppressWarnings(pkgdown::build_site(lazy=TRUE))' - @echo "DONE." + "$(RBIN)/Rscript" -e "rmarkdown::render('README.md', output_format = 'html_document', output_options = list(mathjax = NULL))" $(TGZ): $(pkgfiles) - sed -i -e "s/Date:.*/Date: $(DATE)/" DESCRIPTION - @echo "Roxygenizing package..." - "$(R_HOME)/bin/Rscript" -e 'devtools::document()' - @echo "Building package..." - "$(R_HOME)/bin/R" CMD build . > build.log 2>&1 - @echo "DONE." + "$(RBIN)/R" CMD build . 2>&1 | tee log/build.log + +build: roxy $(TGZ) -build: $(TGZ) +install: build + "$(RBIN)/R" CMD INSTALL $(TGZ) $(WINBIN): build @echo "Building windows binary package..." - "$(R_HOME)/bin/R" CMD INSTALL $(TGZ) --build + "$(RBIN)/R" CMD INSTALL $(TGZ) --build @echo "DONE." winbin: $(WINBIN) -test: build - @echo "Running testthat tests..." - NOT_CRAN=true "$(R_HOME)/bin/Rscript" -e 'options(cli.dynamic = TRUE); devtools::test()' 2>&1 | tee test.log - sed -i -e "s/\r.*\r//" test.log - @echo "DONE." - -quickcheck: build - @echo "Running check..." - "$(R_HOME)/bin/R" CMD check $(TGZ) - @echo "DONE." - -check: build - @echo "Running CRAN check..." - _R_CHECK_CRAN_INCOMING_REMOTE_=false "$(R_HOME)/bin/R" CMD check --as-cran $(TGZ) - @echo "DONE." +check: roxy build + _R_CHECK_CRAN_INCOMING_REMOTE_=false "$(RBIN)/R" CMD check --as-cran --no-tests $(TGZ) 2>&1 | tee log/check.log -install: build - @echo "Installing package..." - "$(R_HOME)/bin/R" CMD INSTALL --no-multiarch $(TGZ) - @echo "DONE." +test: install + "$(RBIN)/Rscript" -e 'options(cli.dynamic = TRUE); devtools::test()' 2>&1 | tee log/test.log + sed -i -e "s/.*\r.*\r//" log/test.log drat: build "$(R_HOME)/bin/Rscript" -e "drat::insertPackage('$(TGZ)', commit = TRUE)" @@ -89,3 +60,11 @@ winbuilder: build curl -T $(TGZ) ftp://anonymous@win-builder.r-project.org/R-release/ @echo "Uploading to R-devel on win-builder" curl -T $(TGZ) ftp://anonymous@win-builder.r-project.org/R-devel/ + +pd: roxy + # In earlier versions, we used suppressWarnings to get + # rid of mbcsToSbcs warnings when plotting the 'µ' character + Rscript -e 'pkgdown::build_site(lazy = TRUE, run_dont_run = TRUE)' + +pd_all: roxy + Rscript -e 'pkgdown::build_site(lazy = FALSE, run_dont_run = TRUE)' @@ -32,8 +32,6 @@ export(endpoint) export(geomean) export(max_twa) export(one_box) -export(perc_runoff_exposit) -export(perc_runoff_reduction_exposit) export(pfm_degradation) export(read.TOXSWA_cwa) export(sawtooth) diff --git a/R/EFSA_GW_interception_2014.R b/R/EFSA_GW_interception_2014.R index 15d7835..386fddf 100644 --- a/R/EFSA_GW_interception_2014.R +++ b/R/EFSA_GW_interception_2014.R @@ -9,33 +9,5 @@ #' \bold{12}(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662 #' @format A matrix containing interception values, currently only for some selected crops #' @examples -#' \dontrun{ -#' # This is the code that was used to define the data -#' bbch <- paste0(0:9, "x") -#' crops <- c( -#' "Beans (field + vegetable)", -#' "Peas", -#' "Summer oilseed rape", "Winter oilseed rape", -#' "Tomatoes", -#' "Spring cereals", "Winter cereals") -#' EFSA_GW_interception_2014 <- matrix(NA, length(crops), length(bbch), -#' dimnames = list(Crop = crops, BBCH = bbch)) -#' EFSA_GW_interception_2014["Beans (field + vegetable)", ] <- -#' c(0, 0.25, rep(0.4, 2), rep(0.7, 5), 0.8) -#' EFSA_GW_interception_2014["Peas", ] <- -#' c(0, 0.35, rep(0.55, 2), rep(0.85, 5), 0.85) -#' EFSA_GW_interception_2014["Summer oilseed rape", ] <- -#' c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9) -#' EFSA_GW_interception_2014["Winter oilseed rape", ] <- -#' c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9) -#' EFSA_GW_interception_2014["Tomatoes", ] <- -#' c(0, 0.5, rep(0.7, 2), rep(0.8, 5), 0.5) -#' EFSA_GW_interception_2014["Spring cereals", ] <- -#' c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8) -#' EFSA_GW_interception_2014["Winter cereals", ] <- -#' c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8) -#' save(EFSA_GW_interception_2014, -#' file = "../data/EFSA_GW_interception_2014.RData") -#' } #' EFSA_GW_interception_2014 -NULL +"EFSA_GW_interception_2014" diff --git a/R/EFSA_washoff_2017.R b/R/EFSA_washoff_2017.R index 450c12e..59e299c 100644 --- a/R/EFSA_washoff_2017.R +++ b/R/EFSA_washoff_2017.R @@ -10,33 +10,5 @@ #' doi:10.2903/j.efsa.2017.4982 #' @format A matrix containing wash-off factors, currently only for some selected crops #' @examples -#' \dontrun{ -#' # This is the code that was used to define the data -#' bbch <- paste0(0:9, "x") -#' crops <- c( -#' "Beans (field + vegetable)", -#' "Peas", -#' "Summer oilseed rape", "Winter oilseed rape", -#' "Tomatoes", -#' "Spring cereals", "Winter cereals") -#' EFSA_washoff_2017 <- matrix(NA, length(crops), length(bbch), -#' dimnames = list(Crop = crops, BBCH = bbch)) -#' EFSA_washoff_2017["Beans (field + vegetable)", ] <- -#' c(NA, 0.6, rep(0.75, 2), rep(0.8, 5), 0.35) -#' EFSA_washoff_2017["Peas", ] <- -#' c(NA, 0.4, rep(0.6, 2), rep(0.65, 5), 0.35) -#' EFSA_washoff_2017["Summer oilseed rape", ] <- -#' c(NA, 0.4, rep(0.5, 2), rep(0.6, 5), 0.5) -#' EFSA_washoff_2017["Winter oilseed rape", ] <- -#' c(NA, 0.1, rep(0.4, 2), rep(0.55, 5), 0.3) -#' EFSA_washoff_2017["Tomatoes", ] <- -#' c(NA, 0.55, rep(0.75, 2), rep(0.7, 5), 0.35) -#' EFSA_washoff_2017["Spring cereals", ] <- -#' c(NA, 0.4, 0.5, 0.5, rep(0.65, 3), rep(0.65, 2), 0.55) -#' EFSA_washoff_2017["Winter cereals", ] <- -#' c(NA, 0.1, 0.4, 0.6, rep(0.55, 3), rep(0.6, 2), 0.4) -#' save(EFSA_washoff_2017, -#' file = "../data/EFSA_washoff_2017.RData") -#' } #' EFSA_washoff_2017 -NULL +"EFSA_washoff_2017" diff --git a/R/PEC_sw_exposit_runoff.R b/R/PEC_sw_exposit_runoff.R index d68a521..8b89cd9 100644 --- a/R/PEC_sw_exposit_runoff.R +++ b/R/PEC_sw_exposit_runoff.R @@ -13,18 +13,11 @@ #' adjacent water body bound to eroding particles} #' } #' @source Excel 3.02 spreadsheet available from -#' \url{https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html} -#' @export perc_runoff_exposit +#' \url{https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html} +#' @docType data #' @examples #' print(perc_runoff_exposit) -{Koc_breaks <- c(0, 20, 50, 100, 200, 500, 1000, 2000, 5000, 10000, 20000, 50000, Inf) -tmp <- paste(Koc_breaks[1:11], Koc_breaks[2:12], sep = "-") -Koc_classes <- c(tmp[1], paste0(">", tmp[2:11]), ">50000")} -perc_runoff_exposit <- data.frame( - Koc_lower_bound = Koc_breaks[1:12], - dissolved = c(0.11, 0.151, 0.197, 0.248, 0.224, 0.184, 0.133, 0.084, 0.037, 0.031, 0.014, 0.001), - bound = c(0, 0, 0, 0.001, 0.004, 0.020, 0.042, 0.091, 0.159, 0.192, 0.291, 0.451)) -rownames(perc_runoff_exposit) <- Koc_classes +"perc_runoff_exposit" #' Runoff reduction percentages as used in Exposit #' @@ -40,31 +33,14 @@ rownames(perc_runoff_exposit) <- Koc_classes #' \item{bound}{The reduction percentage for the particulate phase} #' } #' @source Excel 3.02 spreadsheet available from -#' \url{https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html} +#' \url{https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html} #' #' Agroscope version 3.01a with additional runoff factors for 3 m and 6 m buffer zones received from Muris Korkaric (not published). #' The variant 3.01a2 was introduced for consistency with previous calculations performed by Agroscope for a 3 m buffer zone. -#' @export +#' @docType data #' @examples #' print(perc_runoff_reduction_exposit) -perc_runoff_reduction_exposit <- list( - "3.02" = data.frame( - dissolved = c(0, 40, 60, 80), - bound = c(0, 40, 85, 95), - row.names = c("No buffer", paste(c(5, 10, 20), "m"))), - "3.01a" = data.frame( - dissolved = c(0, 25, 40, 45, 60, 80), - bound = c(0, 30, 40, 55, 85, 95), - row.names = c("No buffer", paste(c(3, 5, 6, 10, 20), "m"))), - "3.01a2" = data.frame( - dissolved = c(0, 25), - bound = c(0, 25), - row.names = c("No buffer", paste(c(3), "m"))), - "2.0" = data.frame( - dissolved = c(0, 97.5), - bound = c(0, 97.5), - row.names = c("No buffer", "20 m")) -) +"perc_runoff_reduction_exposit" #' Calculate PEC surface water due to runoff and erosion as in Exposit 3 #' @@ -93,7 +69,7 @@ perc_runoff_reduction_exposit <- list( #' } #' @export #' @source Excel 3.02 spreadsheet available from -#' \url{https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3} +#' \url{https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html} #' @seealso \code{\link{perc_runoff_exposit}} for runoff loss percentages and \code{\link{perc_runoff_reduction_exposit}} for runoff reduction percentages used #' @examples #' PEC_sw_exposit_runoff(500, Koc = 150) @@ -108,18 +84,18 @@ PEC_sw_exposit_runoff <- function(rate, interception = 0, Koc, DT50 = Inf, t_run if (length(Koc) > 1) stop("Only one compound at a time supported") exposit_reduction_version <- match.arg(exposit_reduction_version) - red_water <- perc_runoff_reduction_exposit[[exposit_reduction_version]]["dissolved"] / 100 - red_bound <- perc_runoff_reduction_exposit[[exposit_reduction_version]]["bound"] / 100 - reduction_runoff <- perc_runoff_reduction_exposit[[exposit_reduction_version]] / 100 + red_water <- pfm::perc_runoff_reduction_exposit[[exposit_reduction_version]]["dissolved"] / 100 + red_bound <- pfm::perc_runoff_reduction_exposit[[exposit_reduction_version]]["bound"] / 100 + reduction_runoff <- pfm::perc_runoff_reduction_exposit[[exposit_reduction_version]] / 100 transfer_runoff <- 1 - reduction_runoff V_runoff <- V_event * (1 - reduction_runoff[["dissolved"]]) # m3 V_flowing_ditch_runoff <- dilution * (V_ditch + V_runoff) f_runoff_exposit <- function(Koc) { - Koc_breaks <- c(perc_runoff_exposit$Koc_lower_bound, Inf) - Koc_classes <- as.character(cut(Koc, Koc_breaks, labels = rownames(perc_runoff_exposit))) - perc_runoff <- perc_runoff_exposit[Koc_classes, c("dissolved", "bound")] + Koc_breaks <- c(pfm::perc_runoff_exposit$Koc_lower_bound, Inf) + Koc_classes <- as.character(cut(Koc, Koc_breaks, labels = rownames(pfm::perc_runoff_exposit))) + perc_runoff <- pfm::perc_runoff_exposit[Koc_classes, c("dissolved", "bound")] if (identical(Koc, 0)) perc_runoff <- c(dissolved = 0, bound = 0) return(unlist(perc_runoff) / 100) } @@ -168,7 +144,7 @@ PEC_sw_exposit_runoff <- function(rate, interception = 0, Koc, DT50 = Inf, t_run #' } #' @export #' @source Excel 3.02 spreadsheet available from -#' \url{https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3} +#' \url{https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html} #' @seealso \code{\link{perc_runoff_exposit}} for runoff loss percentages and \code{\link{perc_runoff_reduction_exposit}} for runoff reduction percentages used #' @examples #' PEC_sw_exposit_drainage(500, Koc = 150) diff --git a/R/drift_data_JKI.R b/R/drift_data_JKI.R index 3b02f43..8f78e4d 100644 --- a/R/drift_data_JKI.R +++ b/R/drift_data_JKI.R @@ -29,59 +29,12 @@ #' @source JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved #' from #' http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html -#' on 2015-06-11 +#' on 2015-06-11, not present any more 2024-01-31 #' #' Rautmann, D., Streloke, M and Winkler, R (2001) New basic drift values in #' the authorization procedure for plant protection products Mitt. Biol. #' Bundesanst. Land- Forstwirtsch. 383, 133-141 #' @keywords datasets #' @examples -#' -#' \dontrun{ -#' # This is the code that was used to extract the data -#' library(readxl) -#' abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls" -#' JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet", "Weinbau frueh", "Weinbau spaet", -#' "Hopfenbau", "Flaechenkulturen > 900 l/ha", "Gleisanlagen") -#' names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late", -#' "Vines early", "Vines late", "Hops", "Areic cultures > 900 L/ha", "Railroad tracks") -#' drift_data_JKI <- list() -#' -#' for (n in 1:8) { -#' drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2) -#' drift_data <- matrix(NA, nrow = 9, ncol = length(JKI_crops)) -#' dimnames(drift_data) <- list(distance = drift_data_raw[[1]][1:9], -#' crop = JKI_crops) -#' if (n == 1) { # Values for railroad tracks only present for one application -#' drift_data[, c(1:3, 5:8)] <- as.matrix(drift_data_raw[c(2:7, 11)][1:9, ]) -#' } else { -#' drift_data[, c(1:3, 5:7)] <- as.matrix(drift_data_raw[c(2:7)][1:9, ]) -#' } -#' drift_data_JKI[[n]] <- drift_data -#' } -#' -#' # Manual data entry from the Rautmann paper -#' drift_data_JKI[[1]]["3", "Ackerbau"] <- 0.95 -#' drift_data_JKI[[1]][, "Weinbau frueh"] <- c(NA, 2.7, 1.18, 0.39, 0.2, 0.13, 0.07, 0.04, 0.03) -#' drift_data_JKI[[2]]["3", "Ackerbau"] <- 0.79 -#' drift_data_JKI[[2]][, "Weinbau frueh"] <- c(NA, 2.53, 1.09, 0.35, 0.18, 0.11, 0.06, 0.03, 0.02) -#' drift_data_JKI[[3]]["3", "Ackerbau"] <- 0.68 -#' drift_data_JKI[[3]][, "Weinbau frueh"] <- c(NA, 2.49, 1.04, 0.32, 0.16, 0.10, 0.05, 0.03, 0.02) -#' drift_data_JKI[[4]]["3", "Ackerbau"] <- 0.62 -#' drift_data_JKI[[4]][, "Weinbau frueh"] <- c(NA, 2.44, 1.02, 0.31, 0.16, 0.10, 0.05, 0.03, 0.02) -#' drift_data_JKI[[5]]["3", "Ackerbau"] <- 0.59 -#' drift_data_JKI[[5]][, "Weinbau frueh"] <- c(NA, 2.37, 1.00, 0.31, 0.15, 0.09, 0.05, 0.03, 0.02) -#' drift_data_JKI[[6]]["3", "Ackerbau"] <- 0.56 -#' drift_data_JKI[[6]][, "Weinbau frueh"] <- c(NA, 2.29, 0.97, 0.30, 0.15, 0.09, 0.05, 0.03, 0.02) -#' drift_data_JKI[[7]]["3", "Ackerbau"] <- 0.55 -#' drift_data_JKI[[7]][, "Weinbau frueh"] <- c(NA, 2.24, 0.94, 0.29, 0.15, 0.09, 0.05, 0.03, 0.02) -#' drift_data_JKI[[8]]["3", "Ackerbau"] <- 0.52 -#' drift_data_JKI[[8]][, "Weinbau frueh"] <- c(NA, 2.16, 0.91, 0.28, 0.14, 0.09, 0.04, 0.03, 0.02) -#' -#' # Save the data -#' save(drift_data_JKI, file = "data/drift_data_JKI.RData") -#' } -#' -#' # And these are the resulting data #' drift_data_JKI NULL diff --git a/R/soil_scenario_data_EFSA_2015.R b/R/soil_scenario_data_EFSA_2015.R index 660cafe..0660d40 100644 --- a/R/soil_scenario_data_EFSA_2015.R +++ b/R/soil_scenario_data_EFSA_2015.R @@ -13,28 +13,8 @@ #' EFSA guidance document for predicting environmental concentrations #' of active substances of plant protection products and transformation products of these #' active substances in soil. \emph{EFSA Journal} \bold{13}(4) 4093 -#' doi:10.2903/j.efsa.2015.4093 +#' \doi{10.2903/j.efsa.2015.4093} #' @keywords datasets #' @examples -#' \dontrun{ -#' # This is the code that was used to define the data -#' soil_scenario_data_EFSA_2015 <- data.frame( -#' Zone = rep(c("North", "Central", "South"), 2), -#' Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"), -#' T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8), -#' T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7), -#' Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"), -#' f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011), -#' theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347), -#' rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51), -#' f_sce = c(3, 2, 2, 2, 1.5, 1.5), -#' f_mod = c(2, 2, 2, 4, 4, 4), -#' stringsAsFactors = FALSE, -#' row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS") -#' ) -#' save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData') -#' } -#' -#' # And this is the resulting dataframe #' soil_scenario_data_EFSA_2015 -NULL +"soil_scenario_data_EFSA_2015" diff --git a/R/soil_scenario_data_EFSA_2017.R b/R/soil_scenario_data_EFSA_2017.R index 79ee15f..f7cbea0 100644 --- a/R/soil_scenario_data_EFSA_2017.R +++ b/R/soil_scenario_data_EFSA_2017.R @@ -13,8 +13,10 @@ #' EFSA guidance document for predicting environmental concentrations #' of active substances of plant protection products and transformation products of these #' active substances in soil. \emph{EFSA Journal} \bold{15}(10) 4982 -#' doi:10.2903/j.efsa.2017.4982 +#' \doi{10.2903/j.efsa.2017.4982} #' @keywords datasets #' @examples #' soil_scenario_data_EFSA_2017 -NULL +#' +#' waldo::compare(soil_scenario_data_EFSA_2017, soil_scenario_data_EFSA_2015) +"soil_scenario_data_EFSA_2017" diff --git a/build.log b/build.log deleted file mode 100644 index b1447b2..0000000 --- a/build.log +++ /dev/null @@ -1,15 +0,0 @@ -* checking for file ‘./DESCRIPTION’ ... OK -* preparing ‘pfm’: -* checking DESCRIPTION meta-information ... OK -* checking for LF line-endings in source and make files and shell scripts -* checking for empty or unneeded directories - NB: this package now depends on R (>= 3.5.0) - WARNING: Added dependency on R >= 3.5.0 because serialized objects in - serialize/load version 3 cannot be read in older versions of R. - File(s) containing such objects: - ‘pfm/data/EFSA_GW_interception_2014.RData’ - ‘pfm/data/EFSA_washoff_2017.RData’ -* building ‘pfm_0.6.0.tar.gz’ -Warning: invalid uid value replaced by that for user 'nobody' -Warning: invalid gid value replaced by that for user 'nobody' - diff --git a/data/EFSA_GW_interception_2014.RData b/data/EFSA_GW_interception_2014.RData Binary files differindex 14fded6..d533b53 100644 --- a/data/EFSA_GW_interception_2014.RData +++ b/data/EFSA_GW_interception_2014.RData diff --git a/data/EFSA_washoff_2017.RData b/data/EFSA_washoff_2017.RData Binary files differindex 699c0c0..18d043f 100644 --- a/data/EFSA_washoff_2017.RData +++ b/data/EFSA_washoff_2017.RData diff --git a/data/FOCUS_GW_scenarios_2012.RData b/data/FOCUS_GW_scenarios_2012.RData Binary files differnew file mode 100644 index 0000000..c8367fa --- /dev/null +++ b/data/FOCUS_GW_scenarios_2012.RData diff --git a/data/perc_runoff.RData b/data/perc_runoff.RData Binary files differnew file mode 100644 index 0000000..249820e --- /dev/null +++ b/data/perc_runoff.RData diff --git a/data/soil_scenario_data_EFSA_2015.RData b/data/soil_scenario_data_EFSA_2015.RData Binary files differindex b30076f..f2caeca 100644 --- a/data/soil_scenario_data_EFSA_2015.RData +++ b/data/soil_scenario_data_EFSA_2015.RData diff --git a/data/soil_scenario_data_EFSA_2017.RData b/data/soil_scenario_data_EFSA_2017.RData Binary files differindex ff8f045..56b0a8f 100644 --- a/data/soil_scenario_data_EFSA_2017.RData +++ b/data/soil_scenario_data_EFSA_2017.RData diff --git a/docs/404.html b/docs/404.html index acdca31..bc1b5ff 100644 --- a/docs/404.html +++ b/docs/404.html @@ -1,66 +1,27 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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- - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-title-body"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -71,35 +32,27 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="https://pkgdown.jrwb.de/pfm/index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> - <li> - <a href="index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> <li> - <a href="reference/index.html">Reference</a> + <a href="https://pkgdown.jrwb.de/pfm/reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> +<ul class="nav navbar-nav navbar-right"></ul> +</div> +<!--/.nav-collapse --> + </div> +<!--/.container --> +</div> +<!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="contents col-md-9"> <div class="page-header"> <h1>Page not found (404)</h1> @@ -110,31 +63,31 @@ Content not found. Please use links in the navbar. </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> </nav> - </div> +</div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p> +<p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer> - </div> +</div> + + </body> </html> - - diff --git a/docs/authors.html b/docs/authors.html index e4155eb..c65d25e 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,66 +1,12 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Authors • pfm</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - -<!-- bootstrap-toc --> -<link rel="stylesheet" href="bootstrap-toc.css"> -<script src="bootstrap-toc.js"></script> - -<!-- Font Awesome icons --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> - -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="pkgdown.css" rel="stylesheet"> -<script src="pkgdown.js"></script> - - - - -<meta property="og:title" content="Authors" /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Authors and Citation • pfm</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"><script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </head> - - <body data-spy="scroll" data-target="#toc"> - <div class="container template-authors"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container template-citation-authors"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -71,46 +17,52 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="contents col-md-9"> - <div class="page-header"> - <h1>Authors</h1> + <div class="section level2 authors-section"> + <div class="page-header"> + <h1>Authors</h1> + </div> + + + <ul class="list-unstyled"><li> + <p><strong>Johannes Ranke</strong>. Author, maintainer. <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> + </p> + </li> + </ul></div> + <div class="section level2 citation-section"> + <div> + <h1 id="citation">Citation</h1> + </div> + </div> + - <ul class="list-unstyled"> - <li> - <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. <a href='https://orcid.org/0000-0003-4371-6538' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a> - </p> - </li> - </ul> + <p>Johannes Ranke (2024). +<em>pfm: Utilities for Pesticide Fate Modelling</em>. +R package version 0.6.1, <a href="https://pkgdown.jrwb.de/pfm">https://pkgdown.jrwb.de/pfm</a>. +</p> + <pre>@Manual{, + title = {pfm: Utilities for Pesticide Fate Modelling}, + author = {{Johannes Ranke}}, + year = {2024}, + note = {R package version 0.6.1}, + url = {https://pkgdown.jrwb.de/pfm}, +}</pre> </div> @@ -118,22 +70,20 @@ - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/index.html b/docs/index.html index fd7cfd1..7658961 100644 --- a/docs/index.html +++ b/docs/index.html @@ -21,6 +21,8 @@ <![endif]--> </head> <body data-spy="scroll" data-target="#toc"> + + <div class="container template-home"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> @@ -33,19 +35,13 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<li> <a href="reference/index.html">Reference</a> </li> </ul> @@ -61,68 +57,74 @@ </header><div class="row"> <div class="contents col-md-9"> -<div id="pfm" class="section level1"> -<div class="page-header"><h1 class="hasAnchor"> -<a href="#pfm" class="anchor"></a>pfm</h1></div> - +<div class="section level1"> +<div class="page-header"><h1 id="pfm">pfm<a class="anchor" aria-label="anchor" href="#pfm"></a> +</h1></div> +<p><a href="https://travis-ci.com/jranke/pfm" class="external-link"><img src="https://travis-ci.com/jranke/pfm.svg?branch=main" alt="Build Status"></a> <a href="https://codecov.io/github/jranke/pfm" class="external-link"><img src="https://codecov.io/github/jranke/pfm/branch/main/graphs/badge.svg" alt="codecov"></a></p> <p>The R package <strong>pfm</strong> provides some utilities for fate modelling, including dealing with FOCUS pesticide fate modelling tools, (currently only TOXSWA cwa and out files), made available under the GNU public license.</p> -<div id="installation" class="section level2"> -<h2 class="hasAnchor"> -<a href="#installation" class="anchor"></a>Installation</h2> -<p>The easiest way to install the package is probably to use <a href="https://cran.r-project.org/package=drat">drat</a>:</p> +<div class="section level2"> +<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a> +</h2> +<p>The easiest way to install the package is probably to use <a href="https://cran.r-project.org/package=drat" class="external-link">drat</a>:</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"drat"</span><span class="op">)</span> -<span class="fu">drat</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/drat/man/addRepo.html">addRepo</a></span><span class="op">(</span><span class="st">"jranke"</span><span class="op">)</span> -<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"pfm"</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"drat"</span><span class="op">)</span></span> +<span><span class="fu">drat</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/drat/man/addRepo.html" class="external-link">addRepo</a></span><span class="op">(</span><span class="st">"jranke"</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"pfm"</span><span class="op">)</span></span></code></pre></div> <p>Alternatively you can install the package using the <code>devtools</code> package. Using <code>quick = TRUE</code> skips docs, multiple-architecture builds, demos, and vignettes.</p> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://devtools.r-lib.org/">devtools</a></span><span class="op">)</span> -<span class="fu"><a href="https://devtools.r-lib.org//reference/remote-reexports.html">install_github</a></span><span class="op">(</span><span class="st">"jranke/pfm"</span>, quick <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://devtools.r-lib.org/" class="external-link">devtools</a></span><span class="op">)</span></span> +<span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"jranke/pfm"</span>, quick <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> </div> -<div id="use" class="section level2"> -<h2 class="hasAnchor"> -<a href="#use" class="anchor"></a>Use</h2> -<p>Please refer to the <a href="http://pkgdown.jrwb.de/pfm/reference/index.html">reference</a>.</p> +<div class="section level2"> +<h2 id="use">Use<a class="anchor" aria-label="anchor" href="#use"></a> +</h2> +<p>Please refer to the <a href="http://pkgdown.jrwb.de/pfm/reference/index.html" class="external-link">reference</a>.</p> </div> -<div id="examples" class="section level2"> -<h2 class="hasAnchor"> -<a href="#examples" class="anchor"></a>Examples</h2> -<p>One recent nice example of the usage of this package is the visualisation of a time weighted average for a sawtooth curve obtained from several overlays of mkinfit predictions as shown <a href="http://pkgdown.jrwb.de/pfm/reference/plot.one_box.html">here</a>.</p> +<div class="section level2"> +<h2 id="examples">Examples<a class="anchor" aria-label="anchor" href="#examples"></a> +</h2> +<p>One recent nice example of the usage of this package is the visualisation of a time weighted average for a sawtooth curve obtained from several overlays of mkinfit predictions as shown <a href="http://pkgdown.jrwb.de/pfm/reference/plot.one_box.html" class="external-link">here</a>.</p> </div> </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <div class="license"> -<h2>License</h2> +<h2 data-toc-skip>License</h2> <ul class="list-unstyled"> <li>GPL</li> </ul> </div> -<div class="developers"> -<h2>Developers</h2> + + +<div class="citation"> +<h2 data-toc-skip>Citation</h2> <ul class="list-unstyled"> -<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li> +<li><a href="authors.html#citation">Citing pfm</a></li> </ul> </div> - <div class="dev-status"> -<h2>Dev status</h2> +<div class="developers"> +<h2 data-toc-skip>Developers</h2> <ul class="list-unstyled"> -<li><a href="https://travis-ci.com/jranke/pfm"><img src="https://travis-ci.com/jranke/pfm.svg?branch=main" alt="Build Status"></a></li> -<li><a href="https://codecov.io/github/jranke/pfm"><img src="https://codecov.io/github/jranke/pfm/branch/main/graphs/badge.svg" alt="codecov"></a></li> +<li>Johannes Ranke <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li> </ul> </div> -</div> + + + + </div> </div> <footer><div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <p></p> +<p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer> @@ -131,5 +133,7 @@ + + </body> </html> diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 1273238..80ea5b8 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -56,8 +56,10 @@ img.icon { float: right; } -img { +/* Ensure in-page images don't run outside their container */ +.contents img { max-width: 100%; + height: auto; } /* Fix bug in bootstrap (only seen in firefox) */ @@ -78,11 +80,10 @@ dd { /* Section anchors ---------------------------------*/ a.anchor { - margin-left: -30px; - display:inline-block; - width: 30px; - height: 30px; - visibility: hidden; + display: none; + margin-left: 5px; + width: 20px; + height: 20px; background-image: url(./link.svg); background-repeat: no-repeat; @@ -90,17 +91,15 @@ a.anchor { background-position: center center; } -.hasAnchor:hover a.anchor { - visibility: visible; -} - -@media (max-width: 767px) { - .hasAnchor:hover a.anchor { - visibility: hidden; - } +h1:hover .anchor, +h2:hover .anchor, +h3:hover .anchor, +h4:hover .anchor, +h5:hover .anchor, +h6:hover .anchor { + display: inline-block; } - /* Fixes for fixed navbar --------------------------*/ .contents h1, .contents h2, .contents h3, .contents h4 { @@ -264,31 +263,26 @@ table { /* Syntax highlighting ---------------------------------------------------- */ -pre { - word-wrap: normal; - word-break: normal; - border: 1px solid #eee; -} - -pre, code { +pre, code, pre code { background-color: #f8f8f8; color: #333; } +pre, pre code { + white-space: pre-wrap; + word-break: break-all; + overflow-wrap: break-word; +} -pre code { - overflow: auto; - word-wrap: normal; - white-space: pre; +pre { + border: 1px solid #eee; } -pre .img { +pre .img, pre .r-plt { margin: 5px 0; } -pre .img img { +pre .img img, pre .r-plt img { background-color: #fff; - display: block; - height: auto; } code a, pre a { @@ -305,9 +299,8 @@ a.sourceLine:hover { .kw {color: #264D66;} /* keyword */ .co {color: #888888;} /* comment */ -.message { color: black; font-weight: bolder;} -.error { color: orange; font-weight: bolder;} -.warning { color: #6A0366; font-weight: bolder;} +.error {font-weight: bolder;} +.warning {font-weight: bolder;} /* Clipboard --------------------------*/ @@ -365,3 +358,27 @@ mark { content: ""; } } + +/* Section anchors --------------------------------- + Added in pandoc 2.11: https://github.com/jgm/pandoc-templates/commit/9904bf71 +*/ + +div.csl-bib-body { } +div.csl-entry { + clear: both; +} +.hanging-indent div.csl-entry { + margin-left:2em; + text-indent:-2em; +} +div.csl-left-margin { + min-width:2em; + float:left; +} +div.csl-right-inline { + margin-left:2em; + padding-left:1em; +} +div.csl-indent { + margin-left: 2em; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 7e7048f..6f0eee4 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -80,7 +80,7 @@ $(document).ready(function() { var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-label='Copy to clipboard' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy'></i></button>"; - $(".examples, div.sourceCode").addClass("hasCopyButton"); + $("div.sourceCode").addClass("hasCopyButton"); // Insert copy buttons: $(copyButton).prependTo(".hasCopyButton"); @@ -91,7 +91,7 @@ // Initialize clipboard: var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', { text: function(trigger) { - return trigger.parentNode.textContent; + return trigger.parentNode.textContent.replace(/\n#>[^\n]*/g, ""); } }); diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index cc57584..62c4837 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,8 +1,8 @@ -pandoc: 2.9.2.1 -pkgdown: 1.6.1 +pandoc: 3.1.1 +pkgdown: 2.0.7 pkgdown_sha: ~ articles: {} -last_built: 2021-11-18T23:17Z +last_built: 2024-01-31T12:15Z urls: reference: https://pkgdown.jrwb.de/pfm/reference article: https://pkgdown.jrwb.de/pfm/articles diff --git a/docs/reference/EFSA_GW_interception_2014.html b/docs/reference/EFSA_GW_interception_2014.html index d7ec108..8bc0b51 100644 --- a/docs/reference/EFSA_GW_interception_2014.html +++ b/docs/reference/EFSA_GW_interception_2014.html @@ -1,67 +1,12 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -72,35 +17,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Subset of EFSA crop interception default values for groundwater modelling</h1> @@ -112,82 +43,58 @@ <p>Subset of EFSA crop interception default values for groundwater modelling</p> </div> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">EFSA_GW_interception_2014</span></span></code></pre></div> + </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div id="format"> + <h2>Format</h2> <p>A matrix containing interception values, currently only for some selected crops</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div id="source"> + <h2>Source</h2> <p>European Food Safety Authority (2014) EFSA Guidance Document for evaluating laboratory and field dissipation studies to obtain DegT50 values of active substances of plant protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>12</b>(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - <span class='co'># This is the code that was used to define the data</span> - <span class='no'>bbch</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='fl'>0</span>:<span class='fl'>9</span>, <span class='st'>"x"</span>) - <span class='no'>crops</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>( - <span class='st'>"Beans (field + vegetable)"</span>, - <span class='st'>"Peas"</span>, - <span class='st'>"Summer oilseed rape"</span>, <span class='st'>"Winter oilseed rape"</span>, - <span class='st'>"Tomatoes"</span>, - <span class='st'>"Spring cereals"</span>, <span class='st'>"Winter cereals"</span>) - <span class='no'>EFSA_GW_interception_2014</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fl'>NA</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>crops</span>), <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>bbch</span>), - <span class='kw'>dimnames</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Crop</span> <span class='kw'>=</span> <span class='no'>crops</span>, <span class='kw'>BBCH</span> <span class='kw'>=</span> <span class='no'>bbch</span>)) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Beans (field + vegetable)"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.25</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.4</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.7</span>, <span class='fl'>5</span>), <span class='fl'>0.8</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Peas"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.35</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.55</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.85</span>, <span class='fl'>5</span>), <span class='fl'>0.85</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Summer oilseed rape"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.4</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>5</span>), <span class='fl'>0.9</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Winter oilseed rape"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.4</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>5</span>), <span class='fl'>0.9</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Tomatoes"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.5</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.7</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>5</span>), <span class='fl'>0.5</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Spring cereals"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0</span>, <span class='fl'>0.2</span>, <span class='fl'>0.8</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.9</span>, <span class='fl'>3</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>2</span>), <span class='fl'>0.8</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Winter cereals"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0</span>, <span class='fl'>0.2</span>, <span class='fl'>0.8</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.9</span>, <span class='fl'>3</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>2</span>), <span class='fl'>0.8</span>) - <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>EFSA_GW_interception_2014</span>, - <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"../data/EFSA_GW_interception_2014.RData"</span>) -} -<span class='no'>EFSA_GW_interception_2014</span></div><div class='output co'>#> BBCH -#> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x -#> Beans (field + vegetable) 0 0.25 0.40 0.40 0.70 0.70 0.70 0.70 0.70 0.80 -#> Peas 0 0.35 0.55 0.55 0.85 0.85 0.85 0.85 0.85 0.85 -#> Summer oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90 -#> Winter oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90 -#> Tomatoes 0 0.50 0.70 0.70 0.80 0.80 0.80 0.80 0.80 0.50 -#> Spring cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80 -#> Winter cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">EFSA_GW_interception_2014</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> BBCH</span> +<span class="r-out co"><span class="r-pr">#></span> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x</span> +<span class="r-out co"><span class="r-pr">#></span> Beans (field + vegetable) 0 0.25 0.40 0.40 0.70 0.70 0.70 0.70 0.70 0.80</span> +<span class="r-out co"><span class="r-pr">#></span> Peas 0 0.35 0.55 0.55 0.85 0.85 0.85 0.85 0.85 0.85</span> +<span class="r-out co"><span class="r-pr">#></span> Summer oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90</span> +<span class="r-out co"><span class="r-pr">#></span> Winter oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90</span> +<span class="r-out co"><span class="r-pr">#></span> Tomatoes 0 0.50 0.70 0.70 0.80 0.80 0.80 0.80 0.80 0.50</span> +<span class="r-out co"><span class="r-pr">#></span> Spring cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80</span> +<span class="r-out co"><span class="r-pr">#></span> Winter cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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- </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Subset of EFSA crop washoff default values</h1> @@ -112,82 +43,58 @@ <p>Subset of EFSA crop washoff default values</p> </div> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">EFSA_washoff_2017</span></span></code></pre></div> + </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div id="format"> + <h2>Format</h2> <p>A matrix containing wash-off factors, currently only for some selected crops</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div id="source"> + <h2>Source</h2> <p>European Food Safety Authority (2017) EFSA guidance document for predicting environmental concentrations of active substances of plant protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>15</b>(10) 4982 doi:10.2903/j.efsa.2017.4982</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - <span class='co'># This is the code that was used to define the data</span> - <span class='no'>bbch</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='fl'>0</span>:<span class='fl'>9</span>, <span class='st'>"x"</span>) - <span class='no'>crops</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>( - <span class='st'>"Beans (field + vegetable)"</span>, - <span class='st'>"Peas"</span>, - <span class='st'>"Summer oilseed rape"</span>, <span class='st'>"Winter oilseed rape"</span>, - <span class='st'>"Tomatoes"</span>, - <span class='st'>"Spring cereals"</span>, <span class='st'>"Winter cereals"</span>) - <span class='no'>EFSA_washoff_2017</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fl'>NA</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>crops</span>), <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>bbch</span>), - <span class='kw'>dimnames</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Crop</span> <span class='kw'>=</span> <span class='no'>crops</span>, <span class='kw'>BBCH</span> <span class='kw'>=</span> <span class='no'>bbch</span>)) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Beans (field + vegetable)"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.6</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.75</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>5</span>), <span class='fl'>0.35</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Peas"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.4</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.6</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.65</span>, <span class='fl'>5</span>), <span class='fl'>0.35</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Summer oilseed rape"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.4</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.5</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.6</span>, <span class='fl'>5</span>), <span class='fl'>0.5</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Winter oilseed rape"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.1</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.4</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.55</span>, <span class='fl'>5</span>), <span class='fl'>0.3</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Tomatoes"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.55</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.75</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.7</span>, <span class='fl'>5</span>), <span class='fl'>0.35</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Spring cereals"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.4</span>, <span class='fl'>0.5</span>, <span class='fl'>0.5</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.65</span>, <span class='fl'>3</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.65</span>, <span class='fl'>2</span>), <span class='fl'>0.55</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Winter cereals"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.1</span>, <span class='fl'>0.4</span>, <span class='fl'>0.6</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.55</span>, <span class='fl'>3</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.6</span>, <span class='fl'>2</span>), <span class='fl'>0.4</span>) - <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>EFSA_washoff_2017</span>, - <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"../data/EFSA_washoff_2017.RData"</span>) -} -<span class='no'>EFSA_washoff_2017</span></div><div class='output co'>#> BBCH -#> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x -#> Beans (field + vegetable) NA 0.60 0.75 0.75 0.80 0.80 0.80 0.80 0.80 0.35 -#> Peas NA 0.40 0.60 0.60 0.65 0.65 0.65 0.65 0.65 0.35 -#> Summer oilseed rape NA 0.40 0.50 0.50 0.60 0.60 0.60 0.60 0.60 0.50 -#> Winter oilseed rape NA 0.10 0.40 0.40 0.55 0.55 0.55 0.55 0.55 0.30 -#> Tomatoes NA 0.55 0.75 0.75 0.70 0.70 0.70 0.70 0.70 0.35 -#> Spring cereals NA 0.40 0.50 0.50 0.65 0.65 0.65 0.65 0.65 0.55 -#> Winter cereals NA 0.10 0.40 0.60 0.55 0.55 0.55 0.60 0.60 0.40</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">EFSA_washoff_2017</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> BBCH</span> +<span class="r-out co"><span class="r-pr">#></span> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x</span> +<span class="r-out co"><span class="r-pr">#></span> Beans (field + vegetable) NA 0.60 0.75 0.75 0.80 0.80 0.80 0.80 0.80 0.35</span> +<span class="r-out co"><span class="r-pr">#></span> Peas NA 0.40 0.60 0.60 0.65 0.65 0.65 0.65 0.65 0.35</span> +<span class="r-out co"><span class="r-pr">#></span> Summer oilseed rape NA 0.40 0.50 0.50 0.60 0.60 0.60 0.60 0.60 0.50</span> +<span class="r-out co"><span class="r-pr">#></span> Winter oilseed rape NA 0.10 0.40 0.40 0.55 0.55 0.55 0.55 0.55 0.30</span> +<span class="r-out co"><span class="r-pr">#></span> Tomatoes NA 0.55 0.75 0.75 0.70 0.70 0.70 0.70 0.70 0.35</span> +<span class="r-out co"><span class="r-pr">#></span> Spring cereals NA 0.40 0.50 0.50 0.65 0.65 0.65 0.65 0.65 0.55</span> +<span class="r-out co"><span class="r-pr">#></span> Winter cereals NA 0.10 0.40 0.60 0.55 0.55 0.55 0.60 0.60 0.40</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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The +soil definitions are from page 46ff. from FOCUS (2012)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,35 +18,21 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>A very small subset of the FOCUS Groundwater scenario definitions</h1> @@ -114,104 +45,107 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> soil definitions are from page 46ff. from FOCUS (2012).</p> </div> - <pre class="usage"><span class='no'>FOCUS_GW_scenarios_2012</span></pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_GW_scenarios_2012</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> <p>An object of class <code>list</code> of length 2.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - + </div> + <div id="references"> + <h2>References</h2> <p>FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. FOrum for the Co-ordination of pesticde fate models and their USe. http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>FOCUS_GW_scenarios_2012</span></div><div class='output co'>#> $names -#> Cha Ham Jok Kre Oke -#> "Châteaudun" "Hamburg" "Jokioinen" "Kremsmünster" "Okehampton" -#> Pia Por Sev Thi -#> "Piacenza" "Porto" "Sevilla" "Thiva" -#> -#> $soils -#> location horizon number pH_H2O perc_clay perc_oc rel_deg -#> 1 Cha Ap 1 8.0 30.0 1.39 1.0 -#> 2 Cha B1 2 8.1 31.0 0.93 0.5 -#> 3 Cha B2 3 8.2 25.0 0.70 0.5 -#> 4 Cha II C1 4 8.5 26.0 0.30 0.3 -#> 5 Cha II C1 5 8.5 26.0 0.30 0.0 -#> 6 Cha II C2 6 8.5 24.0 0.27 0.0 -#> 7 Cha M 7 8.3 31.0 0.21 0.0 -#> 8 Ham Ap 1 6.4 7.2 1.50 1.0 -#> 9 Ham BvI 2 5.6 6.7 1.00 0.5 -#> 10 Ham BvII 3 5.6 0.9 0.20 0.3 -#> 11 Ham Bv/Cv 4 5.7 0.0 0.00 0.3 -#> 12 Ham Cv 5 5.5 0.0 0.00 0.3 -#> 13 Ham Cv 6 5.5 0.0 0.00 0.0 -#> 14 Jok Ap 1 6.2 3.6 4.06 1.0 -#> 15 Jok Bs 2 5.6 1.8 0.84 0.5 -#> 16 Jok BC1 3 5.4 1.2 0.36 0.3 -#> 17 Jok BC2 4 5.4 1.7 0.29 0.3 -#> 18 Jok BC2 5 5.4 1.7 0.29 0.0 -#> 19 Jok Cg 6 5.3 1.9 0.21 0.0 -#> 20 Kre <NA> 1 7.7 14.0 3.60 1.0 -#> 21 Kre <NA> 2 7.0 25.0 1.00 0.5 -#> 22 Kre <NA> 3 7.1 27.0 0.50 0.5 -#> 23 Kre <NA> 4 7.1 27.0 0.50 0.3 -#> 24 Kre <NA> 5 7.1 27.0 0.50 0.0 -#> 25 Oke A 1 5.8 18.0 2.20 1.0 -#> 26 Oke Bw1 2 6.3 17.0 0.70 0.5 -#> 27 Oke BC 3 6.5 14.0 0.40 0.3 -#> 28 Oke C 4 6.6 9.0 0.10 0.3 -#> 29 Oke C 5 6.6 9.0 0.10 0.0 -#> 30 Pia Ap 1 7.0 15.0 1.26 1.0 -#> 31 Pia Ap 2 7.0 15.0 1.26 0.5 -#> 32 Pia Bw 3 6.3 7.0 0.47 0.5 -#> 33 Pia Bw 4 6.3 7.0 0.47 0.3 -#> 34 Pia 2C 5 6.4 0.0 0.00 0.3 -#> 35 Pia 2C 6 6.4 0.0 0.00 0.0 -#> 36 Por <NA> 1 4.9 10.0 1.42 1.0 -#> 37 Por <NA> 2 4.8 8.0 0.78 0.5 -#> 38 Por <NA> 3 4.8 8.0 0.78 0.3 -#> 39 Por <NA> 4 4.8 8.0 0.78 0.0 -#> 40 Sev <NA> 1 7.3 14.0 0.93 1.0 -#> 41 Sev <NA> 2 7.3 13.0 0.93 1.0 -#> 42 Sev <NA> 3 7.8 15.0 0.70 0.5 -#> 43 Sev <NA> 4 8.1 16.0 0.58 0.3 -#> 44 Sev <NA> 5 8.1 16.0 0.58 0.0 -#> 45 Sev <NA> 6 8.2 22.0 0.49 0.0 -#> 46 Thi Ap1 1 7.7 25.3 0.74 1.0 -#> 47 Thi Ap2 2 7.7 25.3 0.74 0.5 -#> 48 Thi Bw 3 7.8 29.6 0.57 0.5 -#> 49 Thi Bw 4 7.8 31.9 0.31 0.3 -#> 50 Thi Ck1 5 7.8 32.9 0.18 0.3 -#> 51 Thi Ck1 6 7.8 32.9 0.18 0.0 -#> </div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">FOCUS_GW_scenarios_2012</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $names</span> +<span class="r-out co"><span class="r-pr">#></span> Cha Ham Jok Kre Oke </span> +<span class="r-out co"><span class="r-pr">#></span> "Châteaudun" "Hamburg" "Jokioinen" "Kremsmünster" "Okehampton" </span> +<span class="r-out co"><span class="r-pr">#></span> Pia Por Sev Thi </span> +<span class="r-out co"><span class="r-pr">#></span> "Piacenza" "Porto" "Sevilla" "Thiva" </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $soils</span> +<span class="r-out co"><span class="r-pr">#></span> location horizon number pH_H2O perc_clay perc_oc rel_deg</span> +<span class="r-out co"><span class="r-pr">#></span> 1 Cha Ap 1 8.0 30.0 1.39 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 Cha B1 2 8.1 31.0 0.93 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 3 Cha B2 3 8.2 25.0 0.70 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 4 Cha II C1 4 8.5 26.0 0.30 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 5 Cha II C1 5 8.5 26.0 0.30 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 6 Cha II C2 6 8.5 24.0 0.27 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 7 Cha M 7 8.3 31.0 0.21 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 8 Ham Ap 1 6.4 7.2 1.50 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 9 Ham BvI 2 5.6 6.7 1.00 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 10 Ham BvII 3 5.6 0.9 0.20 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 11 Ham Bv/Cv 4 5.7 0.0 0.00 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 12 Ham Cv 5 5.5 0.0 0.00 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 13 Ham Cv 6 5.5 0.0 0.00 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 14 Jok Ap 1 6.2 3.6 4.06 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 15 Jok Bs 2 5.6 1.8 0.84 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 16 Jok BC1 3 5.4 1.2 0.36 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 17 Jok BC2 4 5.4 1.7 0.29 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 18 Jok BC2 5 5.4 1.7 0.29 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 19 Jok Cg 6 5.3 1.9 0.21 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 20 Kre <NA> 1 7.7 14.0 3.60 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 21 Kre <NA> 2 7.0 25.0 1.00 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 22 Kre <NA> 3 7.1 27.0 0.50 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 23 Kre <NA> 4 7.1 27.0 0.50 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 24 Kre <NA> 5 7.1 27.0 0.50 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 25 Oke A 1 5.8 18.0 2.20 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 26 Oke Bw1 2 6.3 17.0 0.70 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 27 Oke BC 3 6.5 14.0 0.40 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 28 Oke C 4 6.6 9.0 0.10 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 29 Oke C 5 6.6 9.0 0.10 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 30 Pia Ap 1 7.0 15.0 1.26 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 31 Pia Ap 2 7.0 15.0 1.26 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 32 Pia Bw 3 6.3 7.0 0.47 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 33 Pia Bw 4 6.3 7.0 0.47 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 34 Pia 2C 5 6.4 0.0 0.00 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 35 Pia 2C 6 6.4 0.0 0.00 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 36 Por <NA> 1 4.9 10.0 1.42 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 37 Por <NA> 2 4.8 8.0 0.78 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 38 Por <NA> 3 4.8 8.0 0.78 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 39 Por <NA> 4 4.8 8.0 0.78 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 40 Sev <NA> 1 7.3 14.0 0.93 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 41 Sev <NA> 2 7.3 13.0 0.93 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 42 Sev <NA> 3 7.8 15.0 0.70 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 43 Sev <NA> 4 8.1 16.0 0.58 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 44 Sev <NA> 5 8.1 16.0 0.58 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 45 Sev <NA> 6 8.2 22.0 0.49 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 46 Thi Ap1 1 7.7 25.3 0.74 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 47 Thi Ap2 2 7.7 25.3 0.74 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 48 Thi Bw 3 7.8 29.6 0.57 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 49 Thi Bw 4 7.8 31.9 0.31 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 50 Thi Ck1 5 7.8 32.9 0.18 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 51 Thi Ck1 6 7.8 32.9 0.18 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index bbfb592..0216e4e 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.html +++ b/docs/reference/FOCUS_Step_12_scenarios.html @@ -1,68 +1,13 @@ -<!-- Generated by pkgdown: do not 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<span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</h1> @@ -115,210 +46,78 @@ The text file is not included in the package as its licence is not clear.</p> </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div id="format"> + <h2>Format</h2> <p>A list containing the scenario names in a character vector called 'names', the drift percentiles in a matrix called 'drift', interception percentages in a matrix called 'interception' and the runoff/drainage percentages for Step 2 calculations in a matrix called 'rd'.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - <span class='co'># This is the code that was used to extract the data</span> - <span class='no'>scenario_path</span> <span class='kw'><-</span> <span class='st'>"inst/extdata/FOCUS_Step_12_scenarios.txt"</span> - <span class='no'>scenarios</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/readLines.html'>readLines</a></span>(<span class='no'>scenario_path</span>)[<span class='fl'>9</span>:<span class='fl'>38</span>] - <span class='no'>FOCUS_Step_12_scenarios</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>() - <span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/utils/read.table.html'>read.table</a></span>(<span class='kw'>text</span> <span class='kw'>=</span> <span class='no'>scenarios</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>, <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>check.names</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) - <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span> <span class='kw'>=</span> <span class='no'>sce</span>$<span class='no'>Crop</span> - <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>sce</span>) <span class='kw'><-</span> <span class='no'>sce</span>$<span class='no'>Crop</span> - <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>drift</span> <span class='kw'>=</span> <span class='no'>sce</span>[, <span class='fl'>3</span>:<span class='fl'>11</span>] - <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>interception</span> <span class='kw'>=</span> <span class='no'>sce</span>[, <span class='fl'>12</span>:<span class='fl'>15</span>] - <span class='no'>sce_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/readLines.html'>readLines</a></span>(<span class='no'>scenario_path</span>)[<span class='fl'>41</span>:<span class='fl'>46</span>] - <span class='no'>rd</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/utils/read.table.html'>read.table</a></span>(<span class='kw'>text</span> <span class='kw'>=</span> <span class='no'>sce_2</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>)[<span class='fl'>1</span>:<span class='fl'>2</span>] - <span class='no'>rd_mat</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='no'>rd</span>$<span class='no'>V2</span>, <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>byrow</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) - <span class='fu'><a href='https://rdrr.io/r/base/dimnames.html'>dimnames</a></span>(<span class='no'>rd_mat</span>) <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Oct-Feb"</span>, <span class='st'>"Mar-May"</span>, <span class='st'>"Jun-Sep"</span>), - <span class='kw'>Region</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"North"</span>, <span class='st'>"South"</span>)) - <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>rd</span> <span class='kw'>=</span> <span class='no'>rd_mat</span> - <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>FOCUS_Step_12_scenarios</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"data/FOCUS_Step_12_scenarios.RData"</span>) -} - -<span class='co'># And this is the resulting data</span> -<span class='no'>FOCUS_Step_12_scenarios</span></div><div class='output co'>#> $names -#> [1] "cereals, spring" "cereals, winter" -#> [3] "citrus" "cotton" -#> [5] "field beans" "grass / alfalfa" -#> [7] "hops" "legumes" -#> [9] "maize" "oil seed rape, spring" -#> [11] "oil seed rape, winter" "olives" -#> [13] "pome / stone fruit, early applns" "pome / stone fruit, late applns" -#> [15] "potatoes" "soybeans" -#> [17] "sugar beets" "sunflowers" -#> [19] "tobacco" "vegetables, bulb" -#> [21] "vegetables, fruiting" "vegetables, leafy" -#> [23] "vegetables, root" "vines, early applns" -#> [25] "vines, late applns" "appln, aerial" -#> [27] "appln, hand (crop < 50 cm)" "appln, hand (crop > 50 cm)" -#> [29] "no drift (incorp or seed trtmt)" -#> -#> $drift -#> 1 2 3 4 5 6 -#> cereals, spring 2.759 2.438 2.024 1.862 1.794 1.631 -#> cereals, winter 2.759 2.438 2.024 1.862 1.794 1.631 -#> citrus 15.725 12.129 11.011 10.124 9.743 9.204 -#> cotton 2.759 2.438 2.024 1.862 1.794 1.631 -#> field beans 2.759 2.438 2.024 1.862 1.794 1.631 -#> grass / alfalfa 2.759 2.438 2.024 1.862 1.794 1.631 -#> hops 19.326 17.723 15.928 15.378 15.114 14.902 -#> legumes 2.759 2.438 2.024 1.862 1.794 1.631 -#> maize 2.759 2.438 2.024 1.862 1.794 1.631 -#> oil seed rape, spring 2.759 2.438 2.024 1.862 1.794 1.631 -#> oil seed rape, winter 2.759 2.438 2.024 1.862 1.794 1.631 -#> olives 15.725 12.129 11.011 10.124 9.743 9.204 -#> pome / stone fruit, early applns 29.197 25.531 23.960 23.603 23.116 22.760 -#> pome / stone fruit, late applns 15.725 12.129 11.011 10.124 9.743 9.204 -#> potatoes 2.759 2.438 2.024 1.862 1.794 1.631 -#> soybeans 2.759 2.438 2.024 1.862 1.794 1.631 -#> sugar beets 2.759 2.438 2.024 1.862 1.794 1.631 -#> sunflowers 2.759 2.438 2.024 1.862 1.794 1.631 -#> tobacco 2.759 2.438 2.024 1.862 1.794 1.631 -#> vegetables, bulb 2.759 2.438 2.024 1.862 1.794 1.631 -#> vegetables, fruiting 2.759 2.438 2.024 1.862 1.794 1.631 -#> vegetables, leafy 2.759 2.438 2.024 1.862 1.794 1.631 -#> vegetables, root 2.759 2.438 2.024 1.862 1.794 1.631 -#> vines, early applns 2.699 2.496 2.546 2.499 2.398 2.336 -#> vines, late applns 8.028 7.119 6.898 6.631 6.636 6.431 -#> appln, aerial 33.200 33.200 33.200 33.200 33.200 33.200 -#> appln, hand (crop < 50 cm) 2.759 2.438 2.024 1.862 1.794 1.631 -#> appln, hand (crop > 50 cm) 8.028 7.119 6.898 6.631 6.636 6.431 -#> no drift (incorp or seed trtmt) 0.000 0.000 0.000 0.000 0.000 0.000 -#> 7 8 >8 -#> cereals, spring 1.578 1.512 1.512 -#> cereals, winter 1.578 1.512 1.512 -#> citrus 9.102 8.656 8.656 -#> cotton 1.578 1.512 1.512 -#> field beans 1.578 1.512 1.512 -#> grass / alfalfa 1.578 1.512 1.512 -#> hops 14.628 13.520 13.520 -#> legumes 1.578 1.512 1.512 -#> maize 1.578 1.512 1.512 -#> oil seed rape, spring 1.578 1.512 1.512 -#> oil seed rape, winter 1.578 1.512 1.512 -#> olives 9.102 8.656 8.656 -#> pome / stone fruit, early applns 22.690 22.241 22.241 -#> pome / stone fruit, late applns 9.102 8.656 8.656 -#> potatoes 1.578 1.512 1.512 -#> soybeans 1.578 1.512 1.512 -#> sugar beets 1.578 1.512 1.512 -#> sunflowers 1.578 1.512 1.512 -#> tobacco 1.578 1.512 1.512 -#> vegetables, bulb 1.578 1.512 1.512 -#> vegetables, fruiting 1.578 1.512 1.512 -#> vegetables, leafy 1.578 1.512 1.512 -#> vegetables, root 1.578 1.512 1.512 -#> vines, early applns 2.283 2.265 2.265 -#> vines, late applns 6.227 6.173 6.173 -#> appln, aerial 33.200 33.200 33.200 -#> appln, hand (crop < 50 cm) 1.578 1.512 1.512 -#> appln, hand (crop > 50 cm) 6.227 6.173 6.173 -#> no drift (incorp or seed trtmt) 0.000 0.000 0.000 -#> -#> $interception -#> no interception minimal crop cover -#> cereals, spring 0 0.00 -#> cereals, winter 0 0.00 -#> citrus 0 0.80 -#> cotton 0 0.30 -#> field beans 0 0.25 -#> grass / alfalfa 0 0.40 -#> hops 0 0.20 -#> legumes 0 0.25 -#> maize 0 0.25 -#> oil seed rape, spring 0 0.40 -#> oil seed rape, winter 0 0.40 -#> olives 0 0.70 -#> pome / stone fruit, early applns 0 0.20 -#> pome / stone fruit, late applns 0 0.20 -#> potatoes 0 0.15 -#> soybeans 0 0.20 -#> sugar beets 0 0.20 -#> sunflowers 0 0.20 -#> tobacco 0 0.20 -#> vegetables, bulb 0 0.10 -#> vegetables, fruiting 0 0.25 -#> vegetables, leafy 0 0.25 -#> vegetables, root 0 0.25 -#> vines, early applns 0 0.40 -#> vines, late applns 0 0.40 -#> appln, aerial 0 0.20 -#> appln, hand (crop < 50 cm) 0 0.20 -#> appln, hand (crop > 50 cm) 0 0.20 -#> no drift (incorp or seed trtmt) 0 0.00 -#> average crop cover full canopy -#> cereals, spring 0.20 0.70 -#> cereals, winter 0.20 0.70 -#> citrus 0.80 0.80 -#> cotton 0.60 0.75 -#> field beans 0.40 0.70 -#> grass / alfalfa 0.60 0.75 -#> hops 0.50 0.70 -#> legumes 0.50 0.70 -#> maize 0.50 0.75 -#> oil seed rape, spring 0.70 0.75 -#> oil seed rape, winter 0.70 0.75 -#> olives 0.70 0.70 -#> pome / stone fruit, early applns 0.40 0.65 -#> pome / stone fruit, late applns 0.40 0.65 -#> potatoes 0.50 0.70 -#> soybeans 0.50 0.75 -#> sugar beets 0.70 0.75 -#> sunflowers 0.50 0.75 -#> tobacco 0.70 0.75 -#> vegetables, bulb 0.25 0.40 -#> vegetables, fruiting 0.50 0.70 -#> vegetables, leafy 0.40 0.70 -#> vegetables, root 0.50 0.70 -#> vines, early applns 0.50 0.60 -#> vines, late applns 0.50 0.60 -#> appln, aerial 0.50 0.70 -#> appln, hand (crop < 50 cm) 0.50 0.70 -#> appln, hand (crop > 50 cm) 0.50 0.70 -#> no drift (incorp or seed trtmt) 0.00 0.00 -#> -#> $rd -#> Region -#> Time North South -#> Oct-Feb 5 4 -#> Mar-May 2 4 -#> Jun-Sep 2 3 -#> </div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="co"># This is the code that was used to extract the data</span></span></span> +<span class="r-in"><span> <span class="va">scenario_path</span> <span class="op"><-</span> <span class="st">"inst/extdata/FOCUS_Step_12_scenarios.txt"</span></span></span> +<span class="r-in"><span> <span class="va">scenarios</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="va">scenario_path</span><span class="op">)</span><span class="op">[</span><span class="fl">9</span><span class="op">:</span><span class="fl">38</span><span class="op">]</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in file(con, "r"):</span> cannot open the connection</span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">sce</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/utils/read.table.html" class="external-link">read.table</a></span><span class="op">(</span>text <span class="op">=</span> <span class="va">scenarios</span>, sep <span class="op">=</span> <span class="st">"\t"</span>, header <span class="op">=</span> <span class="cn">TRUE</span>, check.names <span class="op">=</span> <span class="cn">FALSE</span>,</span></span> +<span class="r-in"><span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'scenarios' not found</span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">names</span> <span class="op">=</span> <span class="va">sce</span><span class="op">$</span><span class="va">Crop</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">sce</span><span class="op">)</span> <span class="op"><-</span> <span class="va">sce</span><span class="op">$</span><span class="va">Crop</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">drift</span> <span class="op">=</span> <span class="va">sce</span><span class="op">[</span>, <span class="fl">3</span><span class="op">:</span><span class="fl">11</span><span class="op">]</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">interception</span> <span class="op">=</span> <span class="va">sce</span><span class="op">[</span>, <span class="fl">12</span><span class="op">:</span><span class="fl">15</span><span class="op">]</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span> +<span class="r-in"><span> <span class="va">sce_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="va">scenario_path</span><span class="op">)</span><span class="op">[</span><span class="fl">41</span><span class="op">:</span><span class="fl">46</span><span class="op">]</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in file(con, "r"):</span> cannot open the connection</span> +<span class="r-in"><span> <span class="va">rd</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/utils/read.table.html" class="external-link">read.table</a></span><span class="op">(</span>text <span class="op">=</span> <span class="va">sce_2</span>, sep <span class="op">=</span> <span class="st">"\t"</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce_2' not found</span> +<span class="r-in"><span> <span class="va">rd_mat</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="va">rd</span><span class="op">$</span><span class="va">V2</span>, nrow <span class="op">=</span> <span class="fl">3</span>, byrow <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'rd' not found</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/dimnames.html" class="external-link">dimnames</a></span><span class="op">(</span><span class="va">rd_mat</span><span class="op">)</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>Time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Oct-Feb"</span>, <span class="st">"Mar-May"</span>, <span class="st">"Jun-Sep"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Region <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"North"</span>, <span class="st">"South"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> object 'rd_mat' not found</span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">rd</span> <span class="op">=</span> <span class="va">rd_mat</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'rd_mat' not found</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/save.html" class="external-link">save</a></span><span class="op">(</span><span class="va">FOCUS_Step_12_scenarios</span>, file <span class="op">=</span> <span class="st">"data/FOCUS_Step_12_scenarios.RData"</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>cannot open compressed file 'data/FOCUS_Step_12_scenarios.RData', probable reason 'No such file or directory'</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in gzfile(file, "wb"):</span> cannot open the connection</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># And this is the resulting data</span></span></span> +<span class="r-in"><span><span class="va">FOCUS_Step_12_scenarios</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> list()</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/FOMC_actual_twa.html b/docs/reference/FOMC_actual_twa.html index a365556..1fa9b97 100644 --- a/docs/reference/FOMC_actual_twa.html +++ b/docs/reference/FOMC_actual_twa.html @@ -1,64 +1,12 @@ -<!-- 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navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Actual and maximum moving window time average concentrations for FOMC kinetics</h1> @@ -109,79 +43,77 @@ <p>Actual and maximum moving window time average concentrations for FOMC kinetics</p> </div> - <pre class="usage"><span class='fu'>FOMC_actual_twa</span>( - <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1.0001</span>, - <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>10</span>, - <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>21</span>, <span class='fl'>28</span>, <span class='fl'>42</span>, <span class='fl'>50</span>, <span class='fl'>100</span>) -)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>alpha</th> - <td><p>Parameter of the FOMC model</p></td> - </tr> - <tr> - <th>beta</th> - <td><p>Parameter of the FOMC model</p></td> - </tr> - <tr> - <th>times</th> - <td><p>The output times, and window sizes for time weighted average concentrations</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">FOMC_actual_twa</span><span class="op">(</span></span> +<span> alpha <span class="op">=</span> <span class="fl">1.0001</span>,</span> +<span> beta <span class="op">=</span> <span class="fl">10</span>,</span> +<span> times <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">21</span>, <span class="fl">28</span>, <span class="fl">42</span>, <span class="fl">50</span>, <span class="fl">100</span><span class="op">)</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + <div id="source"> + <h2>Source</h2> <p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, 18 December 2014, p. 251</p> + </div> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>alpha</dt> +<dd><p>Parameter of the FOMC model</p></dd> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>FOMC_actual_twa</span>(<span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1.0001</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>10</span>)</div><div class='output co'>#> actual twa -#> 0 1.00000000 NaN -#> 1 0.90908224 0.9530973 -#> 2 0.83331814 0.9115995 -#> 4 0.71426168 0.8411664 -#> 7 0.58820408 0.7580202 -#> 14 0.41663019 0.6253074 -#> 21 0.32254415 0.5387324 -#> 28 0.26312277 0.4767543 -#> 42 0.19227599 0.3925054 -#> 50 0.16663681 0.3583198 -#> 100 0.09088729 0.2397608</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> - </ul> +<dt>beta</dt> +<dd><p>Parameter of the FOMC model</p></dd> + + +<dt>times</dt> +<dd><p>The output times, and window sizes for time weighted average concentrations</p></dd> + +</dl></div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">FOMC_actual_twa</span><span class="op">(</span>alpha <span class="op">=</span> <span class="fl">1.0001</span>, beta <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> actual twa</span> +<span class="r-out co"><span class="r-pr">#></span> 0 1.00000000 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> 1 0.90908224 0.9530973</span> +<span class="r-out co"><span class="r-pr">#></span> 2 0.83331814 0.9115995</span> +<span class="r-out co"><span class="r-pr">#></span> 4 0.71426168 0.8411664</span> +<span class="r-out co"><span class="r-pr">#></span> 7 0.58820408 0.7580202</span> +<span class="r-out co"><span class="r-pr">#></span> 14 0.41663019 0.6253074</span> +<span class="r-out co"><span class="r-pr">#></span> 21 0.32254415 0.5387324</span> +<span class="r-out co"><span class="r-pr">#></span> 28 0.26312277 0.4767543</span> +<span class="r-out co"><span class="r-pr">#></span> 42 0.19227599 0.3925054</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.16663681 0.3583198</span> +<span class="r-out co"><span class="r-pr">#></span> 100 0.09088729 0.2397608</span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 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src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Groundwater ubiquity score based on Gustafson (1989) — GUS"><meta property="og:description" content="The groundwater ubiquity score GUS is calculated according to the following equation -$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> -<meta name="twitter:card" content="summary" /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -71,35 +19,21 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Groundwater ubiquity score based on Gustafson (1989)</h1> @@ -113,139 +47,136 @@ the following equation $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$</p> </div> - <pre class="usage"><span class='fu'>GUS</span>(<span class='no'>...</span>) - -<span class='co'># S3 method for numeric</span> -<span class='fu'>GUS</span>(<span class='no'>DT50</span>, <span class='no'>Koc</span>, <span class='no'>...</span>) - -<span class='co'># S3 method for chent</span> -<span class='fu'>GUS</span>( - <span class='no'>chent</span>, - <span class='kw'>degradation_value</span> <span class='kw'>=</span> <span class='st'>"DT50ref"</span>, - <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, - <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>, - <span class='kw'>sorption_value</span> <span class='kw'>=</span> <span class='st'>"Kfoc"</span>, - <span class='kw'>degradation_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, - <span class='kw'>sorption_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, - <span class='no'>...</span> -) - -<span class='co'># S3 method for GUS_result</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>...</th> - <td><p>Included in the generic to allow for further arguments later. Therefore -this also had to be added to the specific methods.</p></td> - </tr> - <tr> - <th>DT50</th> - <td><p>Half-life of the chemical in soil. Should be a field + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">GUS</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for numeric</span></span> +<span><span class="fu">GUS</span><span class="op">(</span><span class="va">DT50</span>, <span class="va">Koc</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for chent</span></span> +<span><span class="fu">GUS</span><span class="op">(</span></span> +<span> <span class="va">chent</span>,</span> +<span> degradation_value <span class="op">=</span> <span class="st">"DT50ref"</span>,</span> +<span> lab_field <span class="op">=</span> <span class="st">"laboratory"</span>,</span> +<span> redox <span class="op">=</span> <span class="st">"aerobic"</span>,</span> +<span> sorption_value <span class="op">=</span> <span class="st">"Kfoc"</span>,</span> +<span> degradation_aggregator <span class="op">=</span> <span class="va">geomean</span>,</span> +<span> sorption_aggregator <span class="op">=</span> <span class="va">geomean</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for GUS_result</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>...</dt> +<dd><p>Included in the generic to allow for further arguments later. Therefore +this also had to be added to the specific methods.</p></dd> + + +<dt>DT50</dt> +<dd><p>Half-life of the chemical in soil. Should be a field half-life according to Gustafson (1989). However, leaching to the sub-soil can not completely be excluded in field dissipation experiments and Gustafson did not refer to any normalisation procedure, but says the field study should -be conducted under use conditions.</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>The sorption constant normalised to organic carbon. Gustafson +be conducted under use conditions.</p></dd> + + +<dt>Koc</dt> +<dd><p>The sorption constant normalised to organic carbon. Gustafson does not mention the nonlinearity of the sorption constant commonly found and usually described by Freundlich sorption, therefore it is unclear at which reference concentration the Koc should be observed -(and if the reference concentration would be in soil or in porewater).</p></td> - </tr> - <tr> - <th>chent</th> - <td><p>If a chent is given with appropriate information present in its -chyaml field, this information is used, with defaults specified below.</p></td> - </tr> - <tr> - <th>degradation_value</th> - <td><p>Which of the available degradation values should -be used?</p></td> - </tr> - <tr> - <th>lab_field</th> - <td><p>Should laboratory or field half-lives be used? This +(and if the reference concentration would be in soil or in porewater).</p></dd> + + +<dt>chent</dt> +<dd><p>If a chent is given with appropriate information present in its +chyaml field, this information is used, with defaults specified below.</p></dd> + + +<dt>degradation_value</dt> +<dd><p>Which of the available degradation values should +be used?</p></dd> + + +<dt>lab_field</dt> +<dd><p>Should laboratory or field half-lives be used? This defaults to lab in this implementation, in order to avoid double-accounting for mobility. If comparability with the original GUS values given by Gustafson (1989) is desired, non-normalised first-order -field half-lives obtained under actual use conditions should be used.</p></td> - </tr> - <tr> - <th>redox</th> - <td><p>Aerobic or anaerobic degradation data</p></td> - </tr> - <tr> - <th>sorption_value</th> - <td><p>Which of the available sorption values should be used? +field half-lives obtained under actual use conditions should be used.</p></dd> + + +<dt>redox</dt> +<dd><p>Aerobic or anaerobic degradation data</p></dd> + + +<dt>sorption_value</dt> +<dd><p>Which of the available sorption values should be used? Defaults to Kfoc as this is what is generally available from the European pesticide peer review process. These values generally use a reference concentration of 1 mg/L in porewater, that means they would be expected to -be Koc values at a concentration of 1 mg/L in the water phase.</p></td> - </tr> - <tr> - <th>degradation_aggregator</th> - <td><p>Function for aggregating half-lives</p></td> - </tr> - <tr> - <th>sorption_aggregator</th> - <td><p>Function for aggregation Koc values</p></td> - </tr> - <tr> - <th>x</th> - <td><p>An object of class GUS_result to be printed</p></td> - </tr> - <tr> - <th>digits</th> - <td><p>The number of digits used in the print method</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>A list with the DT50 and Koc used as well as the resulting score - of class GUS_result</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> +be Koc values at a concentration of 1 mg/L in the water phase.</p></dd> + + +<dt>degradation_aggregator</dt> +<dd><p>Function for aggregating half-lives</p></dd> + + +<dt>sorption_aggregator</dt> +<dd><p>Function for aggregation Koc values</p></dd> + +<dt>x</dt> +<dd><p>An object of class GUS_result to be printed</p></dd> + + +<dt>digits</dt> +<dd><p>The number of digits used in the print method</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A list with the DT50 and Koc used as well as the resulting score + of class GUS_result</p> + </div> + <div id="references"> + <h2>References</h2> <p>Gustafson, David I. (1989) Groundwater ubiquity score: a simple method for assessing pesticide leachability. <em>Environmental toxicology and chemistry</em> <b>8</b>(4) 339–57.</p> - - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - </ul> - + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -66,36 +17,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Get the relative accumulation of an FOMC model over multiples of an interval</h1> @@ -104,64 +40,55 @@ </div> <div class="ref-description"> - <p>Get the relative accumulation of an FOMC model over multiples of an interval</p> - </div> - <pre class="usage"><span class='fu'>PEC_FOMC_accu_rel</span>(<span class='no'>n</span>, <span class='no'>interval</span>, <span class='no'>FOMC</span>)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>n</th> - <td><p>number of applications</p></td> - </tr> - <tr> - <th>interval</th> - <td><p>Time between applications</p></td> - </tr> - <tr> - <th>FOMC</th> - <td><p>Named numeric vector containing the FOMC parameters alpha and beta</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_FOMC_accu_rel</span><span class="op">(</span><span class="va">n</span>, <span class="va">interval</span>, <span class="va">FOMC</span><span class="op">)</span></span></code></pre></div> + </div> - <p>A numeric vector containing all n accumulation factors for the n applications</p> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>n</dt> +<dd><p>number of applications</p></dd> + + +<dt>interval</dt> +<dd><p>Time between applications</p></dd> + + +<dt>FOMC</dt> +<dd><p>Named numeric vector containing the FOMC parameters alpha and beta</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - - <li><a href="#value">Value</a></li> - </ul> +<p>A numeric vector containing all n accumulation factors for the n applications</p> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index 3e405a5..f7e1da5 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -1,68 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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If an interval is given, an attempt is made at calculating a long term maximum concentration using the concepts layed out in the PPR panel opinion (EFSA PPR panel 2012 -and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." /> -<meta name="twitter:card" content="summary" /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,35 +21,21 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate predicted environmental concentrations in soil</h1> @@ -117,164 +51,167 @@ the concepts layed out in the PPR panel opinion (EFSA PPR panel 2012 and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017).</p> </div> - <pre class="usage"><span class='fu'>PEC_soil</span>( - <span class='no'>rate</span>, - <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, - <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, - <span class='kw'>mixing_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>, - <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"mg/kg"</span>, - <span class='kw'>PEC_pw_units</span> <span class='kw'>=</span> <span class='st'>"mg/L"</span>, - <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>n_periods</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, - <span class='kw'>tillage_depth</span> <span class='kw'>=</span> <span class='fl'>20</span>, - <span class='kw'>leaching_depth</span> <span class='kw'>=</span> <span class='no'>tillage_depth</span>, - <span class='kw'>crop</span> <span class='kw'>=</span> <span class='st'>"annual"</span>, - <span class='kw'>cultivation</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>chent</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>FOMC</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='no'>Koc</span>/<span class='fl'>1.724</span>, - <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fl'>0</span>, - <span class='kw'>t_act</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"default"</span>, <span class='st'>"EFSA_2017"</span>, <span class='st'>"EFSA_2015"</span>), - <span class='kw'>leaching</span> <span class='kw'>=</span> <span class='no'>scenarios</span> <span class='kw'>==</span> <span class='st'>"EFSA_2017"</span>, - <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>FALSE</span> -)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>rate</th> - <td><p>Application rate in units specified below</p></td> - </tr> - <tr> - <th>rate_units</th> - <td><p>Defaults to g/ha</p></td> - </tr> - <tr> - <th>interception</th> - <td><p>The fraction of the application rate that does not reach the soil</p></td> - </tr> - <tr> - <th>mixing_depth</th> - <td><p>Mixing depth in cm</p></td> - </tr> - <tr> - <th>PEC_units</th> - <td><p>Requested units for the calculated PEC. Only mg/kg currently supported</p></td> - </tr> - <tr> - <th>PEC_pw_units</th> - <td><p>Only mg/L currently supported</p></td> - </tr> - <tr> - <th>interval</th> - <td><p>Period of the deeper mixing. The default is NA, i.e. no + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_soil</span><span class="op">(</span></span> +<span> <span class="va">rate</span>,</span> +<span> rate_units <span class="op">=</span> <span class="st">"g/ha"</span>,</span> +<span> interception <span class="op">=</span> <span class="fl">0</span>,</span> +<span> mixing_depth <span class="op">=</span> <span class="fl">5</span>,</span> +<span> PEC_units <span class="op">=</span> <span class="st">"mg/kg"</span>,</span> +<span> PEC_pw_units <span class="op">=</span> <span class="st">"mg/L"</span>,</span> +<span> interval <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> n_periods <span class="op">=</span> <span class="cn">Inf</span>,</span> +<span> tillage_depth <span class="op">=</span> <span class="fl">20</span>,</span> +<span> leaching_depth <span class="op">=</span> <span class="va">tillage_depth</span>,</span> +<span> crop <span class="op">=</span> <span class="st">"annual"</span>,</span> +<span> cultivation <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> chent <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> DT50 <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> FOMC <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> Koc <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> Kom <span class="op">=</span> <span class="va">Koc</span><span class="op">/</span><span class="fl">1.724</span>,</span> +<span> t_avg <span class="op">=</span> <span class="fl">0</span>,</span> +<span> t_act <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> scenarios <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"default"</span>, <span class="st">"EFSA_2017"</span>, <span class="st">"EFSA_2015"</span><span class="op">)</span>,</span> +<span> leaching <span class="op">=</span> <span class="va">scenarios</span> <span class="op">==</span> <span class="st">"EFSA_2017"</span>,</span> +<span> porewater <span class="op">=</span> <span class="cn">FALSE</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>rate</dt> +<dd><p>Application rate in units specified below</p></dd> + + +<dt>rate_units</dt> +<dd><p>Defaults to g/ha</p></dd> + + +<dt>interception</dt> +<dd><p>The fraction of the application rate that does not reach the soil</p></dd> + + +<dt>mixing_depth</dt> +<dd><p>Mixing depth in cm</p></dd> + + +<dt>PEC_units</dt> +<dd><p>Requested units for the calculated PEC. Only mg/kg currently supported</p></dd> + + +<dt>PEC_pw_units</dt> +<dd><p>Only mg/L currently supported</p></dd> + + +<dt>interval</dt> +<dd><p>Period of the deeper mixing. The default is NA, i.e. no deeper mixing. For annual deeper mixing, set this to 365 when degradation -units are in days</p></td> - </tr> - <tr> - <th>n_periods</th> - <td><p>Number of periods to be considered for long term PEC calculations</p></td> - </tr> - <tr> - <th>tillage_depth</th> - <td><p>Periodic (see interval) deeper mixing in cm</p></td> - </tr> - <tr> - <th>leaching_depth</th> - <td><p>EFSA (2017) uses the mixing depth (ecotoxicological +units are in days</p></dd> + + +<dt>n_periods</dt> +<dd><p>Number of periods to be considered for long term PEC calculations</p></dd> + + +<dt>tillage_depth</dt> +<dd><p>Periodic (see interval) deeper mixing in cm</p></dd> + + +<dt>leaching_depth</dt> +<dd><p>EFSA (2017) uses the mixing depth (ecotoxicological evaluation depth) to calculate leaching for annual crops where tillage takes place. By default, losses from the layer down to the tillage -depth are taken into account in this implementation.</p></td> - </tr> - <tr> - <th>crop</th> - <td><p>Ignored for scenarios other than EFSA_2017. Only annual crops +depth are taken into account in this implementation.</p></dd> + + +<dt>crop</dt> +<dd><p>Ignored for scenarios other than EFSA_2017. Only annual crops are supported when these scenarios are used. Only crops with a single cropping -cycle per year are currently supported.</p></td> - </tr> - <tr> - <th>cultivation</th> - <td><p>Does mechanical cultivation in the sense of EFSA (2017) +cycle per year are currently supported.</p></dd> + + +<dt>cultivation</dt> +<dd><p>Does mechanical cultivation in the sense of EFSA (2017) take place, i.e. twice a year to a depth of 5 cm? Ignored for scenarios -other than EFSA_2017</p></td> - </tr> - <tr> - <th>chent</th> - <td><p>An optional chent object holding substance specific information. Can -also be a name for the substance as a character string</p></td> - </tr> - <tr> - <th>DT50</th> - <td><p>If specified, overrides soil DT50 endpoints from a chent object +other than EFSA_2017</p></dd> + + +<dt>chent</dt> +<dd><p>An optional chent object holding substance specific information. Can +also be a name for the substance as a character string</p></dd> + + +<dt>DT50</dt> +<dd><p>If specified, overrides soil DT50 endpoints from a chent object If DT50 is not specified here and not available from the chent object, zero -degradation is assumed</p></td> - </tr> - <tr> - <th>FOMC</th> - <td><p>If specified, it should be a named numeric vector containing +degradation is assumed</p></dd> + + +<dt>FOMC</dt> +<dd><p>If specified, it should be a named numeric vector containing the FOMC parameters alpha and beta. This overrides any other degradation endpoints, and the degradation during the interval and after the maximum PEC -is calculated using these parameters without temperature correction</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>If specified, overrides Koc endpoints from a chent object</p></td> - </tr> - <tr> - <th>Kom</th> - <td><p>Calculated from Koc by default, but can explicitly be specified -as Kom here</p></td> - </tr> - <tr> - <th>t_avg</th> - <td><p>Averaging times for time weighted average concentrations</p></td> - </tr> - <tr> - <th>t_act</th> - <td><p>Time series for actual concentrations</p></td> - </tr> - <tr> - <th>scenarios</th> - <td><p>If this is 'default', the DT50 will be used without correction +is calculated using these parameters without temperature correction</p></dd> + + +<dt>Koc</dt> +<dd><p>If specified, overrides Koc endpoints from a chent object</p></dd> + + +<dt>Kom</dt> +<dd><p>Calculated from Koc by default, but can explicitly be specified +as Kom here</p></dd> + + +<dt>t_avg</dt> +<dd><p>Averaging times for time weighted average concentrations</p></dd> + + +<dt>t_act</dt> +<dd><p>Time series for actual concentrations</p></dd> + + +<dt>scenarios</dt> +<dd><p>If this is 'default', the DT50 will be used without correction and soil properties as specified in the REACH guidance (R.16, Table R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when -'chents' is specified, the DegT50 with destination 'PECgw' will be used), +'chent' is specified, the DegT50 with destination 'PECgw' will be used), and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also -model and scenario adjustment factors from the EFSA guidance are used.</p></td> - </tr> - <tr> - <th>leaching</th> - <td><p>Should leaching be taken into account? The default is FALSE, -except when the EFSA_2017 scenarios are used.</p></td> - </tr> - <tr> - <th>porewater</th> - <td><p>Should equilibrium porewater concentrations be estimated +model and scenario adjustment factors from the EFSA guidance are used.</p></dd> + + +<dt>leaching</dt> +<dd><p>Should leaching be taken into account? The default is FALSE, +except when the EFSA_2017 scenarios are used.</p></dd> + + +<dt>porewater</dt> +<dd><p>Should equilibrium porewater concentrations be estimated based on Kom and the organic carbon fraction of the soil instead of total soil concentrations? Based on equation (7) given in the PPR panel opinion (EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, -p. 13).</p></td> - </tr> - </table> +p. 13).</p></dd> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The predicted concentration in soil</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> +</dl></div> + <div id="value"> + <h2>Value</h2> + +<p>The predicted concentration in soil</p> + </div> + <div id="details"> + <h2>Details</h2> <p>This assumes that the complete load to soil during the time specified by 'interval' (typically 365 days) is dosed at once. As in the PPR panel opinion cited below (EFSA PPR panel 2012), only temperature correction using the Arrhenius equation is performed.</p> <p>Total soil and porewater PEC values for the scenarios as defined in the EFSA guidance (2017, p. 14/15) can easily be calculated.</p> - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - + </div> + <div id="note"> + <h2>Note</h2> <p>While time weighted average (TWA) concentrations given in the examples from the EFSA guidance from 2015 (p. 80) are be reproduced, this is not true for the TWA concentrations given for the same example in the EFSA guidance @@ -289,8 +226,9 @@ from 2017 (p. 92).</p> e.g. in the EFSA scenarios, the DT50 for groundwater modelling (destination 'PECgw') is taken from the chent object, otherwise the DT50 with destination 'PECsoil'.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - + </div> + <div id="references"> + <h2>References</h2> <p>EFSA Panel on Plant Protection Products and their Residues (2012) Scientific Opinion on the science behind the guidance for scenario selection and scenario parameterisation for predicting environmental @@ -306,75 +244,80 @@ from 2017 (p. 92).</p> protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093 doi:10.2903/j.efsa.2015.4093</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>100</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0.25</span>)</div><div class='output co'>#> scenario -#> t_avg default -#> 0 0.1</div><div class='input'> -<span class='co'># This is example 1 starting at p. 92 of the EFSA guidance (2017)</span> -<span class='co'># Note that TWA concentrations differ from the ones given in the guidance</span> -<span class='co'># for an unknown reason (the values from EFSA (2015) can be reproduced).</span> -<span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>), - <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2017"</span>)</div><div class='output co'>#> scenario -#> t_avg CTN CTC CTS -#> 0 19.76834 13.8619 10.53795 -#> 21 19.59345 13.7169 10.39882</div><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>), - <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2017"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> scenario -#> t_avg CLN CLC CLS -#> 0 0.5541984 0.6779249 0.9816693 -#> 21 0.5484576 0.6693125 0.9609119</div><div class='input'> -<span class='co'># This is example 1 starting at p. 79 of the EFSA guidance (2015)</span> -<span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>), - <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>)</div><div class='output co'>#> scenario -#> t_avg CTN CTC CTS -#> 0 21.96827 11.53750 9.145259 -#> 21 21.78517 11.40701 9.017370</div><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>), - <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> scenario -#> t_avg CLN CLC CLS -#> 0 0.7589401 0.6674322 0.9147861 -#> 21 0.7506036 0.6590345 0.8987279</div><div class='input'> -<span class='co'># The following is from example 4 starting at p. 85 of the EFSA guidance (2015)</span> -<span class='co'># Metabolite M2</span> -<span class='co'># Calculate total and porewater soil concentrations for tier 1 scenarios</span> -<span class='co'># Relative molar mass is 100/300, formation fraction is 0.7 * 1</span> -<span class='no'>results_pfm</span> <span class='kw'><-</span> <span class='fu'>PEC_soil</span>(<span class='fl'>100</span>/<span class='fl'>300</span> * <span class='fl'>0.7</span> * <span class='fl'>1</span> * <span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>), - <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>) -<span class='no'>results_pfm_pw</span> <span class='kw'><-</span> <span class='fu'>PEC_soil</span>(<span class='fl'>100</span>/<span class='fl'>300</span> * <span class='fl'>0.7</span> * <span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>), - <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#details">Details</a></li> - <li><a href="#note">Note</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">100</span>, interception <span class="op">=</span> <span class="fl">0.25</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> scenario</span> +<span class="r-out co"><span class="r-pr">#></span> t_avg default</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0.1</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This is example 1 starting at p. 92 of the EFSA guidance (2017)</span></span></span> +<span class="r-in"><span><span class="co"># Note that TWA concentrations differ from the ones given in the guidance</span></span></span> +<span class="r-in"><span><span class="co"># for an unknown reason (the values from EFSA (2015) can be reproduced).</span></span></span> +<span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_avg <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Kom <span class="op">=</span> <span class="fl">1000</span>, scenarios <span class="op">=</span> <span class="st">"EFSA_2017"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> scenario</span> +<span class="r-out co"><span class="r-pr">#></span> t_avg CTN CTC CTS</span> +<span class="r-out co"><span class="r-pr">#></span> 0 19.76834 13.8619 10.53795</span> +<span class="r-out co"><span class="r-pr">#></span> 21 19.59345 13.7169 10.39882</span> +<span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_av <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Kom <span class="op">=</span> <span class="fl">1000</span>, scenarios <span class="op">=</span> <span class="st">"EFSA_2017"</span>, porewater <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> scenario</span> +<span class="r-out co"><span class="r-pr">#></span> t_avg CLN CLC CLS</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0.5541984 0.6779249 0.9816693</span> +<span class="r-out co"><span class="r-pr">#></span> 21 0.5484576 0.6693125 0.9609119</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This is example 1 starting at p. 79 of the EFSA guidance (2015)</span></span></span> +<span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_avg <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> scenarios <span class="op">=</span> <span class="st">"EFSA_2015"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> scenario</span> +<span class="r-out co"><span class="r-pr">#></span> t_avg CTN CTC CTS</span> +<span class="r-out co"><span class="r-pr">#></span> 0 21.96827 11.53750 9.145259</span> +<span class="r-out co"><span class="r-pr">#></span> 21 21.78517 11.40701 9.017370</span> +<span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_av <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Kom <span class="op">=</span> <span class="fl">1000</span>, scenarios <span class="op">=</span> <span class="st">"EFSA_2015"</span>, porewater <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> scenario</span> +<span class="r-out co"><span class="r-pr">#></span> t_avg CLN CLC CLS</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0.7589401 0.6674322 0.9147861</span> +<span class="r-out co"><span class="r-pr">#></span> 21 0.7506036 0.6590345 0.8987279</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The following is from example 4 starting at p. 85 of the EFSA guidance (2015)</span></span></span> +<span class="r-in"><span><span class="co"># Metabolite M2</span></span></span> +<span class="r-in"><span><span class="co"># Calculate total and porewater soil concentrations for tier 1 scenarios</span></span></span> +<span class="r-in"><span><span class="co"># Relative molar mass is 100/300, formation fraction is 0.7 * 1</span></span></span> +<span class="r-in"><span><span class="va">results_pfm</span> <span class="op"><-</span> <span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">100</span><span class="op">/</span><span class="fl">300</span> <span class="op">*</span> <span class="fl">0.7</span> <span class="op">*</span> <span class="fl">1</span> <span class="op">*</span> <span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_avg <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> scenarios <span class="op">=</span> <span class="st">"EFSA_2015"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">results_pfm_pw</span> <span class="op"><-</span> <span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">100</span><span class="op">/</span><span class="fl">300</span> <span class="op">*</span> <span class="fl">0.7</span> <span class="op">*</span> <span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_av <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Kom <span class="op">=</span> <span class="fl">100</span>, scenarios <span class="op">=</span> <span class="st">"EFSA_2015"</span>, porewater <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> 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version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate initial and accumulation PEC soil for a set of metabolites</h1> @@ -104,68 +40,59 @@ </div> <div class="ref-description"> - <p>Calculate initial and accumulation PEC soil for a set of metabolites</p> - </div> - <pre class="usage"><span class='fu'>PEC_soil_mets</span>(<span class='no'>rate</span>, <span class='no'>mw_parent</span>, <span class='no'>mets</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='no'>...</span>)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>rate</th> - <td><p>Application rate in units specified below</p></td> - </tr> - <tr> - <th>mw_parent</th> - <td><p>The molecular weight of the parent compound</p></td> - </tr> - <tr> - <th>mets</th> - <td><p>A dataframe with metabolite identifiers as rownames + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_soil_mets</span><span class="op">(</span><span class="va">rate</span>, <span class="va">mw_parent</span>, <span class="va">mets</span>, interval <span class="op">=</span> <span class="fl">365</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>rate</dt> +<dd><p>Application rate in units specified below</p></dd> + + +<dt>mw_parent</dt> +<dd><p>The molecular weight of the parent compound</p></dd> + + +<dt>mets</dt> +<dd><p>A dataframe with metabolite identifiers as rownames and columns "mw", "occ" and "DT50" holding their molecular weight, -maximum occurrence in soil and their soil DT50</p></td> - </tr> - <tr> - <th>interval</th> - <td><p>The interval for accumulation calculations</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments are passed to PEC_soil</p></td> - </tr> - </table> - +maximum occurrence in soil and their soil DT50</p></dd> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - </ul> + +<dt>interval</dt> +<dd><p>The interval for accumulation calculations</p></dd> + + +<dt>...</dt> +<dd><p>Further arguments are passed to PEC_soil</p></dd> + +</dl></div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html index bdcf5af..b0be7f3 100644 --- a/docs/reference/PEC_sw_drainage_UK.html +++ 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website" /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</h1> @@ -111,97 +45,97 @@ published on the CRC website" /> published on the CRC website</p> </div> - <pre class="usage"><span class='fu'>PEC_sw_drainage_UK</span>( - <span class='no'>rate</span>, - <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, - <span class='no'>Koc</span>, - <span class='kw'>latest_application</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>soil_DT50</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>model_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span> -)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>rate</th> - <td><p>Application rate in g/ha</p></td> - </tr> - <tr> - <th>interception</th> - <td><p>The fraction of the application rate that does not reach the soil</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>The sorption coefficient normalised to organic carbon in L/kg</p></td> - </tr> - <tr> - <th>latest_application</th> - <td><p>Latest application date, formatted as e.g. "01 July"</p></td> - </tr> - <tr> - <th>soil_DT50</th> - <td><p>Soil degradation half-life, if SFO kinetics are to be used</p></td> - </tr> - <tr> - <th>model</th> - <td><p>The soil degradation model to be used. Either one of "FOMC", -"DFOP", "HS", or "IORE", or an mkinmod object</p></td> - </tr> - <tr> - <th>model_parms</th> - <td><p>A named numeric vector containing the model parameters</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The predicted concentration in surface water in µg/L</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_drainage_UK</span><span class="op">(</span></span> +<span> <span class="va">rate</span>,</span> +<span> interception <span class="op">=</span> <span class="fl">0</span>,</span> +<span> <span class="va">Koc</span>,</span> +<span> latest_application <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> soil_DT50 <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> model <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> model_parms <span class="op">=</span> <span class="cn">NULL</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>rate</dt> +<dd><p>Application rate in g/ha</p></dd> + + +<dt>interception</dt> +<dd><p>The fraction of the application rate that does not reach the soil</p></dd> + + +<dt>Koc</dt> +<dd><p>The sorption coefficient normalised to organic carbon in L/kg</p></dd> + + +<dt>latest_application</dt> +<dd><p>Latest application date, formatted as e.g. "01 July"</p></dd> + + +<dt>soil_DT50</dt> +<dd><p>Soil degradation half-life, if SFO kinetics are to be used</p></dd> + + +<dt>model</dt> +<dd><p>The soil degradation model to be used. Either one of "FOMC", +"DFOP", "HS", or "IORE", or an mkinmod object</p></dd> + +<dt>model_parms</dt> +<dd><p>A named numeric vector containing the model parameters</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The predicted concentration in surface water in µg/L</p> + </div> + <div id="references"> + <h2>References</h2> <p>HSE's Chemicals Regulation Division (CRD) Active substance PECsw calculations (for UK specific authorisation requests) - <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm</a> + <a href="https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm" class="external-link">https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm</a> accessed 2019-09-27</p> <p>Drainage PECs Version 1.0 (2015) Spreadsheet published at - <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> + <a href="https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx" class="external-link">https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> accessed 2019-09-27</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>PEC_sw_drainage_UK</span>(<span class='fl'>150</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>100</span>)</div><div class='output co'>#> [1] 8.076923</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_sw_drainage_UK</span><span class="op">(</span><span class="fl">150</span>, Koc <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 8.076923</span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html index e2c325b..c017454 100644 --- a/docs/reference/PEC_sw_drift.html +++ b/docs/reference/PEC_sw_drift.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift • pfm</title> - 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- - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +with input via spray drift."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,35 +19,21 @@ with input via spray drift." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate predicted environmental concentrations in surface water due to drift</h1> @@ -116,106 +47,118 @@ concentration in surface water based on complete, instantaneous mixing with input via spray drift.</p> </div> - <pre class="usage"><span class='fu'>PEC_sw_drift</span>( - <span class='no'>rate</span>, - <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>, - <span class='kw'>drift_percentages</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>drift_data</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"JKI"</span>, <span class='st'>"RF"</span>), - <span class='kw'>crop</span> <span class='kw'>=</span> <span class='st'>"Ackerbau"</span>, - <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>), - <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, - <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"µg/L"</span> -)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>rate</th> - <td><p>Application rate in units specified below</p></td> - </tr> - <tr> - <th>applications</th> - <td><p>Number of applications for selection of drift percentile</p></td> - </tr> - <tr> - <th>water_depth</th> - <td><p>Depth of the water body in cm</p></td> - </tr> - <tr> - <th>drift_percentages</th> - <td><p>Percentage drift values for which to calculate PECsw. -'drift_data' and 'distances' if not NULL.</p></td> - </tr> - <tr> - <th>drift_data</th> - <td><p>Source of drift percentage data. If 'JKI', the [drift_data_JKI] + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_drift</span><span class="op">(</span></span> +<span> <span class="va">rate</span>,</span> +<span> applications <span class="op">=</span> <span class="fl">1</span>,</span> +<span> water_depth <span class="op">=</span> <span class="fl">30</span>,</span> +<span> drift_percentages <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> drift_data <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"JKI"</span>, <span class="st">"RF"</span><span class="op">)</span>,</span> +<span> crop <span class="op">=</span> <span class="st">"Ackerbau"</span>,</span> +<span> distances <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">5</span>, <span class="fl">10</span>, <span class="fl">20</span><span class="op">)</span>,</span> +<span> rate_units <span class="op">=</span> <span class="st">"g/ha"</span>,</span> +<span> PEC_units <span class="op">=</span> <span class="st">"µg/L"</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>rate</dt> +<dd><p>Application rate in units specified below</p></dd> + + +<dt>applications</dt> +<dd><p>Number of applications for selection of drift percentile</p></dd> + + +<dt>water_depth</dt> +<dd><p>Depth of the water body in cm</p></dd> + + +<dt>drift_percentages</dt> +<dd><p>Percentage drift values for which to calculate PECsw. +'drift_data' and 'distances' if not NULL.</p></dd> + + +<dt>drift_data</dt> +<dd><p>Source of drift percentage data. If 'JKI', the [drift_data_JKI] included in the package is used. If 'RF', the Rautmann formula is used, if -implemented for the crop type and number of applications</p></td> - </tr> - <tr> - <th>crop</th> - <td><p>Crop name (use German names for JKI data), defaults to "Ackerbau"</p></td> - </tr> - <tr> - <th>distances</th> - <td><p>The distances in m for which to get PEC values</p></td> - </tr> - <tr> - <th>rate_units</th> - <td><p>Defaults to g/ha</p></td> - </tr> - <tr> - <th>PEC_units</th> - <td><p>Requested units for the calculated PEC. Only µg/L currently supported</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The predicted concentration in surface water</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>PEC_sw_drift</span>(<span class='fl'>100</span>)</div><div class='output co'>#> 1 m 5 m 10 m 20 m -#> 0.92333333 0.19000000 0.09666667 0.05000000 </div><div class='input'><span class='co'># Alternatively, we can use the formula for a single application to "Ackerbau" from the paper</span> -<span class='fu'>PEC_sw_drift</span>(<span class='fl'>100</span>, <span class='kw'>drift_data</span> <span class='kw'>=</span> <span class='st'>"RF"</span>)</div><div class='output co'>#> 1 m 5 m 10 m 20 m -#> 0.92350000 0.19114149 0.09699222 0.04921742 </div><div class='input'> -<span class='co'># This makes it possible to also use different substances</span> -<span class='fu'>PEC_sw_drift</span>(<span class='fl'>100</span>, <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>5</span>, <span class='fl'>6</span>, <span class='fl'>10</span>, <span class='fl'>20</span>, <span class='fl'>50</span>, <span class='fl'>100</span>), <span class='kw'>drift_data</span> <span class='kw'>=</span> <span class='st'>"RF"</span>)</div><div class='output co'>#> 1 m 3 m 5 m 6 m 10 m 20 m 50 m -#> 0.92350000 0.31512171 0.19114149 0.15990435 0.09699222 0.04921742 0.02007497 -#> 100 m -#> 0.01018678 </div><div class='input'> -<span class='co'># Using custom drift percentages is also supported</span> -<span class='fu'>PEC_sw_drift</span>(<span class='fl'>100</span>, <span class='kw'>drift_percentages</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>2.77</span>, <span class='fl'>0.95</span>, <span class='fl'>0.57</span>, <span class='fl'>0.48</span>, <span class='fl'>0.29</span>, <span class='fl'>0.15</span>, <span class='fl'>0.06</span>, <span class='fl'>0.03</span>))</div><div class='output co'>#> 2.77 % 0.95 % 0.57 % 0.48 % 0.29 % 0.15 % 0.06 % -#> 0.92333333 0.31666667 0.19000000 0.16000000 0.09666667 0.05000000 0.02000000 -#> 0.03 % -#> 0.01000000 </div></pre> +implemented for the crop type and number of applications</p></dd> + + +<dt>crop</dt> +<dd><p>Crop name (use German names for JKI data), defaults to "Ackerbau"</p></dd> + + +<dt>distances</dt> +<dd><p>The distances in m for which to get PEC values</p></dd> + + +<dt>rate_units</dt> +<dd><p>Defaults to g/ha</p></dd> + + +<dt>PEC_units</dt> +<dd><p>Requested units for the calculated PEC. Only µg/L currently supported</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The predicted concentration in surface water</p> + </div> + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 1 m 5 m 10 m 20 m </span> +<span class="r-out co"><span class="r-pr">#></span> 0.92333333 0.19000000 0.09666667 0.05000000 </span> +<span class="r-in"><span><span class="co"># Alternatively, we can use the formula for a single application to "Ackerbau" from the paper</span></span></span> +<span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, drift_data <span class="op">=</span> <span class="st">"RF"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 1 m 5 m 10 m 20 m </span> +<span class="r-out co"><span class="r-pr">#></span> 0.92350000 0.19114149 0.09699222 0.04921742 </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This makes it possible to also use different substances</span></span></span> +<span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, distances <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">6</span>, <span class="fl">10</span>, <span class="fl">20</span>, <span class="fl">50</span>, <span class="fl">100</span><span class="op">)</span>, drift_data <span class="op">=</span> <span class="st">"RF"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 1 m 3 m 5 m 6 m 10 m 20 m 50 m </span> +<span class="r-out co"><span class="r-pr">#></span> 0.92350000 0.31512171 0.19114149 0.15990435 0.09699222 0.04921742 0.02007497 </span> +<span class="r-out co"><span class="r-pr">#></span> 100 m </span> +<span class="r-out co"><span class="r-pr">#></span> 0.01018678 </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Using custom drift percentages is also supported</span></span></span> +<span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, drift_percentages <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2.77</span>, <span class="fl">0.95</span>, <span class="fl">0.57</span>, <span class="fl">0.48</span>, <span class="fl">0.29</span>, <span class="fl">0.15</span>, <span class="fl">0.06</span>, <span class="fl">0.03</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.77 % 0.95 % 0.57 % 0.48 % 0.29 % 0.15 % 0.06 % </span> +<span class="r-out co"><span class="r-pr">#></span> 0.92333333 0.31666667 0.19000000 0.16000000 0.09666667 0.05000000 0.02000000 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.03 % </span> +<span class="r-out co"><span class="r-pr">#></span> 0.01000000 </span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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Although there are four groups of +compounds ("Gefährdungsgruppen"), only one distinction is made in the calculations, between compounds with low mobility (group 1) and compounds with modest to high mobility (groups 2, 3 and 4). In this implementation, the group is derived only from the Koc, if not given explicitly. For -details, see the discussion of the function arguments below." /> -<meta name="twitter:card" content="summary" /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +details, see the discussion of the function arguments below.'><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -75,35 +23,21 @@ details, see the discussion of the function arguments below." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate PEC surface water due to drainage as in Exposit 3</h1> @@ -121,123 +55,126 @@ the group is derived only from the Koc, if not given explicitly. For details, see the discussion of the function arguments below.</p> </div> - <pre class="usage"><span class='fu'>PEC_sw_exposit_drainage</span>( - <span class='no'>rate</span>, - <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, - <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>mobility</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"low"</span>, <span class='st'>"high"</span>), - <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, - <span class='kw'>t_drainage</span> <span class='kw'>=</span> <span class='fl'>3</span>, - <span class='kw'>V_ditch</span> <span class='kw'>=</span> <span class='fl'>30</span>, - <span class='kw'>V_drainage</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>spring</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>autumn</span> <span class='kw'>=</span> <span class='fl'>100</span>), - <span class='kw'>dilution</span> <span class='kw'>=</span> <span class='fl'>2</span> -)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>rate</th> - <td><p>The application rate in g/ha</p></td> - </tr> - <tr> - <th>interception</th> - <td><p>The fraction intercepted by the crop</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>The sorption coefficient to soil organic carbon used to determine the mobility. A trigger -value of 550 L/kg is used in order to decide if Koc >> 500.</p></td> - </tr> - <tr> - <th>mobility</th> - <td><p>Overrides what is determined from the Koc.</p></td> - </tr> - <tr> - <th>DT50</th> - <td><p>The soil half-life in days</p></td> - </tr> - <tr> - <th>t_drainage</th> - <td><p>The time between application and the drainage event, where degradation occurs, in days</p></td> - </tr> - <tr> - <th>V_ditch</th> - <td><p>The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3</p></td> - </tr> - <tr> - <th>V_drainage</th> - <td><p>The drainage volume, equivalent to 1 mm precipitation on 1 ha for spring/summer or 10 mm for -autumn/winter/early spring.</p></td> - </tr> - <tr> - <th>dilution</th> - <td><p>The dilution factor</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_exposit_drainage</span><span class="op">(</span></span> +<span> <span class="va">rate</span>,</span> +<span> interception <span class="op">=</span> <span class="fl">0</span>,</span> +<span> Koc <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> mobility <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="st">"low"</span>, <span class="st">"high"</span><span class="op">)</span>,</span> +<span> DT50 <span class="op">=</span> <span class="cn">Inf</span>,</span> +<span> t_drainage <span class="op">=</span> <span class="fl">3</span>,</span> +<span> V_ditch <span class="op">=</span> <span class="fl">30</span>,</span> +<span> V_drainage <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>spring <span class="op">=</span> <span class="fl">10</span>, autumn <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span> +<span> dilution <span class="op">=</span> <span class="fl">2</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + <div id="source"> + <h2>Source</h2> <p>Excel 3.02 spreadsheet available from - <a href='https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3'>https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <a href="https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html" class="external-link">https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html</a></p> + </div> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>rate</dt> +<dd><p>The application rate in g/ha</p></dd> + + +<dt>interception</dt> +<dd><p>The fraction intercepted by the crop</p></dd> + + +<dt>Koc</dt> +<dd><p>The sorption coefficient to soil organic carbon used to determine the mobility. A trigger +value of 550 L/kg is used in order to decide if Koc >> 500.</p></dd> + + +<dt>mobility</dt> +<dd><p>Overrides what is determined from the Koc.</p></dd> + + +<dt>DT50</dt> +<dd><p>The soil half-life in days</p></dd> + + +<dt>t_drainage</dt> +<dd><p>The time between application and the drainage event, where degradation occurs, in days</p></dd> + + +<dt>V_ditch</dt> +<dd><p>The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3</p></dd> - <p>A list containing the following components</p><dl class='dl-horizontal'> - <dt>perc_runoff</dt><dd><p>The runoff percentages for dissolved and bound substance</p></dd> - <dt>runoff</dt><dd><p>A matrix containing dissolved and bound input for the different distances</p></dd> - <dt>PEC_sw_runoff</dt><dd><p>A matrix containing PEC values for dissolved and bound substance + +<dt>V_drainage</dt> +<dd><p>The drainage volume, equivalent to 1 mm precipitation on 1 ha for spring/summer or 10 mm for +autumn/winter/early spring.</p></dd> + + +<dt>dilution</dt> +<dd><p>The dilution factor</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A list containing the following components</p> +<p></p> +<dl><dt>perc_runoff</dt> +<dd><p>The runoff percentages for dissolved and bound substance</p></dd> + + <dt>runoff</dt> +<dd><p>A matrix containing dissolved and bound input for the different distances</p></dd> + + <dt>PEC_sw_runoff</dt> +<dd><p>A matrix containing PEC values for dissolved and bound substance for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.</p></dd> + -</dl> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p><code><a href='perc_runoff_exposit.html'>perc_runoff_exposit</a></code> for runoff loss percentages and <code><a href='perc_runoff_reduction_exposit.html'>perc_runoff_reduction_exposit</a></code> for runoff reduction percentages used</p></div> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>PEC_sw_exposit_drainage</span>(<span class='fl'>500</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>150</span>)</div><div class='output co'>#> $perc_drainage_total -#> spring autumn -#> 0.2 1.0 -#> -#> $perc_peak -#> spring autumn -#> 12.5 25.0 -#> -#> $PEC_sw_drainage -#> spring autumn -#> 1.562500 4.807692 -#> </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> - </ul> +</dl></div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> for runoff loss percentages and <code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> for runoff reduction percentages used</p></div> + </div> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="fu">PEC_sw_exposit_drainage</span><span class="op">(</span><span class="fl">500</span>, Koc <span class="op">=</span> <span class="fl">150</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $perc_drainage_total</span> +<span class="r-out co"><span class="r-pr">#></span> spring autumn </span> +<span class="r-out co"><span class="r-pr">#></span> 0.2 1.0 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $perc_peak</span> +<span class="r-out co"><span class="r-pr">#></span> spring autumn </span> +<span class="r-out co"><span class="r-pr">#></span> 12.5 25.0 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sw_drainage</span> +<span class="r-out co"><span class="r-pr">#></span> spring autumn </span> +<span class="r-out co"><span class="r-pr">#></span> 1.562500 4.807692 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - 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- </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate PEC surface water due to runoff and erosion as in Exposit 3</h1> @@ -111,152 +45,157 @@ in the worksheet "Konzept Runoff"." /> in the worksheet "Konzept Runoff".</p> </div> - <pre class="usage"><span class='fu'>PEC_sw_exposit_runoff</span>( - <span class='no'>rate</span>, - <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, - <span class='no'>Koc</span>, - <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, - <span class='kw'>t_runoff</span> <span class='kw'>=</span> <span class='fl'>3</span>, - <span class='kw'>exposit_reduction_version</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"3.02"</span>, <span class='st'>"3.01a"</span>, <span class='st'>"3.01a2"</span>, <span class='st'>"2.0"</span>), - <span class='kw'>V_ditch</span> <span class='kw'>=</span> <span class='fl'>30</span>, - <span class='kw'>V_event</span> <span class='kw'>=</span> <span class='fl'>100</span>, - <span class='kw'>dilution</span> <span class='kw'>=</span> <span class='fl'>2</span> -)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>rate</th> - <td><p>The application rate in g/ha</p></td> - </tr> - <tr> - <th>interception</th> - <td><p>The fraction intercepted by the crop</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>The sorption coefficient to soil organic carbon</p></td> - </tr> - <tr> - <th>DT50</th> - <td><p>The soil half-life in days</p></td> - </tr> - <tr> - <th>t_runoff</th> - <td><p>The time between application and the runoff event, where degradation occurs, in days</p></td> - </tr> - <tr> - <th>exposit_reduction_version</th> - <td><p>The version of the reduction factors to be used. "3.02" is the current + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_exposit_runoff</span><span class="op">(</span></span> +<span> <span class="va">rate</span>,</span> +<span> interception <span class="op">=</span> <span class="fl">0</span>,</span> +<span> <span class="va">Koc</span>,</span> +<span> DT50 <span class="op">=</span> <span class="cn">Inf</span>,</span> +<span> t_runoff <span class="op">=</span> <span class="fl">3</span>,</span> +<span> exposit_reduction_version <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"3.02"</span>, <span class="st">"3.01a"</span>, <span class="st">"3.01a2"</span>, <span class="st">"2.0"</span><span class="op">)</span>,</span> +<span> V_ditch <span class="op">=</span> <span class="fl">30</span>,</span> +<span> V_event <span class="op">=</span> <span class="fl">100</span>,</span> +<span> dilution <span class="op">=</span> <span class="fl">2</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="source"> + <h2>Source</h2> + <p>Excel 3.02 spreadsheet available from + <a href="https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html" class="external-link">https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html</a></p> + </div> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>rate</dt> +<dd><p>The application rate in g/ha</p></dd> + + +<dt>interception</dt> +<dd><p>The fraction intercepted by the crop</p></dd> + + +<dt>Koc</dt> +<dd><p>The sorption coefficient to soil organic carbon</p></dd> + + +<dt>DT50</dt> +<dd><p>The soil half-life in days</p></dd> + + +<dt>t_runoff</dt> +<dd><p>The time between application and the runoff event, where degradation occurs, in days</p></dd> + + +<dt>exposit_reduction_version</dt> +<dd><p>The version of the reduction factors to be used. "3.02" is the current version used in Germany, "3.01a" is the version with additional percentages for 3 m and 6 m buffer zones used in Switzerland. "3.01a2" is a version introduced for consistency with previous calculations performed for a 3 m buffer zone in Switzerland, with the same reduction being applied to the dissolved -and the bound fraction.</p></td> - </tr> - <tr> - <th>V_ditch</th> - <td><p>The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3</p></td> - </tr> - <tr> - <th>V_event</th> - <td><p>The unreduced runoff volume, equivalent to 10 mm precipitation on 1 ha</p></td> - </tr> - <tr> - <th>dilution</th> - <td><p>The dilution factor</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> +and the bound fraction.</p></dd> - <p>Excel 3.02 spreadsheet available from - <a href='https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3'>https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A list containing the following components</p><dl class='dl-horizontal'> - <dt>perc_runoff</dt><dd><p>The runoff percentages for dissolved and bound substance</p></dd> - <dt>runoff</dt><dd><p>A matrix containing dissolved and bound input for the different distances</p></dd> - <dt>PEC_sw_runoff</dt><dd><p>A matrix containing PEC values for dissolved and bound substance +<dt>V_ditch</dt> +<dd><p>The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3</p></dd> + + +<dt>V_event</dt> +<dd><p>The unreduced runoff volume, equivalent to 10 mm precipitation on 1 ha</p></dd> + + +<dt>dilution</dt> +<dd><p>The dilution factor</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A list containing the following components</p> +<p></p> +<dl><dt>perc_runoff</dt> +<dd><p>The runoff percentages for dissolved and bound substance</p></dd> + + <dt>runoff</dt> +<dd><p>A matrix containing dissolved and bound input for the different distances</p></dd> + + <dt>PEC_sw_runoff</dt> +<dd><p>A matrix containing PEC values for dissolved and bound substance for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.</p></dd> + -</dl> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p><code><a href='perc_runoff_exposit.html'>perc_runoff_exposit</a></code> for runoff loss percentages and <code><a href='perc_runoff_reduction_exposit.html'>perc_runoff_reduction_exposit</a></code> for runoff reduction percentages used</p></div> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>PEC_sw_exposit_runoff</span>(<span class='fl'>500</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>150</span>)</div><div class='output co'>#> $perc_runoff -#> dissolved bound -#> 0.248 0.001 -#> -#> $runoff -#> dissolved bound total -#> No buffer 1.240 0.00500 1.24500 -#> 5 m 0.744 0.00300 0.74700 -#> 10 m 0.496 0.00075 0.49675 -#> 20 m 0.248 0.00025 0.24825 -#> -#> $PEC_sw_runoff -#> dissolved bound total -#> No buffer 4.769231 0.019230769 4.788462 -#> 5 m 4.133333 0.016666667 4.150000 -#> 10 m 3.542857 0.005357143 3.548214 -#> 20 m 2.480000 0.002500000 2.482500 -#> </div><div class='input'> <span class='fu'>PEC_sw_exposit_runoff</span>(<span class='fl'>600</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>10000</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>195</span>, <span class='kw'>exposit</span> <span class='kw'>=</span> <span class='st'>"3.01a"</span>)</div><div class='output co'>#> $perc_runoff -#> dissolved bound -#> 0.037 0.159 -#> -#> $runoff -#> dissolved bound total -#> No buffer 0.21964521 0.94388078 1.16352600 -#> 3 m 0.16473391 0.66071655 0.82545046 -#> 5 m 0.13178713 0.56632847 0.69811560 -#> 6 m 0.12080487 0.42474635 0.54555122 -#> 10 m 0.08785809 0.14158212 0.22944020 -#> 20 m 0.04392904 0.04719404 0.09112308 -#> -#> $PEC_sw_runoff -#> dissolved bound total -#> No buffer 0.8447893 3.6303107 4.4751000 -#> 3 m 0.7844472 3.1462693 3.9307165 -#> 5 m 0.7321507 3.1462693 3.8784200 -#> 6 m 0.7106169 2.4985080 3.2091248 -#> 10 m 0.6275578 1.0113008 1.6388586 -#> 20 m 0.4392904 0.4719404 0.9112308 -#> </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> - </ul> +</dl></div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> for runoff loss percentages and <code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> for runoff reduction percentages used</p></div> + </div> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="fu">PEC_sw_exposit_runoff</span><span class="op">(</span><span class="fl">500</span>, Koc <span class="op">=</span> <span class="fl">150</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $perc_runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound </span> +<span class="r-out co"><span class="r-pr">#></span> 0.248 0.001 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 1.240 0.00500 1.24500</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 0.744 0.00300 0.74700</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 0.496 0.00075 0.49675</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 0.248 0.00025 0.24825</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sw_runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 4.769231 0.019230769 4.788462</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 4.133333 0.016666667 4.150000</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 3.542857 0.005357143 3.548214</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 2.480000 0.002500000 2.482500</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span> <span class="fu">PEC_sw_exposit_runoff</span><span class="op">(</span><span class="fl">600</span>, Koc <span class="op">=</span> <span class="fl">10000</span>, DT50 <span class="op">=</span> <span class="fl">195</span>, exposit <span class="op">=</span> <span class="st">"3.01a"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $perc_runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound </span> +<span class="r-out co"><span class="r-pr">#></span> 0.037 0.159 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0.21964521 0.94388078 1.16352600</span> +<span class="r-out co"><span class="r-pr">#></span> 3 m 0.16473391 0.66071655 0.82545046</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 0.13178713 0.56632847 0.69811560</span> +<span class="r-out co"><span class="r-pr">#></span> 6 m 0.12080487 0.42474635 0.54555122</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 0.08785809 0.14158212 0.22944020</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 0.04392904 0.04719404 0.09112308</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sw_runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0.8447893 3.6303107 4.4751000</span> +<span class="r-out co"><span class="r-pr">#></span> 3 m 0.7844472 3.1462693 3.9307165</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 0.7321507 3.1462693 3.8784200</span> +<span class="r-out co"><span class="r-pr">#></span> 6 m 0.7106169 2.4985080 3.2091248</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 0.6275578 1.0113008 1.6388586</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 0.4392904 0.4719404 0.9112308</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - 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Note that results for multiple applications should be compared to the corresponding results for a single application. At current, this is not done automatically in this implementation. Only Step 1 PECs are calculated. However, -input files are generated that are suitable as input also for Step 2 -to be used with the FOCUS calculator." /> -<meta name="twitter:card" content="summary" /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +input files can be generated that are suitable as input for +the FOCUS calculator."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -75,35 +23,21 @@ to be used with the FOCUS calculator." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate PEC surface water at FOCUS Step 1</h1> @@ -117,119 +51,118 @@ authored by Michael Klein, in R. Note that results for multiple applications should be compared to the corresponding results for a single application. At current, this is not done automatically in this implementation. Only Step 1 PECs are calculated. However, -input files are generated that are suitable as input also for Step 2 -to be used with the FOCUS calculator.</p> +input files can be generated that are suitable as input for +the FOCUS calculator.</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_focus</span><span class="op">(</span></span> +<span> <span class="va">parent</span>,</span> +<span> <span class="va">rate</span>,</span> +<span> n <span class="op">=</span> <span class="fl">1</span>,</span> +<span> i <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> comment <span class="op">=</span> <span class="st">""</span>,</span> +<span> met <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> f_drift <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> f_rd <span class="op">=</span> <span class="fl">0.1</span>,</span> +<span> scenario <span class="op">=</span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">names</span>,</span> +<span> region <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"n"</span>, <span class="st">"s"</span><span class="op">)</span>,</span> +<span> season <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="st">"of"</span>, <span class="st">"mm"</span>, <span class="st">"js"</span><span class="op">)</span>,</span> +<span> interception <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"no interception"</span>, <span class="st">"minimal crop cover"</span>, <span class="st">"average crop cover"</span>,</span> +<span> <span class="st">"full canopy"</span><span class="op">)</span>,</span> +<span> met_form_water <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> txt_file <span class="op">=</span> <span class="st">"pesticide.txt"</span>,</span> +<span> overwrite <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> append <span class="op">=</span> <span class="cn">FALSE</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> - <pre class="usage"><span class='fu'>PEC_sw_focus</span>( - <span class='no'>parent</span>, - <span class='no'>rate</span>, - <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>""</span>, - <span class='kw'>met</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>f_rd</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, - <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span>, - <span class='kw'>region</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"n"</span>, <span class='st'>"s"</span>), - <span class='kw'>season</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"of"</span>, <span class='st'>"mm"</span>, <span class='st'>"js"</span>), - <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"no interception"</span>, <span class='st'>"minimal crop cover"</span>, <span class='st'>"average crop cover"</span>, - <span class='st'>"full canopy"</span>), - <span class='kw'>met_form_water</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>txt_file</span> <span class='kw'>=</span> <span class='st'>"pesticide.txt"</span>, - <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>append</span> <span class='kw'>=</span> <span class='fl'>TRUE</span> -)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>parent</th> - <td><p>A list containing substance specific parameters, e.g. -conveniently generated by <code><a href='chent_focus_sw.html'>chent_focus_sw</a></code>.</p></td> - </tr> - <tr> - <th>rate</th> - <td><p>The application rate in g/ha. Overriden when -applications are given explicitly</p></td> - </tr> - <tr> - <th>n</th> - <td><p>The number of applications</p></td> - </tr> - <tr> - <th>i</th> - <td><p>The application interval</p></td> - </tr> - <tr> - <th>comment</th> - <td><p>A comment for the input file</p></td> - </tr> - <tr> - <th>met</th> - <td><p>A list containing metabolite specific parameters. e.g. -conveniently generated by <code><a href='chent_focus_sw.html'>chent_focus_sw</a></code>. If not NULL, -the PEC is calculated for this compound, not the parent.</p></td> - </tr> - <tr> - <th>f_drift</th> - <td><p>The fraction of the application rate reaching the waterbody + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>parent</dt> +<dd><p>A list containing substance specific parameters, e.g. +conveniently generated by [chent_focus_sw].</p></dd> + + +<dt>rate</dt> +<dd><p>The application rate in g/ha. Overriden when +applications are given explicitly</p></dd> + + +<dt>n</dt> +<dd><p>The number of applications</p></dd> + + +<dt>i</dt> +<dd><p>The application interval</p></dd> + + +<dt>comment</dt> +<dd><p>A comment for the input file</p></dd> + + +<dt>met</dt> +<dd><p>A list containing metabolite specific parameters. e.g. +conveniently generated by [chent_focus_sw]. If not NULL, +the PEC is calculated for this compound, not the parent.</p></dd> + + +<dt>f_drift</dt> +<dd><p>The fraction of the application rate reaching the waterbody via drift. If NA, this is derived from the scenario name and the number of applications via the drift data defined by the -<code><a href='FOCUS_Step_12_scenarios.html'>FOCUS_Step_12_scenarios</a></code></p></td> - </tr> - <tr> - <th>f_rd</th> - <td><p>The fraction of the amount applied reaching the waterbody via +[FOCUS_Step_12_scenarios]</p></dd> + + +<dt>f_rd</dt> +<dd><p>The fraction of the amount applied reaching the waterbody via runoff/drainage. At Step 1, it is assumed to be 10<!-- %, be it the --> -parent or a metabolite</p></td> - </tr> - <tr> - <th>scenario</th> - <td><p>The name of the scenario. Must be one of the scenario -names given in <code><a href='FOCUS_Step_12_scenarios.html'>FOCUS_Step_12_scenarios</a></code></p></td> - </tr> - <tr> - <th>region</th> - <td><p>'n' for Northern Europe or 's' for Southern Europe. If NA, only -Step 1 PECsw are calculated</p></td> - </tr> - <tr> - <th>season</th> - <td><p>'of' for October to February, 'mm' for March to May, and 'js' -for June to September. If NA, only step 1 PECsw are calculated</p></td> - </tr> - <tr> - <th>interception</th> - <td><p>One of 'no interception' (default), 'minimal crop cover', -'average crop cover' or 'full canopy'</p></td> - </tr> - <tr> - <th>met_form_water</th> - <td><p>Should the metabolite formation in water be taken into +parent or a metabolite</p></dd> + + +<dt>scenario</dt> +<dd><p>The name of the scenario. Must be one of the scenario +names given in [FOCUS_Step_12_scenarios]</p></dd> + + +<dt>region</dt> +<dd><p>'n' for Northern Europe or 's' for Southern Europe. If NA, only +Step 1 PECsw are calculated</p></dd> + + +<dt>season</dt> +<dd><p>'of' for October to February, 'mm' for March to May, and 'js' +for June to September. If NA, only step 1 PECsw are calculated</p></dd> + + +<dt>interception</dt> +<dd><p>One of 'no interception' (default), 'minimal crop cover', +'average crop cover' or 'full canopy'</p></dd> + + +<dt>met_form_water</dt> +<dd><p>Should the metabolite formation in water be taken into account? This can be switched off to check the influence and to compare -with previous versions of the Steps 12 calculator</p></td> - </tr> - <tr> - <th>txt_file</th> - <td><p>the name, and potentially the full path to the +with previous versions of the Steps 12 calculator</p></dd> + + +<dt>txt_file</dt> +<dd><p>the name, and potentially the full path to the Steps.12 input text file to which the specification of the run(s) -should be written</p></td> - </tr> - <tr> - <th>overwrite</th> - <td><p>Should an existing file a the location specified in -<code>txt_file</code> be overwritten? Only takes effect if append is FALSE.</p></td> - </tr> - <tr> - <th>append</th> - <td><p>Should the input text file be appended?</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> +should be written</p></dd> + + +<dt>overwrite</dt> +<dd><p>Should an existing file a the location specified in +<code>txt_file</code> be overwritten? Only takes effect if append is FALSE.</p></dd> + +<dt>append</dt> +<dd><p>Should the input text file be appended, if it exists?</p></dd> + +</dl></div> + <div id="note"> + <h2>Note</h2> <p>The formulas for input to the waterbody via runoff/drainage of the parent and subsequent formation of the metabolite in water is not documented in the model description coming with the calculator. As one would @@ -237,142 +170,141 @@ should be written</p></td> multiplying the application rate with the molar weight correction and the formation fraction in water/sediment systems.</p> <p>Step 2 is not implemented.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - + </div> + <div id="references"> + <h2>References</h2> <p>FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4). FOrum for the Co-ordination of pesticde fate models and their USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic<!-- %20FOCUS_SWS_vc1.4.pdf --></p> <p>Website of the Steps 1 and 2 calculator at the Joint Research Center of the European Union: http://esdac.jrc.ec.europa.eu/projects/stepsonetwo</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># Parent only</span> -<span class='no'>dummy_1</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"Dummy 1"</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>6000</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>344.8</span>) -<span class='fu'>PEC_sw_focus</span>(<span class='no'>dummy_1</span>, <span class='fl'>3000</span>, <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>append</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> $f_drift -#> [1] 0 -#> -#> $eq_rate_drift_s -#> [1] 3000 -#> -#> $eq_rate_rd_s -#> [1] 3000 -#> -#> $eq_rate_rd_parent_s -#> [1] NA -#> -#> $input_drift_s -#> [1] 0 -#> -#> $input_rd_s -#> [1] 300 -#> -#> $f_rd_sw -#> [1] 0.6850566 -#> -#> $f_rd_sed -#> [1] 0.3149434 -#> -#> $PEC -#> type -#> Time PECsw TWAECsw PECsed TWAECsed -#> 0 6.850566e+02 NA 2.362075e+03 NA -#> 1 6.103161e+02 647.68635 2.104370e+03 2233.2225 -#> 2 5.437298e+02 612.03420 1.874780e+03 2110.2939 -#> 4 4.315586e+02 548.76030 1.488014e+03 1892.1255 -#> 7 3.051580e+02 469.88375 1.052185e+03 1620.1592 -#> 14 1.359325e+02 339.57370 4.686951e+02 1170.8501 -#> 21 6.055102e+01 257.45458 2.087799e+02 887.7034 -#> 28 2.697241e+01 203.47173 9.300089e+01 701.5705 -#> 42 5.352005e+00 140.10377 1.845371e+01 483.0778 -#> 50 2.123945e+00 118.24602 7.323361e+00 407.7123 -#> 100 6.585062e-03 59.30629 2.270529e-02 204.4881 -#> -#> $PEC_sw_max -#> [1] 685.0566 -#> -#> $PEC_sed_max -#> [1] 2362.075 -#> </div><div class='input'> -<span class='co'># Metabolite</span> -<span class='no'>new_dummy</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"New Dummy"</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>100</span>) -<span class='no'>M1</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"M1"</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>50</span>, - <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>0.5</span>) -<span class='fu'>PEC_sw_focus</span>(<span class='no'>new_dummy</span>, <span class='fl'>1000</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='st'>"cereals, winter"</span>, <span class='kw'>met</span> <span class='kw'>=</span> <span class='no'>M1</span>)</div><div class='output co'>#> $f_drift -#> [1] 0.02759 -#> -#> $eq_rate_drift_s -#> [1] 0 -#> -#> $eq_rate_rd_s -#> [1] 200 -#> -#> $eq_rate_rd_parent_s -#> [1] 0 -#> -#> $input_drift_s -#> [1] 0 -#> -#> $input_rd_s -#> [1] 20 -#> -#> $f_rd_sw -#> [1] 0.9375 -#> -#> $f_rd_sed -#> [1] 0.0625 -#> -#> $PEC -#> type -#> Time PECsw TWAECsw PECsed TWAECsed -#> 0 62.50000 NA 31.25000 NA -#> 1 62.06828 62.28414 31.03414 31.14207 -#> 2 61.63954 62.06890 30.81977 31.03445 -#> 4 60.79093 61.64158 30.39547 30.82079 -#> 7 59.53987 61.00800 29.76994 30.50400 -#> 14 56.71995 59.56326 28.35997 29.78163 -#> 21 54.03358 58.16414 27.01679 29.08207 -#> 28 51.47444 56.80902 25.73722 28.40451 -#> 42 46.71404 54.22460 23.35702 27.11230 -#> 50 44.19417 52.81945 22.09709 26.40973 -#> 100 31.25000 45.08422 15.62500 22.54211 -#> -#> $PEC_sw_max -#> [1] 62.5 -#> -#> $PEC_sed_max -#> [1] 31.25 -#> </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#note">Note</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Parent only</span></span></span> +<span class="r-in"><span><span class="va">dummy_1</span> <span class="op"><-</span> <span class="fu"><a href="chent_focus_sw.html">chent_focus_sw</a></span><span class="op">(</span><span class="st">"Dummy 1"</span>, cwsat <span class="op">=</span> <span class="fl">6000</span>, DT50_ws <span class="op">=</span> <span class="fl">6</span>, Koc <span class="op">=</span> <span class="fl">344.8</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">PEC_sw_focus</span><span class="op">(</span><span class="va">dummy_1</span>, <span class="fl">3000</span>, f_drift <span class="op">=</span> <span class="fl">0</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $f_drift</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_drift_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 3000</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_rd_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 3000</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_rd_parent_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $input_drift_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $input_rd_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 300</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $f_rd_sw</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.6850566</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $f_rd_sed</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.3149434</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC</span> +<span class="r-out co"><span class="r-pr">#></span> type</span> +<span class="r-out co"><span class="r-pr">#></span> Time PECsw TWAECsw PECsed TWAECsed</span> +<span class="r-out co"><span class="r-pr">#></span> 0 6.850566e+02 NA 2.362075e+03 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 1 6.103161e+02 647.68635 2.104370e+03 2233.2225</span> +<span class="r-out co"><span class="r-pr">#></span> 2 5.437298e+02 612.03420 1.874780e+03 2110.2939</span> +<span class="r-out co"><span class="r-pr">#></span> 4 4.315586e+02 548.76030 1.488014e+03 1892.1255</span> +<span class="r-out co"><span class="r-pr">#></span> 7 3.051580e+02 469.88375 1.052185e+03 1620.1592</span> +<span class="r-out co"><span class="r-pr">#></span> 14 1.359325e+02 339.57370 4.686951e+02 1170.8501</span> +<span class="r-out co"><span class="r-pr">#></span> 21 6.055102e+01 257.45458 2.087799e+02 887.7034</span> +<span class="r-out co"><span class="r-pr">#></span> 28 2.697241e+01 203.47173 9.300089e+01 701.5705</span> +<span class="r-out co"><span class="r-pr">#></span> 42 5.352005e+00 140.10377 1.845371e+01 483.0778</span> +<span class="r-out co"><span class="r-pr">#></span> 50 2.123945e+00 118.24602 7.323361e+00 407.7123</span> +<span class="r-out co"><span class="r-pr">#></span> 100 6.585062e-03 59.30629 2.270529e-02 204.4881</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sw_max</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 685.0566</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sed_max</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 2362.075</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Metabolite</span></span></span> +<span class="r-in"><span><span class="va">new_dummy</span> <span class="op"><-</span> <span class="fu"><a href="chent_focus_sw.html">chent_focus_sw</a></span><span class="op">(</span><span class="st">"New Dummy"</span>, mw <span class="op">=</span> <span class="fl">250</span>, Koc <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">M1</span> <span class="op"><-</span> <span class="fu"><a href="chent_focus_sw.html">chent_focus_sw</a></span><span class="op">(</span><span class="st">"M1"</span>, mw <span class="op">=</span> <span class="fl">100</span>, cwsat <span class="op">=</span> <span class="fl">100</span>, DT50_ws <span class="op">=</span> <span class="fl">100</span>, Koc <span class="op">=</span> <span class="fl">50</span>,</span></span> +<span class="r-in"><span> max_ws <span class="op">=</span> <span class="fl">0</span>, max_soil <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">PEC_sw_focus</span><span class="op">(</span><span class="va">new_dummy</span>, <span class="fl">1000</span>, scenario <span class="op">=</span> <span class="st">"cereals, winter"</span>, met <span class="op">=</span> <span class="va">M1</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $f_drift</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.02759</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_drift_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_rd_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 200</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_rd_parent_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $input_drift_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $input_rd_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 20</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $f_rd_sw</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.9375</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $f_rd_sed</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.0625</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC</span> +<span class="r-out co"><span class="r-pr">#></span> type</span> +<span class="r-out co"><span class="r-pr">#></span> Time PECsw TWAECsw PECsed TWAECsed</span> +<span class="r-out co"><span class="r-pr">#></span> 0 62.50000 NA 31.25000 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 1 62.06828 62.28414 31.03414 31.14207</span> +<span class="r-out co"><span class="r-pr">#></span> 2 61.63954 62.06890 30.81977 31.03445</span> +<span class="r-out co"><span class="r-pr">#></span> 4 60.79093 61.64158 30.39547 30.82079</span> +<span class="r-out co"><span class="r-pr">#></span> 7 59.53987 61.00800 29.76994 30.50400</span> +<span class="r-out co"><span class="r-pr">#></span> 14 56.71995 59.56326 28.35997 29.78163</span> +<span class="r-out co"><span class="r-pr">#></span> 21 54.03358 58.16414 27.01679 29.08207</span> +<span class="r-out co"><span class="r-pr">#></span> 28 51.47444 56.80902 25.73722 28.40451</span> +<span class="r-out co"><span class="r-pr">#></span> 42 46.71404 54.22460 23.35702 27.11230</span> +<span class="r-out co"><span class="r-pr">#></span> 50 44.19417 52.81945 22.09709 26.40973</span> +<span class="r-out co"><span class="r-pr">#></span> 100 31.25000 45.08422 15.62500 22.54211</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sw_max</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 62.5</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sed_max</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 31.25</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html index 458eeb7..247c8d7 100644 --- a/docs/reference/PEC_sw_sed.html +++ 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version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate predicted environmental concentrations in sediment from surface @@ -114,89 +48,89 @@ water concentrations</h1> PEC calculator</p> </div> - <pre class="usage"><span class='fu'>PEC_sw_sed</span>( - <span class='no'>PEC_sw</span>, - <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>100</span>, - <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"percentage"</span>, - <span class='kw'>sediment_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>, - <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>, - <span class='kw'>sediment_density</span> <span class='kw'>=</span> <span class='fl'>1.3</span>, - <span class='kw'>PEC_sed_units</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"µg/kg"</span>, <span class='st'>"mg/kg"</span>) -)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>PEC_sw</th> - <td><p>Numeric vector or matrix of surface water concentrations in µg/L for -which the corresponding sediment concentration is to be estimated</p></td> - </tr> - <tr> - <th>percentage</th> - <td><p>The percentage in sediment, used for the percentage method</p></td> - </tr> - <tr> - <th>method</th> - <td><p>The method used for the calculation</p></td> - </tr> - <tr> - <th>sediment_depth</th> - <td><p>Depth of the sediment layer</p></td> - </tr> - <tr> - <th>water_depth</th> - <td><p>Depth of the water body in cm</p></td> - </tr> - <tr> - <th>sediment_density</th> - <td><p>The density of the sediment in L/kg (equivalent to -g/cm3)</p></td> - </tr> - <tr> - <th>PEC_sed_units</th> - <td><p>The units of the estimated sediment PEC value</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The predicted concentration in sediment</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>PEC_sw_sed</span>(<span class='fu'><a href='PEC_sw_drift.html'>PEC_sw_drift</a></span>(<span class='fl'>100</span>, <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fl'>1</span>), <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>50</span>)</div><div class='output co'>#> 1 m -#> 2.130769 </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> - </ul> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_sed</span><span class="op">(</span></span> +<span> <span class="va">PEC_sw</span>,</span> +<span> percentage <span class="op">=</span> <span class="fl">100</span>,</span> +<span> method <span class="op">=</span> <span class="st">"percentage"</span>,</span> +<span> sediment_depth <span class="op">=</span> <span class="fl">5</span>,</span> +<span> water_depth <span class="op">=</span> <span class="fl">30</span>,</span> +<span> sediment_density <span class="op">=</span> <span class="fl">1.3</span>,</span> +<span> PEC_sed_units <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"µg/kg"</span>, <span class="st">"mg/kg"</span><span class="op">)</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>PEC_sw</dt> +<dd><p>Numeric vector or matrix of surface water concentrations in µg/L for +which the corresponding sediment concentration is to be estimated</p></dd> + + +<dt>percentage</dt> +<dd><p>The percentage in sediment, used for the percentage method</p></dd> + + +<dt>method</dt> +<dd><p>The method used for the calculation</p></dd> + + +<dt>sediment_depth</dt> +<dd><p>Depth of the sediment layer</p></dd> + + +<dt>water_depth</dt> +<dd><p>Depth of the water body in cm</p></dd> + +<dt>sediment_density</dt> +<dd><p>The density of the sediment in L/kg (equivalent to +g/cm3)</p></dd> + + +<dt>PEC_sed_units</dt> +<dd><p>The units of the estimated sediment PEC value</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The predicted concentration in sediment</p> + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_sw_sed</span><span class="op">(</span><span class="fu"><a href="PEC_sw_drift.html">PEC_sw_drift</a></span><span class="op">(</span><span class="fl">100</span>, distances <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>, percentage <span class="op">=</span> <span class="fl">50</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 1 m </span> +<span class="r-out co"><span class="r-pr">#></span> 2.130769 </span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png Binary files differnew file mode 100644 index 0000000..8269e66 --- /dev/null +++ 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navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Actual and maximum moving window time average concentrations for SFO kinetics</h1> @@ -109,71 +43,69 @@ <p>Actual and maximum moving window time average concentrations for SFO kinetics</p> </div> - <pre class="usage"><span class='fu'>SFO_actual_twa</span>(<span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>21</span>, <span class='fl'>28</span>, <span class='fl'>42</span>, <span class='fl'>50</span>, <span class='fl'>100</span>))</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>DT50</th> - <td><p>The half-life.</p></td> - </tr> - <tr> - <th>times</th> - <td><p>The output times, and window sizes for time weighted average concentrations</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SFO_actual_twa</span><span class="op">(</span>DT50 <span class="op">=</span> <span class="fl">1000</span>, times <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">21</span>, <span class="fl">28</span>, <span class="fl">42</span>, <span class="fl">50</span>, <span class="fl">100</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> + </div> + <div id="source"> + <h2>Source</h2> <p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, 18 December 2014, p. 251</p> + </div> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>DT50</dt> +<dd><p>The half-life.</p></dd> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>SFO_actual_twa</span>(<span class='fl'>10</span>)</div><div class='output co'>#> actual twa -#> 0 1.0000000000 NaN -#> 1 0.9330329915 0.9661297 -#> 2 0.8705505633 0.9337803 -#> 4 0.7578582833 0.8733416 -#> 7 0.6155722067 0.7923030 -#> 14 0.3789291416 0.6400113 -#> 21 0.2332582479 0.5267498 -#> 28 0.1435872944 0.4412651 -#> 42 0.0544094102 0.3248093 -#> 50 0.0312500000 0.2795222 -#> 100 0.0009765625 0.1441286</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> - </ul> +<dt>times</dt> +<dd><p>The output times, and window sizes for time weighted average concentrations</p></dd> + +</dl></div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">SFO_actual_twa</span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> actual twa</span> +<span class="r-out co"><span class="r-pr">#></span> 0 1.0000000000 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> 1 0.9330329915 0.9661297</span> +<span class="r-out co"><span class="r-pr">#></span> 2 0.8705505633 0.9337803</span> +<span class="r-out co"><span class="r-pr">#></span> 4 0.7578582833 0.8733416</span> +<span class="r-out co"><span class="r-pr">#></span> 7 0.6155722067 0.7923030</span> +<span class="r-out co"><span class="r-pr">#></span> 14 0.3789291416 0.6400113</span> +<span class="r-out co"><span class="r-pr">#></span> 21 0.2332582479 0.5267498</span> +<span class="r-out co"><span class="r-pr">#></span> 28 0.1435872944 0.4412651</span> +<span class="r-out co"><span class="r-pr">#></span> 42 0.0544094102 0.3248093</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.0312500000 0.2795222</span> +<span class="r-out co"><span class="r-pr">#></span> 100 0.0009765625 0.1441286</span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" 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id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Determine the SSLRC mobility classification for a chemical substance from its Koc</h1> @@ -105,86 +41,81 @@ checked against the spreadsheet published on the CRC website" /> </div> <div class="ref-description"> - <p>This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website</p> - </div> - <pre class="usage"><span class='fu'>SSLRC_mobility_classification</span>(<span class='no'>Koc</span>)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>Koc</th> - <td><p>The sorption coefficient normalised to organic carbon in L/kg</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SSLRC_mobility_classification</span><span class="op">(</span><span class="va">Koc</span><span class="op">)</span></span></code></pre></div> + </div> - <p>A list containing the classification and the percentage of the - compound transported per 10 mm drain water</p> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>Koc</dt> +<dd><p>The sorption coefficient normalised to organic carbon in L/kg</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> +<p>A list containing the classification and the percentage of the + compound transported per 10 mm drain water</p> + </div> + <div id="references"> + <h2>References</h2> <p>HSE's Chemicals Regulation Division (CRD) Active substance PECsw calculations (for UK specific authorisation requests) - <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm</a> + <a href="https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm" class="external-link">https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm</a> accessed 2019-09-27</p> <p>Drainage PECs Version 1.0 (2015) Spreadsheet published at - <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> + <a href="https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx" class="external-link">https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> accessed 2019-09-27</p> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>SSLRC_mobility_classification</span>(<span class='fl'>100</span>)</div><div class='output co'>#> $`Mobility classification` -#> [1] "Moderately mobile" -#> -#> $`Percentage drained per mm of drain water` -#> [1] 0.7 -#> </div><div class='input'><span class='fu'>SSLRC_mobility_classification</span>(<span class='fl'>10000</span>)</div><div class='output co'>#> $`Mobility classification` -#> [1] "Non mobile" -#> -#> $`Percentage drained per mm of drain water` -#> [1] 0.008 -#> </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - - <li><a href="#value">Value</a></li> - - <li><a href="#references">References</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">SSLRC_mobility_classification</span><span class="op">(</span><span class="fl">100</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $`Mobility classification`</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "Moderately mobile"</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $`Percentage drained per mm of drain water`</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.7</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span><span class="fu">SSLRC_mobility_classification</span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $`Mobility classification`</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "Non mobile"</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $`Percentage drained per mm of drain water`</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.008</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" 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Usually, an instance of this class will be generated -by read.TOXSWA_cwa." /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +by read.TOXSWA_cwa."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -76,35 +21,21 @@ by read.TOXSWA_cwa." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>R6 class for holding TOXSWA water concentration data and associated statistics</h1> @@ -117,179 +48,236 @@ by read.TOXSWA_cwa." /> and some associated statistics. like maximum moving window average concentrations, and dataframes holding the events exceeding specified thresholds. Usually, an instance of this class will be generated -by <code><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></code>.</p> +by <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></code>.</p> </div> + <div id="format"> + <h2>Format</h2> + <p>An <code>R6Class</code> generator object.</p> + </div> + <div id="public-fields"> + <h2>Public fields</h2> + <p></p><div class="r6-fields"><dl><dt><code>filename</code></dt> +<dd><p>Length one character vector holding the filename.</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>An <code>R6Class</code> generator object.</p> - <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2> +<dt><code>basedir</code></dt> +<dd><p>Length one character vector holding the directory where the file came from.</p></dd> + - <p><div class="r6-fields"></p><dl'> -<dt><code>filename</code></dt><dd><p>Length one character vector holding the filename.</p></dd> +<dt><code>zipfile</code></dt> +<dd><p>If not null, giving the path to the zip file from which the file was read.</p></dd> -<dt><code>basedir</code></dt><dd><p>Length one character vector holding the directory where the file came from.</p></dd> -<dt><code>zipfile</code></dt><dd><p>If not null, giving the path to the zip file from which the file was read.</p></dd> +<dt><code>segment</code></dt> +<dd><p>Length one integer, specifying for which segment the cwa data were read.</p></dd> -<dt><code>segment</code></dt><dd><p>Length one integer, specifying for which segment the cwa data were read.</p></dd> -<dt><code>substance</code></dt><dd><p>The TOXSWA name of the substance.</p></dd> +<dt><code>substance</code></dt> +<dd><p>The TOXSWA name of the substance.</p></dd> -<dt><code>cwas</code></dt><dd><p>Dataframe holding the concentrations.</p></dd> -<dt><code>events</code></dt><dd><p>List of dataframes holding the event statistics for each threshold.</p></dd> +<dt><code>cwas</code></dt> +<dd><p>Dataframe holding the concentrations.</p></dd> -<dt><code>windows</code></dt><dd><p>Matrix of maximum time weighted average concentrations (TWAC_max) + +<dt><code>events</code></dt> +<dd><p>List of dataframes holding the event statistics for each threshold.</p></dd> + + +<dt><code>windows</code></dt> +<dd><p>Matrix of maximum time weighted average concentrations (TWAC_max) and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) for the requested moving window sizes in days.</p></dd> -</dl><p></div></p> - <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> +</dl><p></p></div> + </div> + <div id="methods"> + <h2>Methods</h2> -<h3>Public methods</h3> - -<ul> -<li><p><a href='#method-new'><code>TOXSWA_cwa$new()</code></a></p></li> -<li><p><a href='#method-moving_windows'><code>TOXSWA_cwa$moving_windows()</code></a></p></li> -<li><p><a href='#method-get_events'><code>TOXSWA_cwa$get_events()</code></a></p></li> -<li><p><a href='#method-print'><code>TOXSWA_cwa$print()</code></a></p></li> -<li><p><a href='#method-clone'><code>TOXSWA_cwa$clone()</code></a></p></li> -</ul> -<p><hr> -<a id="method-new"></a></p><h3>Method <code>new()</code></h3> -<p>Create a TOXSWA_cwa object from a file</p><h3>Usage</h3> -<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>new</span>( - <span class='no'>filename</span>, - <span class='no'>basedir</span>, - <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>segment</span> <span class='kw'>=</span> <span class='st'>"last"</span>, - <span class='kw'>substance</span> <span class='kw'>=</span> <span class='st'>"parent"</span>, - <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span> -)</pre><p></div></p> - -<h3>Arguments</h3> -<p><div class="arguments"></p><dl'> -<dt><code>filename</code></dt><dd><p>The filename</p></dd> - -<dt><code>basedir</code></dt><dd><p>The directory to look in</p></dd> - -<dt><code>zipfile</code></dt><dd><p>Optional path to a zipfile holding the file</p></dd> - -<dt><code>segment</code></dt><dd><p>Either "last" or the number of the segment for which to read the data</p></dd> - -<dt><code>substance</code></dt><dd><p>The TOXSWA substance name (for TOXSWA 4 or higher)</p></dd> - -<dt><code>total</code></dt><dd><p>Should total concentrations be read in? If FALSE, free concentrations are read</p></dd> - -</dl><p></div></p> -<p><hr> -<a id="method-moving_windows"></a></p><h3>Method <code>moving_windows()</code></h3> -<p>Add to the `windows` field described above.</p><h3>Usage</h3> -<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>moving_windows</span>(<span class='no'>windows</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p> - -<h3>Arguments</h3> -<p><div class="arguments"></p><dl'> -<dt><code>windows</code></dt><dd><p>Window sizes in days</p></dd> - -<dt><code>total</code></dt><dd><p>If TRUE, the total concentration including the amount adsorbed to +<div class="section"> +<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> + +<ul><li><p><a href="#method-TOXSWA_cwa-new"><code>TOXSWA_cwa$new()</code></a></p></li> +<li><p><a href="#method-TOXSWA_cwa-moving_windows"><code>TOXSWA_cwa$moving_windows()</code></a></p></li> +<li><p><a href="#method-TOXSWA_cwa-get_events"><code>TOXSWA_cwa$get_events()</code></a></p></li> +<li><p><a href="#method-TOXSWA_cwa-print"><code>TOXSWA_cwa$print()</code></a></p></li> +<li><p><a href="#method-TOXSWA_cwa-clone"><code>TOXSWA_cwa$clone()</code></a></p></li> +</ul></div><p></p><hr><a id="method-TOXSWA_cwa-new"></a><div class="section"> +<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> +<p>Create a TOXSWA_cwa object from a file</p><div class="section"> +<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/TOXSWA_cwa.html">TOXSWA_cwa</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span> +<span> <span class="va">filename</span>,</span> +<span> <span class="va">basedir</span>,</span> +<span> zipfile <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> segment <span class="op">=</span> <span class="st">"last"</span>,</span> +<span> substance <span class="op">=</span> <span class="st">"parent"</span>,</span> +<span> total <span class="op">=</span> <span class="cn">FALSE</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4> +<p></p><div class="arguments"><dl><dt><code>filename</code></dt> +<dd><p>The filename</p></dd> + + +<dt><code>basedir</code></dt> +<dd><p>The directory to look in</p></dd> + + +<dt><code>zipfile</code></dt> +<dd><p>Optional path to a zipfile holding the file</p></dd> + + +<dt><code>segment</code></dt> +<dd><p>Either "last" or the number of the segment for which to read the data</p></dd> + + +<dt><code>substance</code></dt> +<dd><p>The TOXSWA substance name (for TOXSWA 4 or higher)</p></dd> + + +<dt><code>total</code></dt> +<dd><p>Should total concentrations be read in? If FALSE, free concentrations are read</p></dd> + + +</dl><p></p></div> +</div> + +</div><p></p><hr><a id="method-TOXSWA_cwa-moving_windows"></a><div class="section"> +<h3 id="method-moving-windows-">Method <code>moving_windows()</code><a class="anchor" aria-label="anchor" href="#method-moving-windows-"></a></h3> +<p>Add to the `windows` field described above.</p><div class="section"> +<h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">moving_windows</span><span class="op">(</span><span class="va">windows</span>, total <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4> +<p></p><div class="arguments"><dl><dt><code>windows</code></dt> +<dd><p>Window sizes in days</p></dd> + + +<dt><code>total</code></dt> +<dd><p>If TRUE, the total concentration including the amount adsorbed to suspended matter will be used.</p></dd> -</dl><p></div></p> -<p><hr> -<a id="method-get_events"></a></p><h3>Method <code>get_events()</code></h3> + +</dl><p></p></div> +</div> + +</div><p></p><hr><a id="method-TOXSWA_cwa-get_events"></a><div class="section"> +<h3 id="method-get-events-">Method <code>get_events()</code><a class="anchor" aria-label="anchor" href="#method-get-events-"></a></h3> <p>Populate a datataframe with event information for the specified threshold value. The resulting dataframe is stored in the `events` -field of the object.</p><h3>Usage</h3> -<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>get_events</span>(<span class='no'>thresholds</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p> +field of the object.</p><div class="section"> +<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">get_events</span><span class="op">(</span><span class="va">thresholds</span>, total <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4> +<p></p><div class="arguments"><dl><dt><code>thresholds</code></dt> +<dd><p>Threshold values in µg/L.</p></dd> -<h3>Arguments</h3> -<p><div class="arguments"></p><dl'> -<dt><code>thresholds</code></dt><dd><p>Threshold values in µg/L.</p></dd> -<dt><code>total</code></dt><dd><p>If TRUE, the total concentration including the amount adsorbed to +<dt><code>total</code></dt> +<dd><p>If TRUE, the total concentration including the amount adsorbed to suspended matter will be used.</p></dd> -</dl><p></div></p> -<p><hr> -<a id="method-print"></a></p><h3>Method <code><a href='https://rdrr.io/r/base/print.html'>print()</a></code></h3> -<p>Print a `TOXSWA_cwa` object</p><h3>Usage</h3> -<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>()</pre><p></div></p> - -<p><hr> -<a id="method-clone"></a></p><h3>Method <code>clone()</code></h3> -<p>The objects of this class are cloneable with this method.</p><h3>Usage</h3> -<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>clone</span>(<span class='kw'>deep</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p> - -<h3>Arguments</h3> -<p><div class="arguments"></p><dl'> -<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd> - -</dl><p></div></p> - - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>H_sw_R1_stream</span> <span class='kw'><-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00003s_pa.cwa"</span>, - <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>, - <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/system.file.html'>system.file</a></span>(<span class='st'>"testdata/SwashProjects.zip"</span>, - <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>)) -<span class='no'>H_sw_R1_stream</span>$<span class='fu'>get_events</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>2</span>, <span class='fl'>10</span>)) -<span class='no'>H_sw_R1_stream</span>$<span class='fu'>moving_windows</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>7</span>, <span class='fl'>21</span>)) -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>H_sw_R1_stream</span>)</div><div class='output co'>#> <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 -#> datetime t t_firstjan t_rel_to_max cwa_mug_per_L -#> 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0 -#> 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0 -#> 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0 -#> 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0 -#> 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0 -#> 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0 -#> cwa_tot_mug_per_L -#> 20 0 -#> 40 0 -#> 60 0 -#> 80 0 -#> 100 0 -#> 120 0 -#> Moving window analysis -#> window max_TWAC max_AUC_h max_AUC_d -#> 1 7 days 2.3926551 401.9660 16.74859 -#> 2 21 days 0.8369248 421.8101 17.57542 -#> Event statistics for threshold 2 -#> t_start cwa_max duration pre_interval AUC_h AUC_d -#> 1 44.375 4.167238 0.208 44.375 17.77202 0.740501 -#> 2 55.042 40.584010 0.583 10.459 398.21189 16.592162 -#> Event statistics for threshold 10 -#> t_start cwa_max duration pre_interval AUC_h AUC_d -#> 1 55.083 40.58401 0.459 55.083 379.433 15.80971</div></pre> + +</dl><p></p></div> +</div> + +</div><p></p><hr><a id="method-TOXSWA_cwa-print"></a><div class="section"> +<h3 id="method-print-">Method <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code><a class="anchor" aria-label="anchor" href="#method-print-"></a></h3> +<p>Print a `TOXSWA_cwa` object</p><div class="section"> +<h4 id="usage-3">Usage<a class="anchor" aria-label="anchor" href="#usage-3"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">print</span><span class="op">(</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-TOXSWA_cwa-clone"></a><div class="section"> +<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3> +<p>The objects of this class are cloneable with this method.</p><div class="section"> +<h4 id="usage-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></a></h4> +<p></p><div class="arguments"><dl><dt><code>deep</code></dt> +<dd><p>Whether to make a deep clone.</p></dd> + + +</dl><p></p></div> +</div> + +</div> + + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">H_sw_R1_stream</span> <span class="op"><-</span> <span class="fu"><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span><span class="op">(</span><span class="st">"00003s_pa.cwa"</span>,</span></span> +<span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> +<span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>,</span></span> +<span class="r-in"><span> package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">H_sw_R1_stream</span><span class="op">$</span><span class="fu">get_events</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span>, <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">H_sw_R1_stream</span><span class="op">$</span><span class="fu">moving_windows</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">7</span>, <span class="fl">21</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">H_sw_R1_stream</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 </span> +<span class="r-out co"><span class="r-pr">#></span> datetime t t_firstjan t_rel_to_max cwa_mug_per_L</span> +<span class="r-out co"><span class="r-pr">#></span> 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0</span> +<span class="r-out co"><span class="r-pr">#></span> 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0</span> +<span class="r-out co"><span class="r-pr">#></span> 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0</span> +<span class="r-out co"><span class="r-pr">#></span> 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0</span> +<span class="r-out co"><span class="r-pr">#></span> 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0</span> +<span class="r-out co"><span class="r-pr">#></span> 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0</span> +<span class="r-out co"><span class="r-pr">#></span> cwa_tot_mug_per_L</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0</span> +<span class="r-out co"><span class="r-pr">#></span> 60 0</span> +<span class="r-out co"><span class="r-pr">#></span> 80 0</span> +<span class="r-out co"><span class="r-pr">#></span> 100 0</span> +<span class="r-out co"><span class="r-pr">#></span> 120 0</span> +<span class="r-out co"><span class="r-pr">#></span> Moving window analysis</span> +<span class="r-out co"><span class="r-pr">#></span> window max_TWAC max_AUC_h max_AUC_d</span> +<span class="r-out co"><span class="r-pr">#></span> 1 7 days 2.3926551 401.9660 16.74859</span> +<span class="r-out co"><span class="r-pr">#></span> 2 21 days 0.8369248 421.8101 17.57542</span> +<span class="r-out co"><span class="r-pr">#></span> Event statistics for threshold 2 </span> +<span class="r-out co"><span class="r-pr">#></span> t_start cwa_max duration pre_interval AUC_h AUC_d</span> +<span class="r-out co"><span class="r-pr">#></span> 1 44.375 4.167238 0.208 44.375 17.77202 0.740501</span> +<span class="r-out co"><span class="r-pr">#></span> 2 55.042 40.584010 0.583 10.459 398.21189 16.592162</span> +<span class="r-out co"><span class="r-pr">#></span> Event statistics for threshold 10 </span> +<span class="r-out co"><span class="r-pr">#></span> t_start cwa_max duration pre_interval AUC_h AUC_d</span> +<span class="r-out co"><span class="r-pr">#></span> 1 55.083 40.58401 0.459 55.083 379.433 15.80971</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" 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src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Estimation of the transpiration stream concentration factor — TSCF"><meta property="og:description" content="The FOCUS groundwater guidance (FOCUS 2014, p. 41) states that a reliable measured log Kow for neutral pH must be available in order to apply the Briggs equation. It is not clarified when it can be regarded reliable, but the equation is stated to be produced for non-ionic compounds, suggesting that the compound should not be ionogenic (weak acid/base) -or ionic." /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +or ionic."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -77,35 +22,21 @@ or ionic." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Estimation of the transpiration stream concentration factor</h1> @@ -122,60 +53,63 @@ the compound should not be ionogenic (weak acid/base) or ionic.</p> </div> - <pre class="usage"><span class='fu'>TSCF</span>(<span class='no'>log_Kow</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"briggs82"</span>, <span class='st'>"dettenmaier09"</span>))</pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">TSCF</span><span class="op">(</span><span class="va">log_Kow</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"briggs82"</span>, <span class="st">"dettenmaier09"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> + </div> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>log_Kow</th> - <td><p>The decadic logarithm of the octanol-water partition constant</p></td> - </tr> - <tr> - <th>method</th> - <td><p>Short name of the estimation method.</p></td> - </tr> - </table> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>log_Kow</dt> +<dd><p>The decadic logarithm of the octanol-water partition constant</p></dd> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - <p>The Dettenmaier equation is given to show that other views on the subject exist.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> +<dt>method</dt> +<dd><p>Short name of the estimation method.</p></dd> +</dl></div> + <div id="details"> + <h2>Details</h2> + <p>The Dettenmaier equation is given to show that other views on the subject exist.</p> + </div> + <div id="references"> + <h2>References</h2> <p>FOCUS (2014) Generic Guidance for Tier 1 FOCUS Ground Water Assessments. Version 2.2, May 2014 Dettenmaier EM, Doucette WJ and Bugbee B (2009) Chemical hydrophobicity and uptake by plant roots. Environ. Sci. Technol 43, 324 - 329</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>TSCF</span>, -<span class='fl'>1</span>, <span class='fl'>5</span>, <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"log Kow"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"TSCF"</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1.1</span>))</div><div class='input'><span class='no'>TSCF_2</span> <span class='kw'><-</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>TSCF</span>(<span class='no'>x</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"dettenmaier09"</span>) -<span class='fu'><a href='https://rdrr.io/r/graphics/curve.html'>curve</a></span>(<span class='no'>TSCF_2</span>, -<span class='fl'>1</span>, <span class='fl'>5</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></span>(<span class='st'>"topright"</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>2</span>, <span class='kw'>bty</span> <span class='kw'>=</span> <span class='st'>"n"</span>, - <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Briggs et al. (1982)"</span>, <span class='st'>"Dettenmaier et al. (2009)"</span>))</div><div class='img'><img src='TSCF-1.png' alt='' width='700' height='433' /></div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">TSCF</span>, <span class="op">-</span><span class="fl">1</span>, <span class="fl">5</span>, xlab <span class="op">=</span> <span class="st">"log Kow"</span>, ylab <span class="op">=</span> <span class="st">"TSCF"</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1.1</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">TSCF_2</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">TSCF</span><span class="op">(</span><span class="va">x</span>, method <span class="op">=</span> <span class="st">"dettenmaier09"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/curve.html" class="external-link">curve</a></span><span class="op">(</span><span class="va">TSCF_2</span>, <span class="op">-</span><span class="fl">1</span>, <span class="fl">5</span>, add <span class="op">=</span> <span class="cn">TRUE</span>, lty <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></span><span class="op">(</span><span class="st">"topright"</span>, lty <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">2</span>, bty <span class="op">=</span> <span class="st">"n"</span>,</span></span> +<span class="r-in"><span> legend <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Briggs et al. (1982)"</span>, <span class="st">"Dettenmaier et al. (2009)"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="TSCF-1.png" alt="" width="700" height="433"></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html index 70fd16d..13129b8 100644 --- a/docs/reference/chent_focus_sw.html +++ b/docs/reference/chent_focus_sw.html @@ -1,64 +1,12 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -69,35 +17,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Create a chemical compound object for FOCUS Step 1 calculations</h1> @@ -109,98 +43,93 @@ <p>Create a chemical compound object for FOCUS Step 1 calculations</p> </div> - <pre class="usage"><span class='fu'>chent_focus_sw</span>( - <span class='no'>name</span>, - <span class='no'>Koc</span>, - <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>DT50_soil</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>DT50_water</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>DT50_sediment</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>1000</span>, - <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>1</span> -)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>name</th> - <td><p>Length one character vector containing the name</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>Partition coefficient between organic carbon and water -in L/kg.</p></td> - </tr> - <tr> - <th>DT50_ws</th> - <td><p>Half-life in water/sediment systems in days</p></td> - </tr> - <tr> - <th>DT50_soil</th> - <td><p>Half-life in soil in days</p></td> - </tr> - <tr> - <th>DT50_water</th> - <td><p>Half-life in water in days (Step 2)</p></td> - </tr> - <tr> - <th>DT50_sediment</th> - <td><p>Half-life in sediment in days (Step 2)</p></td> - </tr> - <tr> - <th>cwsat</th> - <td><p>Water solubility in mg/L</p></td> - </tr> - <tr> - <th>mw</th> - <td><p>Molar weight in g/mol.</p></td> - </tr> - <tr> - <th>max_soil</th> - <td><p>Maximum observed fraction (dimensionless) in soil</p></td> - </tr> - <tr> - <th>max_ws</th> - <td><p>Maximum observed fraction (dimensionless) in water/sediment -systems</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>A list with the substance specific properties</p> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">chent_focus_sw</span><span class="op">(</span></span> +<span> <span class="va">name</span>,</span> +<span> <span class="va">Koc</span>,</span> +<span> DT50_ws <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> DT50_soil <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> DT50_water <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> DT50_sediment <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> cwsat <span class="op">=</span> <span class="fl">1000</span>,</span> +<span> mw <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> max_soil <span class="op">=</span> <span class="fl">1</span>,</span> +<span> max_ws <span class="op">=</span> <span class="fl">1</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>name</dt> +<dd><p>Length one character vector containing the name</p></dd> + + +<dt>Koc</dt> +<dd><p>Partition coefficient between organic carbon and water +in L/kg.</p></dd> + + +<dt>DT50_ws</dt> +<dd><p>Half-life in water/sediment systems in days</p></dd> + + +<dt>DT50_soil</dt> +<dd><p>Half-life in soil in days</p></dd> + + +<dt>DT50_water</dt> +<dd><p>Half-life in water in days (Step 2)</p></dd> + + +<dt>DT50_sediment</dt> +<dd><p>Half-life in sediment in days (Step 2)</p></dd> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - </ul> + +<dt>cwsat</dt> +<dd><p>Water solubility in mg/L</p></dd> + + +<dt>mw</dt> +<dd><p>Molar weight in g/mol.</p></dd> + + +<dt>max_soil</dt> +<dd><p>Maximum observed fraction (dimensionless) in soil</p></dd> + + +<dt>max_ws</dt> +<dd><p>Maximum observed fraction (dimensionless) in water/sediment +systems</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A list with the substance specific properties</p> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - 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<li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Deposition from spray drift expressed as percent of the applied dose as @@ -118,23 +49,24 @@ published by the German Julius-Kühn Institute (JKI).</p> </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div id="format"> + <h2>Format</h2> <p>A list currently containing matrices with spray drift percentage data for field crops (Ackerbau), and Pome/stone fruit, early and late (Obstbau frueh, spaet).</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div id="source"> + <h2>Source</h2> <p>JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved from http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html -on 2015-06-11</p> +on 2015-06-11, not present any more 2024-01-31</p> <p>Rautmann, D., Streloke, M and Winkler, R (2001) New basic drift values in the authorization procedure for plant protection products Mitt. Biol. Bundesanst. Land- Forstwirtsch. 383, 133-141</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - + </div> + <div id="details"> + <h2>Details</h2> <p>The data were extracted from the spreadsheet cited below using the R code given in the example section. The spreadsheet is not included in the package as its licence is not clear.</p> @@ -148,272 +80,226 @@ these values are used for spray applications with handheld/knapsack equipment (tragbare Spritz- und Sprühgerate).</p> <p>Values for non-professional use listed in the JKI spreadsheet were not included.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - <span class='co'># This is the code that was used to extract the data</span> - <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>readxl</span>) - <span class='no'>abdrift_path</span> <span class='kw'><-</span> <span class='st'>"inst/extdata/Tabelle der Abdrifteckwerte.xls"</span> - <span class='no'>JKI_crops</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Ackerbau"</span>, <span class='st'>"Obstbau frueh"</span>, <span class='st'>"Obstbau spaet"</span>, <span class='st'>"Weinbau frueh"</span>, <span class='st'>"Weinbau spaet"</span>, - <span class='st'>"Hopfenbau"</span>, <span class='st'>"Flaechenkulturen > 900 l/ha"</span>, <span class='st'>"Gleisanlagen"</span>) - <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>JKI_crops</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Field crops"</span>, <span class='st'>"Pome/stone fruit, early"</span>, <span class='st'>"Pome/stone fruit, late"</span>, - <span class='st'>"Vines early"</span>, <span class='st'>"Vines late"</span>, <span class='st'>"Hops"</span>, <span class='st'>"Areic cultures > 900 L/ha"</span>, <span class='st'>"Railroad tracks"</span>) - <span class='no'>drift_data_JKI</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>() - - <span class='kw'>for</span> (<span class='no'>n</span> <span class='kw'>in</span> <span class='fl'>1</span>:<span class='fl'>8</span>) { - <span class='no'>drift_data_raw</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/readxl/man/read_excel.html'>read_excel</a></span>(<span class='no'>abdrift_path</span>, <span class='kw'>sheet</span> <span class='kw'>=</span> <span class='no'>n</span> + <span class='fl'>1</span>, <span class='kw'>skip</span> <span class='kw'>=</span> <span class='fl'>2</span>) - <span class='no'>drift_data</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fl'>NA</span>, <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>9</span>, <span class='kw'>ncol</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>JKI_crops</span>)) - <span class='fu'><a href='https://rdrr.io/r/base/dimnames.html'>dimnames</a></span>(<span class='no'>drift_data</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>distance</span> <span class='kw'>=</span> <span class='no'>drift_data_raw</span><span class='kw'>[[</span><span class='fl'>1</span>]][<span class='fl'>1</span>:<span class='fl'>9</span>], - <span class='kw'>crop</span> <span class='kw'>=</span> <span class='no'>JKI_crops</span>) - <span class='kw'>if</span> (<span class='no'>n</span> <span class='kw'>==</span> <span class='fl'>1</span>) { <span class='co'># Values for railroad tracks only present for one application</span> - <span class='no'>drift_data</span>[, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>:<span class='fl'>3</span>, <span class='fl'>5</span>:<span class='fl'>8</span>)] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>as.matrix</a></span>(<span class='no'>drift_data_raw</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>2</span>:<span class='fl'>7</span>, <span class='fl'>11</span>)][<span class='fl'>1</span>:<span class='fl'>9</span>, ]) - } <span class='kw'>else</span> { - <span class='no'>drift_data</span>[, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>:<span class='fl'>3</span>, <span class='fl'>5</span>:<span class='fl'>7</span>)] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>as.matrix</a></span>(<span class='no'>drift_data_raw</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>2</span>:<span class='fl'>7</span>)][<span class='fl'>1</span>:<span class='fl'>9</span>, ]) - } - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='no'>n</span>]] <span class='kw'><-</span> <span class='no'>drift_data</span> - } - - <span class='co'># Manual data entry from the Rautmann paper</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>1</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.95</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>1</span>]][, <span class='st'>"Weinbau frueh"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>2.7</span>, <span class='fl'>1.18</span>, <span class='fl'>0.39</span>, <span class='fl'>0.2</span>, <span class='fl'>0.13</span>, <span class='fl'>0.07</span>, <span class='fl'>0.04</span>, <span class='fl'>0.03</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>2</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.79</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>2</span>]][, <span class='st'>"Weinbau frueh"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>2.53</span>, <span class='fl'>1.09</span>, <span class='fl'>0.35</span>, <span class='fl'>0.18</span>, <span class='fl'>0.11</span>, <span class='fl'>0.06</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>3</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.68</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>3</span>]][, <span class='st'>"Weinbau frueh"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>2.49</span>, <span class='fl'>1.04</span>, <span class='fl'>0.32</span>, <span class='fl'>0.16</span>, <span class='fl'>0.10</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>4</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.62</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>4</span>]][, <span class='st'>"Weinbau frueh"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>2.44</span>, <span class='fl'>1.02</span>, <span class='fl'>0.31</span>, <span class='fl'>0.16</span>, <span class='fl'>0.10</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>5</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.59</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>5</span>]][, <span class='st'>"Weinbau frueh"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>2.37</span>, <span class='fl'>1.00</span>, <span class='fl'>0.31</span>, <span class='fl'>0.15</span>, <span class='fl'>0.09</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>6</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.56</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>6</span>]][, <span class='st'>"Weinbau frueh"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>2.29</span>, <span class='fl'>0.97</span>, <span class='fl'>0.30</span>, <span class='fl'>0.15</span>, <span class='fl'>0.09</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>7</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.55</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>7</span>]][, <span class='st'>"Weinbau frueh"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>2.24</span>, <span class='fl'>0.94</span>, <span class='fl'>0.29</span>, <span class='fl'>0.15</span>, <span class='fl'>0.09</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>8</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.52</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>8</span>]][, <span class='st'>"Weinbau frueh"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>2.16</span>, <span class='fl'>0.91</span>, <span class='fl'>0.28</span>, <span class='fl'>0.14</span>, <span class='fl'>0.09</span>, <span class='fl'>0.04</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - - <span class='co'># Save the data</span> - <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>drift_data_JKI</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"data/drift_data_JKI.RData"</span>) -} - -<span class='co'># And these are the resulting data</span> -<span class='no'>drift_data_JKI</span></div><div class='output co'>#> [[1]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 2.77 NA NA NA NA -#> 3 0.95 29.20 15.73 2.70 8.02 -#> 5 0.57 19.89 8.41 1.18 3.62 -#> 10 0.29 11.81 3.60 0.39 1.23 -#> 15 0.20 5.55 1.81 0.20 0.65 -#> 20 0.15 2.77 1.09 0.13 0.42 -#> 30 0.10 1.04 0.54 0.07 0.22 -#> 40 0.07 0.52 0.32 0.04 0.14 -#> 50 0.06 0.30 0.22 0.03 0.10 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 4.440 NA -#> 3 19.33 NA 0.018721696 -#> 5 11.57 0.180 0.014363896 -#> 10 5.77 0.050 0.010026007 -#> 15 3.84 0.020 0.008124366 -#> 20 1.79 0.012 0.006998158 -#> 30 0.56 0.005 0.005670811 -#> 40 0.25 0.003 NA -#> 50 0.13 0.002 0.004350831 -#> -#> [[2]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 2.38 NA NA NA NA -#> 3 0.79 25.53 12.13 2.53 7.23 -#> 5 0.47 16.87 6.81 1.09 3.22 -#> 10 0.24 9.61 3.11 0.35 1.07 -#> 15 0.16 5.61 1.58 0.18 0.56 -#> 20 0.12 2.59 0.90 0.11 0.36 -#> 30 0.08 0.87 0.40 0.06 0.19 -#> 40 0.06 0.40 0.23 0.03 0.12 -#> 50 0.05 0.22 0.15 0.02 0.08 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 3.780 NA -#> 3 17.73 NA NA -#> 5 9.60 0.160 NA -#> 10 4.18 0.040 NA -#> 15 2.57 0.020 NA -#> 20 1.21 0.011 NA -#> 30 0.38 0.005 NA -#> 40 0.17 0.003 NA -#> 50 0.09 0.002 NA -#> -#> [[3]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 2.01 NA NA NA NA -#> 3 0.68 23.96 11.01 2.49 6.90 -#> 5 0.41 15.79 6.04 1.04 3.07 -#> 10 0.20 8.96 2.67 0.32 1.02 -#> 15 0.14 4.24 1.39 0.16 0.54 -#> 20 0.10 2.01 0.80 0.10 0.34 -#> 30 0.07 0.70 0.36 0.05 0.18 -#> 40 0.05 0.33 0.21 0.03 0.11 -#> 50 0.04 0.19 0.13 0.02 0.08 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 3.420 NA -#> 3 15.93 NA NA -#> 5 8.57 0.150 NA -#> 10 3.70 0.040 NA -#> 15 2.26 0.020 NA -#> 20 1.05 0.010 NA -#> 30 0.34 0.004 NA -#> 40 0.15 0.003 NA -#> 50 0.08 0.002 NA -#> -#> [[4]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 1.85 NA NA NA NA -#> 3 0.62 23.61 10.12 2.44 6.71 -#> 5 0.38 15.42 5.60 1.02 2.99 -#> 10 0.19 8.66 2.50 0.31 0.99 -#> 15 0.13 4.01 1.28 0.16 0.52 -#> 20 0.10 1.89 0.75 0.10 0.33 -#> 30 0.06 0.66 0.35 0.05 0.17 -#> 40 0.05 0.31 0.20 0.03 0.11 -#> 50 0.04 0.17 0.13 0.02 0.08 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 2.290 NA -#> 3 15.38 NA NA -#> 5 8.26 0.120 NA -#> 10 3.55 0.030 NA -#> 15 2.17 0.020 NA -#> 20 0.93 0.009 NA -#> 30 0.31 0.004 NA -#> 40 0.14 0.002 NA -#> 50 0.08 0.002 NA -#> -#> [[5]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 1.75 NA NA NA NA -#> 3 0.59 23.12 9.74 2.37 6.59 -#> 5 0.36 15.06 5.41 1.00 2.93 -#> 10 0.18 8.42 2.43 0.31 0.98 -#> 15 0.12 3.83 1.24 0.15 0.51 -#> 20 0.09 1.81 0.72 0.09 0.33 -#> 30 0.06 0.63 0.34 0.05 0.17 -#> 40 0.05 0.30 0.20 0.03 0.11 -#> 50 0.04 0.17 0.13 0.02 0.08 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 2.120 NA -#> 3 15.12 NA NA -#> 5 7.99 0.110 NA -#> 10 3.36 0.030 NA -#> 15 2.03 0.010 NA -#> 20 0.88 0.008 NA -#> 30 0.29 0.004 NA -#> 40 0.14 0.002 NA -#> 50 0.07 0.002 NA -#> -#> [[6]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 1.64 NA NA NA NA -#> 3 0.56 22.76 9.21 2.29 6.41 -#> 5 0.34 14.64 5.18 0.97 2.85 -#> 10 0.17 8.04 2.38 0.30 0.95 -#> 15 0.11 3.71 1.20 0.15 0.50 -#> 20 0.09 1.75 0.68 0.09 0.32 -#> 30 0.06 0.61 0.31 0.05 0.17 -#> 40 0.04 0.29 0.17 0.03 0.11 -#> 50 0.03 0.16 0.11 0.02 0.07 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 1.980 NA -#> 3 14.90 NA NA -#> 5 7.79 0.100 NA -#> 10 3.23 0.030 NA -#> 15 1.93 0.010 NA -#> 20 0.83 0.008 NA -#> 30 0.28 0.004 NA -#> 40 0.13 0.002 NA -#> 50 0.07 0.001 NA -#> -#> [[7]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 1.61 NA NA NA NA -#> 3 0.55 22.69 9.10 2.24 6.33 -#> 5 0.33 14.45 5.11 0.94 2.81 -#> 10 0.17 7.83 2.33 0.29 0.94 -#> 15 0.11 3.62 1.20 0.15 0.49 -#> 20 0.08 1.71 0.67 0.09 0.31 -#> 30 0.06 0.60 0.30 0.05 0.16 -#> 40 0.04 0.28 0.17 0.03 0.10 -#> 50 0.03 0.16 0.11 0.02 0.07 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 1.930 NA -#> 3 14.63 NA NA -#> 5 7.60 0.100 NA -#> 10 3.13 0.030 NA -#> 15 1.86 0.010 NA -#> 20 0.81 0.008 NA -#> 30 0.26 0.004 NA -#> 40 0.12 0.002 NA -#> 50 0.06 0.001 NA -#> -#> [[8]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 1.52 NA NA NA NA -#> 3 0.52 22.24 8.66 2.16 6.26 -#> 5 0.31 14.09 4.92 0.91 2.78 -#> 10 0.16 7.58 2.29 0.28 0.93 -#> 15 0.11 3.48 1.14 0.14 0.49 -#> 20 0.08 1.65 0.65 0.09 0.31 -#> 30 0.05 0.57 0.29 0.04 0.16 -#> 40 0.04 0.27 0.16 0.03 0.10 -#> 50 0.03 0.15 0.11 0.02 0.07 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 1.640 NA -#> 3 13.53 NA NA -#> 5 7.15 0.090 NA -#> 10 3.01 0.020 NA -#> 15 1.82 0.010 NA -#> 20 0.78 0.007 NA -#> 30 0.25 0.003 NA -#> 40 0.12 0.002 NA -#> 50 0.06 0.001 NA -#> </div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">drift_data_JKI</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [[1]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 2.77 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.95 29.20 15.73 2.70 8.02</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.57 19.89 8.41 1.18 3.62</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.29 11.81 3.60 0.39 1.23</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.20 5.55 1.81 0.20 0.65</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.15 2.77 1.09 0.13 0.42</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.10 1.04 0.54 0.07 0.22</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.07 0.52 0.32 0.04 0.14</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.06 0.30 0.22 0.03 0.10</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 4.440 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 19.33 NA 0.018721696</span> +<span class="r-out co"><span class="r-pr">#></span> 5 11.57 0.180 0.014363896</span> +<span class="r-out co"><span class="r-pr">#></span> 10 5.77 0.050 0.010026007</span> +<span class="r-out co"><span class="r-pr">#></span> 15 3.84 0.020 0.008124366</span> +<span class="r-out co"><span class="r-pr">#></span> 20 1.79 0.012 0.006998158</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.56 0.005 0.005670811</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.25 0.003 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.13 0.002 0.004350831</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[2]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 2.38 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.79 25.53 12.13 2.53 7.23</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.47 16.87 6.81 1.09 3.22</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.24 9.61 3.11 0.35 1.07</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.16 5.61 1.58 0.18 0.56</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.12 2.59 0.90 0.11 0.36</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.08 0.87 0.40 0.06 0.19</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.06 0.40 0.23 0.03 0.12</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.05 0.22 0.15 0.02 0.08</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 3.780 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 17.73 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 9.60 0.160 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 4.18 0.040 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 2.57 0.020 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 1.21 0.011 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.38 0.005 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.17 0.003 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.09 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[3]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 2.01 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.68 23.96 11.01 2.49 6.90</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.41 15.79 6.04 1.04 3.07</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.20 8.96 2.67 0.32 1.02</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.14 4.24 1.39 0.16 0.54</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.10 2.01 0.80 0.10 0.34</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.07 0.70 0.36 0.05 0.18</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.05 0.33 0.21 0.03 0.11</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.04 0.19 0.13 0.02 0.08</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 3.420 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 15.93 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 8.57 0.150 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.70 0.040 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 2.26 0.020 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 1.05 0.010 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.34 0.004 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.15 0.003 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.08 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[4]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1.85 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.62 23.61 10.12 2.44 6.71</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.38 15.42 5.60 1.02 2.99</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.19 8.66 2.50 0.31 0.99</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.13 4.01 1.28 0.16 0.52</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.10 1.89 0.75 0.10 0.33</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.06 0.66 0.35 0.05 0.17</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.05 0.31 0.20 0.03 0.11</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.04 0.17 0.13 0.02 0.08</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 2.290 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 15.38 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 8.26 0.120 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.55 0.030 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 2.17 0.020 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.93 0.009 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.31 0.004 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.14 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.08 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[5]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1.75 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.59 23.12 9.74 2.37 6.59</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.36 15.06 5.41 1.00 2.93</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.18 8.42 2.43 0.31 0.98</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.12 3.83 1.24 0.15 0.51</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.09 1.81 0.72 0.09 0.33</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.06 0.63 0.34 0.05 0.17</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.05 0.30 0.20 0.03 0.11</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.04 0.17 0.13 0.02 0.08</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 2.120 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 15.12 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 7.99 0.110 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.36 0.030 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 2.03 0.010 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.88 0.008 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.29 0.004 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.14 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.07 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[6]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1.64 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.56 22.76 9.21 2.29 6.41</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.34 14.64 5.18 0.97 2.85</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.17 8.04 2.38 0.30 0.95</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.11 3.71 1.20 0.15 0.50</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.09 1.75 0.68 0.09 0.32</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.06 0.61 0.31 0.05 0.17</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.04 0.29 0.17 0.03 0.11</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.03 0.16 0.11 0.02 0.07</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 1.980 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 14.90 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 7.79 0.100 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.23 0.030 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 1.93 0.010 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.83 0.008 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.28 0.004 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.13 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.07 0.001 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[7]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1.61 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.55 22.69 9.10 2.24 6.33</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.33 14.45 5.11 0.94 2.81</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.17 7.83 2.33 0.29 0.94</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.11 3.62 1.20 0.15 0.49</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.08 1.71 0.67 0.09 0.31</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.06 0.60 0.30 0.05 0.16</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.04 0.28 0.17 0.03 0.10</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.03 0.16 0.11 0.02 0.07</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 1.930 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 14.63 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 7.60 0.100 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.13 0.030 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 1.86 0.010 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.81 0.008 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.26 0.004 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.12 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.06 0.001 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[8]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1.52 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.52 22.24 8.66 2.16 6.26</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.31 14.09 4.92 0.91 2.78</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.16 7.58 2.29 0.28 0.93</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.11 3.48 1.14 0.14 0.49</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.08 1.65 0.65 0.09 0.31</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.05 0.57 0.29 0.04 0.16</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.04 0.27 0.16 0.03 0.10</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.03 0.15 0.11 0.02 0.07</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 1.640 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 13.53 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 7.15 0.090 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.01 0.020 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 1.82 0.010 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.78 0.007 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.25 0.003 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.12 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.06 0.001 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 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Such information is extracted and optionally aggregated by -this function." /> -<meta name="twitter:card" content="summary" /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +this function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -72,35 +20,21 @@ this function." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Retrieve endpoint information from the chyaml field of a chent object</h1> @@ -115,136 +49,131 @@ chyaml field. Such information is extracted and optionally aggregated by this function.</p> </div> - <pre class="usage"><span class='fu'>endpoint</span>( - <span class='no'>chent</span>, - <span class='kw'>medium</span> <span class='kw'>=</span> <span class='st'>"soil"</span>, - <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"degradation"</span>, <span class='st'>"sorption"</span>), - <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"laboratory"</span>, <span class='st'>"field"</span>), - <span class='kw'>redox</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"aerobic"</span>, <span class='st'>"anaerobic"</span>), - <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"DT50ref"</span>, <span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), - <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, - <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span> -) - -<span class='fu'>soil_DT50</span>( - <span class='no'>chent</span>, - <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, - <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, - <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, - <span class='kw'>value</span> <span class='kw'>=</span> <span class='st'>"DT50ref"</span>, - <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>, - <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span> -) - -<span class='fu'>soil_Kfoc</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='st'>"Kfoc"</span>, <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) - -<span class='fu'>soil_N</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>mean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) - -<span class='fu'>soil_sorption</span>( - <span class='no'>chent</span>, - <span class='kw'>values</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), - <span class='kw'>aggregators</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='no'>mean</span>), - <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='fl'>3</span>), - <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span> -)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>chent</th> - <td><p>The chent object to get the information from</p></td> - </tr> - <tr> - <th>medium</th> - <td><p>The medium for which information is sought</p></td> - </tr> - <tr> - <th>type</th> - <td><p>The information type</p></td> - </tr> - <tr> - <th>lab_field</th> - <td><p>If not NA, do we want laboratory or field endpoints</p></td> - </tr> - <tr> - <th>redox</th> - <td><p>If not NA, are we looking for aerobic or anaerobic data</p></td> - </tr> - <tr> - <th>value</th> - <td><p>The name of the value we want. The list given in the -usage section is not exclusive</p></td> - </tr> - <tr> - <th>aggregator</th> - <td><p>The aggregator function. Can be mean, -<code><a href='geomean.html'>geomean</a></code>, or identity, for example.</p></td> - </tr> - <tr> - <th>raw</th> - <td><p>Should the number(s) be returned as stored in the chent + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">endpoint</span><span class="op">(</span></span> +<span> <span class="va">chent</span>,</span> +<span> medium <span class="op">=</span> <span class="st">"soil"</span>,</span> +<span> type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"degradation"</span>, <span class="st">"sorption"</span><span class="op">)</span>,</span> +<span> lab_field <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="st">"laboratory"</span>, <span class="st">"field"</span><span class="op">)</span>,</span> +<span> redox <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="st">"aerobic"</span>, <span class="st">"anaerobic"</span><span class="op">)</span>,</span> +<span> value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"DT50ref"</span>, <span class="st">"Kfoc"</span>, <span class="st">"N"</span><span class="op">)</span>,</span> +<span> aggregator <span class="op">=</span> <span class="va">geomean</span>,</span> +<span> raw <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> signif <span class="op">=</span> <span class="fl">3</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="fu">soil_DT50</span><span class="op">(</span></span> +<span> <span class="va">chent</span>,</span> +<span> aggregator <span class="op">=</span> <span class="va">geomean</span>,</span> +<span> signif <span class="op">=</span> <span class="fl">3</span>,</span> +<span> lab_field <span class="op">=</span> <span class="st">"laboratory"</span>,</span> +<span> value <span class="op">=</span> <span class="st">"DT50ref"</span>,</span> +<span> redox <span class="op">=</span> <span class="st">"aerobic"</span>,</span> +<span> raw <span class="op">=</span> <span class="cn">FALSE</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="fu">soil_Kfoc</span><span class="op">(</span><span class="va">chent</span>, aggregator <span class="op">=</span> <span class="va">geomean</span>, signif <span class="op">=</span> <span class="fl">3</span>, value <span class="op">=</span> <span class="st">"Kfoc"</span>, raw <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">soil_N</span><span class="op">(</span><span class="va">chent</span>, aggregator <span class="op">=</span> <span class="va">mean</span>, signif <span class="op">=</span> <span class="fl">3</span>, raw <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">soil_sorption</span><span class="op">(</span></span> +<span> <span class="va">chent</span>,</span> +<span> values <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Kfoc"</span>, <span class="st">"N"</span><span class="op">)</span>,</span> +<span> aggregators <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>Kfoc <span class="op">=</span> <span class="va">geomean</span>, Koc <span class="op">=</span> <span class="va">geomean</span>, N <span class="op">=</span> <span class="va">mean</span><span class="op">)</span>,</span> +<span> signif <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>Kfoc <span class="op">=</span> <span class="fl">3</span>, N <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>,</span> +<span> raw <span class="op">=</span> <span class="cn">FALSE</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>chent</dt> +<dd><p>The chent object to get the information from</p></dd> + + +<dt>medium</dt> +<dd><p>The medium for which information is sought</p></dd> + + +<dt>type</dt> +<dd><p>The information type</p></dd> + + +<dt>lab_field</dt> +<dd><p>If not NA, do we want laboratory or field endpoints</p></dd> + + +<dt>redox</dt> +<dd><p>If not NA, are we looking for aerobic or anaerobic data</p></dd> + + +<dt>value</dt> +<dd><p>The name of the value we want. The list given in the +usage section is not exclusive</p></dd> + + +<dt>aggregator</dt> +<dd><p>The aggregator function. Can be mean, +<code><a href="geomean.html">geomean</a></code>, or identity, for example.</p></dd> + + +<dt>raw</dt> +<dd><p>Should the number(s) be returned as stored in the chent object (could be a character value) to retain original information -about precision?</p></td> - </tr> - <tr> - <th>signif</th> - <td><p>How many significant digits do we want</p></td> - </tr> - <tr> - <th>values</th> - <td><p>The values to be returned</p></td> - </tr> - <tr> - <th>aggregators</th> - <td><p>A named vector of aggregator functions to be used</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The result from applying the aggregator function to +about precision?</p></dd> + + +<dt>signif</dt> +<dd><p>How many significant digits do we want</p></dd> + + +<dt>values</dt> +<dd><p>The values to be returned</p></dd> + + +<dt>aggregators</dt> +<dd><p>A named vector of aggregator functions to be used</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The result from applying the aggregator function to the values converted to a numeric vector, rounded to the given number of significant digits, or, if raw = TRUE, the values as a character value, retaining any implicit information on precision that may be present.</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - + </div> + <div id="details"> + <h2>Details</h2> <p>The functions <code>soil_*</code> are functions to extract soil specific endpoints. For the Freundlich exponent, the capital letter <code>N</code> is used in order to facilitate dealing with such data in R. In pesticide fate modelling, this exponent is often called 1/n.</p> + </div> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#details">Details</a></li> - </ul> - - </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html index 34befc3..540b33b 100644 --- a/docs/reference/geomean.html +++ b/docs/reference/geomean.html @@ -1,68 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Calculate the geometric mean — geomean • pfm</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> - -<!-- Font Awesome icons --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> - -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - - -<meta property="og:title" content="Calculate the geometric mean — geomean" /> -<meta property="og:description" content="Based on some posts in a thread on Stackoverflow +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Calculate the geometric mean — geomean • pfm</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate the geometric mean — geomean"><meta property="og:description" content="Based on some posts in a thread on Stackoverflow http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in This function returns NA if NA values are present and na.rm = FALSE (default). If negative values are present, it gives an error message. -If at least one element of the vector is 0, it returns 0." /> -<meta name="twitter:card" content="summary" /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +If at least one element of the vector is 0, it returns 0."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,35 +21,21 @@ If at least one element of the vector is 0, it returns 0." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate the geometric mean</h1> @@ -111,64 +45,68 @@ If at least one element of the vector is 0, it returns 0." /> <div class="ref-description"> <p>Based on some posts in a thread on Stackoverflow -<a href='http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in'>http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in</a> +<a href="http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in" class="external-link">http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in</a> This function returns NA if NA values are present and na.rm = FALSE (default). If negative values are present, it gives an error message. If at least one element of the vector is 0, it returns 0.</p> </div> - <pre class="usage"><span class='fu'>geomean</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">geomean</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> + </div> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>Vector of numbers</p></td> - </tr> - <tr> - <th>na.rm</th> - <td><p>Should NA values be omitted?</p></td> - </tr> - </table> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>Vector of numbers</p></dd> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>The geometric mean</p> +<dt>na.rm</dt> +<dd><p>Should NA values be omitted?</p></dd> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>geomean</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] 3</div><div class='input'><span class='fu'>geomean</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>NA</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] NA</div><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'>geomean</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, -<span class='fl'>3</span>, <span class='fl'>9</span>)) <span class='co'># returns an error</span></div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> - </ul> +</dl></div> + <div id="value"> + <h2>Value</h2> + +<p>The geometric mean</p> + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">geomean</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">9</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 3</span> +<span class="r-in"><span><span class="fu">geomean</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">3</span>, <span class="cn">NA</span>, <span class="fl">9</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] NA</span> +<span class="r-in"><span><span class="fu">geomean</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="op">-</span><span class="fl">3</span>, <span class="fl">9</span><span class="op">)</span><span class="op">)</span> <span class="co"># returns an error</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in geomean(c(1, -3, 9)):</span> Only defined for positive numbers</span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/get_vertex.html b/docs/reference/get_vertex.html index 3d0bc2d..c6dc00c 100644 --- a/docs/reference/get_vertex.html +++ b/docs/reference/get_vertex.html @@ -1,62 +1,13 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Fit a parabola through three points — get_vertex • pfm</title> - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - 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- </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Fit a parabola through three points</h1> @@ -105,55 +41,46 @@ https://stackoverflow.com/a/717791" /> </div> <div class="ref-description"> - <p>This was inspired by an answer on stackoverflow https://stackoverflow.com/a/717791</p> - </div> - <pre class="usage"><span class='fu'>get_vertex</span>(<span class='no'>x</span>, <span class='no'>y</span>)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>Three x coordinates</p></td> - </tr> - <tr> - <th>y</th> - <td><p>Three y coordinates</p></td> - </tr> - </table> - + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_vertex</span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></code></pre></div> + </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - </ul> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>Three x coordinates</p></dd> + + +<dt>y</dt> +<dd><p>Three y coordinates</p></dd> + +</dl></div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-index"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -71,391 +17,226 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="contents col-md-9"> <div class="page-header"> <h1>Reference</h1> </div> - <table class="ref-index"> - - <colgroup> - - <col class="alias" /> - <col class="title" /> - </colgroup> - - <tbody> - <tr> - <th colspan="2"> - <h2 id="section-general-utility-functions" class="hasAnchor"><a href="#section-general-utility-functions" class="anchor"></a>General utility functions</h2> - <p class="section-desc"><p>Functions that are independent of specific fate modelling areas</p></p> + <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2"> + <h2 id="general-utility-functions">General utility functions <a href="#general-utility-functions" class="anchor" aria-hidden="true"></a></h2> + <p class="section-desc"></p><p>Functions that are independent of specific fate modelling areas</p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="geomean.html">geomean()</a></code> </p> </td> <td><p>Calculate the geometric mean</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="one_box.html">one_box()</a></code> </p> </td> <td><p>Create a time series of decline data</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="plot.one_box.html">plot(<i><one_box></i>)</a></code> </p> </td> <td><p>Plot time series of decline data</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="sawtooth.html">sawtooth()</a></code> </p> </td> <td><p>Create decline time series for multiple applications</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="twa.html">twa()</a></code> </p> </td> <td><p>Calculate a time weighted average concentration</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="max_twa.html">max_twa()</a></code> </p> </td> <td><p>The maximum time weighted average concentration for a moving window</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="pfm_degradation.html">pfm_degradation()</a></code> </p> </td> <td><p>Calculate a time course of relative concentrations based on an mkinmod model</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="SFO_actual_twa.html">SFO_actual_twa()</a></code> </p> </td> <td><p>Actual and maximum moving window time average concentrations for SFO kinetics</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="FOMC_actual_twa.html">FOMC_actual_twa()</a></code> </p> </td> <td><p>Actual and maximum moving window time average concentrations for FOMC kinetics</p></td> - </tr><tr> - - <td> - <p><code><a href="set_nd_nq.html">set_nd_nq()</a></code> <code><a href="set_nd_nq.html">set_nd_nq_focus()</a></code> </p> - </td> - <td><p>Set non-detects and unquantified values in residue series without replicates</p></td> - </tr><tr> - - <td> + </tr><tr><td> + <p><code><a href="reexports.html">reexports</a></code> <code><a href="reexports.html">set_nd_nq</a></code> <code><a href="reexports.html">set_nd_nq_focus</a></code> </p> + </td> + <td><p>Objects exported from other packages</p></td> + </tr><tr><td> <p><code><a href="TSCF.html">TSCF()</a></code> </p> </td> <td><p>Estimation of the transpiration stream concentration factor</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-predicted-environmental-concentrations-in-soil" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-soil" class="anchor"></a>Predicted environmental concentrations in soil</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="predicted-environmental-concentrations-in-soil">Predicted environmental concentrations in soil <a href="#predicted-environmental-concentrations-in-soil" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="PEC_soil.html">PEC_soil()</a></code> </p> </td> <td><p>Calculate predicted environmental concentrations in soil</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_soil_mets.html">PEC_soil_mets()</a></code> </p> </td> <td><p>Calculate initial and accumulation PEC soil for a set of metabolites</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code> </p> </td> <td><p>Properties of the predefined scenarios from the EFSA guidance from 2015</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="soil_scenario_data_EFSA_2017.html">soil_scenario_data_EFSA_2017</a></code> </p> </td> <td><p>Properties of the predefined scenarios from the EFSA guidance from 2017</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_FOMC_accu_rel.html">PEC_FOMC_accu_rel()</a></code> </p> </td> <td><p>Get the relative accumulation of an FOMC model over multiples of an interval</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="EFSA_washoff_2017.html">EFSA_washoff_2017</a></code> </p> </td> <td><p>Subset of EFSA crop washoff default values</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-predicted-environmental-concentrations-in-groundwater" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-groundwater" class="anchor"></a>Predicted environmental concentrations in groundwater</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="predicted-environmental-concentrations-in-groundwater">Predicted environmental concentrations in groundwater <a href="#predicted-environmental-concentrations-in-groundwater" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="FOCUS_GW_scenarios_2012.html">FOCUS_GW_scenarios_2012</a></code> </p> </td> <td><p>A very small subset of the FOCUS Groundwater scenario definitions</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="EFSA_GW_interception_2014.html">EFSA_GW_interception_2014</a></code> </p> </td> <td><p>Subset of EFSA crop interception default values for groundwater modelling</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-predicted-environmental-concentrations-in-surface-water" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-surface-water" class="anchor"></a>Predicted environmental concentrations in surface water</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="predicted-environmental-concentrations-in-surface-water">Predicted environmental concentrations in surface water <a href="#predicted-environmental-concentrations-in-surface-water" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="PEC_sw_drift.html">PEC_sw_drift()</a></code> </p> </td> <td><p>Calculate predicted environmental concentrations in surface water due to drift</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="drift_data_JKI.html">drift_data_JKI</a></code> </p> </td> <td><p>Deposition from spray drift expressed as percent of the applied dose as published by the JKI</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK()</a></code> </p> </td> <td><p>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_sw_sed.html">PEC_sw_sed()</a></code> </p> </td> <td><p>Calculate predicted environmental concentrations in sediment from surface water concentrations</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_sw_focus.html">PEC_sw_focus()</a></code> </p> </td> <td><p>Calculate PEC surface water at FOCUS Step 1</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="chent_focus_sw.html">chent_focus_sw()</a></code> </p> </td> <td><p>Create a chemical compound object for FOCUS Step 1 calculations</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></code> </p> </td> <td><p>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_sw_exposit_drainage.html">PEC_sw_exposit_drainage()</a></code> </p> </td> <td><p>Calculate PEC surface water due to drainage as in Exposit 3</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_sw_exposit_runoff.html">PEC_sw_exposit_runoff()</a></code> </p> </td> <td><p>Calculate PEC surface water due to runoff and erosion as in Exposit 3</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> </p> </td> <td><p>Runoff loss percentages as used in Exposit 3</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> </p> </td> <td><p>Runoff reduction percentages as used in Exposit</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code> </p> </td> <td><p>R6 class for holding TOXSWA water concentration data and associated statistics</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa()</a></code> </p> </td> <td><p>Read TOXSWA surface water concentrations</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="plot.TOXSWA_cwa.html">plot(<i><TOXSWA_cwa></i>)</a></code> </p> </td> <td><p>Plot TOXSWA surface water concentrations</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-classifications-and-indicators" class="hasAnchor"><a href="#section-classifications-and-indicators" class="anchor"></a>Classifications and indicators</h2> - <p class="section-desc"><p>Evaluating environmental fate properties</p></p> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="classifications-and-indicators">Classifications and indicators <a href="#classifications-and-indicators" class="anchor" aria-hidden="true"></a></h2> + <p class="section-desc"></p><p>Evaluating environmental fate properties</p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="SSLRC_mobility_classification.html">SSLRC_mobility_classification()</a></code> </p> </td> <td><p>Determine the SSLRC mobility classification for a chemical substance from its Koc</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="GUS.html">GUS()</a></code> <code><a href="GUS.html">print(<i><GUS_result></i>)</a></code> </p> </td> <td><p>Groundwater ubiquity score based on Gustafson (1989)</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-work-with-chent-objects-containing-relevant-information" class="hasAnchor"><a href="#section-work-with-chent-objects-containing-relevant-information" class="anchor"></a>Work with chent objects containing relevant information</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="work-with-chent-objects-containing-relevant-information">Work with chent objects containing relevant information <a href="#work-with-chent-objects-containing-relevant-information" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="endpoint.html">endpoint()</a></code> <code><a href="endpoint.html">soil_DT50()</a></code> <code><a href="endpoint.html">soil_Kfoc()</a></code> <code><a href="endpoint.html">soil_N()</a></code> <code><a href="endpoint.html">soil_sorption()</a></code> </p> </td> <td><p>Retrieve endpoint information from the chyaml field of a chent object</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-utilities" class="hasAnchor"><a href="#section-utilities" class="anchor"></a>Utilities</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="utilities">Utilities <a href="#utilities" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="get_vertex.html">get_vertex()</a></code> </p> </td> <td><p>Fit a parabola through three points</p></td> - </tr> - </tbody> - 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It is therefore recommended to check this using plot.one_box using the window size for the argument -max_twa." /> -<meta name="twitter:card" content="summary" /> - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +max_twa."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -70,36 +21,21 @@ max_twa." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>The maximum time weighted average concentration for a moving window</h1> @@ -108,101 +44,90 @@ max_twa." /> </div> <div class="ref-description"> - - <p>If you generate your time series using <code><a href='sawtooth.html'>sawtooth</a></code>, + <p>If you generate your time series using <code><a href="sawtooth.html">sawtooth</a></code>, you need to make sure that the length of the time series allows for finding the maximum. It is therefore recommended to check this using -<code><a href='plot.one_box.html'>plot.one_box</a></code> using the window size for the argument +<code><a href="plot.one_box.html">plot.one_box</a></code> using the window size for the argument <code>max_twa</code>.</p> - </div> - <pre class="usage"><span class='fu'>max_twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</span>)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>An object of type <code><a href='one_box.html'>one_box</a></code></p></td> - </tr> - <tr> - <th>window</th> - <td><p>The size of the moving window</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">max_twa</span><span class="op">(</span><span class="va">x</span>, window <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>An object of type <code><a href="one_box.html">one_box</a></code></p></dd> + +<dt>window</dt> +<dd><p>The size of the moving window</p></dd> + +</dl></div> + <div id="details"> + <h2>Details</h2> <p>The method working directly on fitted <code>mkinfit</code> objects uses the equations given in the PEC soil section of the FOCUS guidance and is restricted SFO, FOMC and DFOP models and to the parent compound</p> - - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + </div> + <div id="references"> + <h2>References</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p><code><a href='twa.html'>twa</a></code></p></div> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>pred</span> <span class='kw'><-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>), - <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>1</span>))) -<span class='fu'>max_twa</span>(<span class='no'>pred</span>)</div><div class='output co'>#> $max -#> parent -#> 0.9537545 -#> -#> $window_start -#> parent -#> 0 -#> -#> $window_end -#> parent -#> 21 -#> </div><div class='input'><span class='no'>pred_FOMC</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>max_twa</span>(<span class='no'>pred_FOMC</span>)</div><div class='output co'>#> 21 -#> 18.22124 </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - - <li><a href="#details">Details</a></li> - - <li><a href="#references">References</a></li> - - <li><a href="#see-also">See also</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> + <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="twa.html">twa</a></code></p></div> + </div> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">pred</span> <span class="op"><-</span> <span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> applications <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">7</span><span class="op">)</span>, amount <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">max_twa</span><span class="op">(</span><span class="va">pred</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $max</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 0.9537545 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_start</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 0 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_end</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 21 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span><span class="va">pred_FOMC</span> <span class="op"><-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">max_twa</span><span class="op">(</span><span class="va">pred_FOMC</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 21 </span> +<span class="r-out co"><span class="r-pr">#></span> 18.22124 </span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -69,35 +17,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Create a time series of decline data</h1> @@ -109,99 +43,105 @@ <p>Create a time series of decline data</p> </div> - <pre class="usage"><span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>ini</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>) - -<span class='co'># S3 method for numeric</span> -<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>) - -<span class='co'># S3 method for character</span> -<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>parms</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>) - -<span class='co'># S3 method for mkinfit</span> -<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)</pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">one_box</span><span class="op">(</span><span class="va">x</span>, <span class="va">ini</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for numeric</span></span> +<span><span class="fu">one_box</span><span class="op">(</span><span class="va">x</span>, ini <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for character</span></span> +<span><span class="fu">one_box</span><span class="op">(</span><span class="va">x</span>, ini <span class="op">=</span> <span class="fl">1</span>, <span class="va">parms</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu">one_box</span><span class="op">(</span><span class="va">x</span>, ini <span class="op">=</span> <span class="st">"model"</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span></code></pre></div> + </div> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>When numeric, this is the half-life to be used for an exponential + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>When numeric, this is the half-life to be used for an exponential decline. When a character string specifying a parent decline model is given e.g. <code>FOMC</code>, <code>parms</code> must contain the corresponding parameters. -If x is an <code>mkinfit</code> object, the decline is calculated from this -object.</p></td> - </tr> - <tr> - <th>ini</th> - <td><p>The initial amount. If x is an <code>mkinfit</code> object, and +If x is an <code><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></code> object, the decline is calculated from this +object.</p></dd> + + +<dt>ini</dt> +<dd><p>The initial amount. If x is an <code><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></code> object, and ini is 'model', the fitted initial concentrations are used. Otherwise, ini must be numeric. If it has length one, it is used for the parent and initial values of metabolites are zero, otherwise, it must give values for -all observed variables.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to methods</p></td> - </tr> - <tr> - <th>t_end</th> - <td><p>End of the time series</p></td> - </tr> - <tr> - <th>res</th> - <td><p>Resolution of the time series</p></td> - </tr> - <tr> - <th>parms</th> - <td><p>A named numeric vector containing the model parameters</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>An object of class <code>one_box</code>, inheriting from <code><a href='https://rdrr.io/r/stats/ts.html'>ts</a></code>.</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># Only use a half-life</span> -<span class='no'>pred_0</span> <span class='kw'><-</span> <span class='fu'>one_box</span>(<span class='fl'>10</span>) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>pred_0</span>)</div><div class='img'><img src='one_box-1.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># Use a fitted mkinfit model</span> -<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>mkin</span>) -<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='https://pkgdown.jrwb.de/mkin/reference/mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='no'>pred_1</span> <span class='kw'><-</span> <span class='fu'>one_box</span>(<span class='no'>fit</span>) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>pred_1</span>)</div><div class='img'><img src='one_box-2.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># Use a model with more than one observed variable</span> -<span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://pkgdown.jrwb.de/mkin/reference/mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://pkgdown.jrwb.de/mkin/reference/mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://pkgdown.jrwb.de/mkin/reference/mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://pkgdown.jrwb.de/mkin/reference/mkinfit.html'>mkinfit</a></span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'>one_box</span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>pred_2</span>)</div><div class='img'><img src='one_box-3.png' alt='' width='700' height='433' /></div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> - </ul> +all observed variables.</p></dd> + + +<dt>...</dt> +<dd><p>Further arguments passed to methods</p></dd> + +<dt>t_end</dt> +<dd><p>End of the time series</p></dd> + + +<dt>res</dt> +<dd><p>Resolution of the time series</p></dd> + + +<dt>parms</dt> +<dd><p>A named numeric vector containing the model parameters</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>An object of class <code>one_box</code>, inheriting from <code><a href="https://rdrr.io/r/stats/ts.html" class="external-link">ts</a></code>.</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Only use a half-life</span></span></span> +<span class="r-in"><span><span class="va">pred_0</span> <span class="op"><-</span> <span class="fu">one_box</span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_0</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="one_box-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Use a fitted mkinfit model</span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/" class="external-link">mkin</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">pred_1</span> <span class="op"><-</span> <span class="fu">one_box</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_1</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="one_box-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Use a model with more than one observed variable</span></span></span> +<span class="r-in"><span><span class="va">m_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="va">m_2</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span><span class="va">pred_2</span> <span class="op"><-</span> <span class="fu">one_box</span><span class="op">(</span><span class="va">fit_2</span>, ini <span class="op">=</span> <span class="st">"model"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_2</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="one_box-3.png" alt="" width="700" height="433"></span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" 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href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Runoff loss percentages as used in Exposit 3</h1> @@ -112,64 +43,71 @@ <p>A table of the loss percentages used in Exposit 3 for the twelve different Koc classes</p> </div> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">perc_runoff_exposit</span></span></code></pre></div> + </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div id="format"> + <h2>Format</h2> <p>A data frame with percentage values for the dissolved fraction and the fraction - bound to eroding particles, with Koc classes used as row names</p><dl'> - <dt>Koc_lower_bound</dt><dd><p>The lower bound of the Koc class</p></dd> - <dt>dissolved</dt><dd><p>The percentage of the applied substance transferred to an + bound to eroding particles, with Koc classes used as row names</p><dl><dt>Koc_lower_bound</dt> +<dd><p>The lower bound of the Koc class</p></dd> + + <dt>dissolved</dt> +<dd><p>The percentage of the applied substance transferred to an adjacent water body in the dissolved phase</p></dd> - <dt>bound</dt><dd><p>The percentage of the applied substance transferred to an - adjacent water body bound to eroding particles</p></dd> - -</dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt>bound</dt> +<dd><p>The percentage of the applied substance transferred to an + adjacent water body bound to eroding particles</p></dd> + +</dl></div> + <div id="source"> + <h2>Source</h2> <p>Excel 3.02 spreadsheet available from - <a href='https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html'>https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html</a></p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>perc_runoff_exposit</span>)</div><div class='output co'>#> Koc_lower_bound dissolved bound -#> 0-20 0 0.110 0.000 -#> >20-50 20 0.151 0.000 -#> >50-100 50 0.197 0.000 -#> >100-200 100 0.248 0.001 -#> >200-500 200 0.224 0.004 -#> >500-1000 500 0.184 0.020 -#> >1000-2000 1000 0.133 0.042 -#> >2000-5000 2000 0.084 0.091 -#> >5000-10000 5000 0.037 0.159 -#> >10000-20000 10000 0.031 0.192 -#> >20000-50000 20000 0.014 0.291 -#> >50000 50000 0.001 0.451</div></pre> + <a href="https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html" class="external-link">https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">perc_runoff_exposit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Koc_lower_bound dissolved bound</span> +<span class="r-out co"><span class="r-pr">#></span> 0-20 0 0.110 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> >20-50 20 0.151 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> >50-100 50 0.197 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> >100-200 100 0.248 0.001</span> +<span class="r-out co"><span class="r-pr">#></span> >200-500 200 0.224 0.004</span> +<span class="r-out co"><span class="r-pr">#></span> >500-1000 500 0.184 0.020</span> +<span class="r-out co"><span class="r-pr">#></span> >1000-2000 1000 0.133 0.042</span> +<span class="r-out co"><span class="r-pr">#></span> >2000-5000 2000 0.084 0.091</span> +<span class="r-out co"><span class="r-pr">#></span> >5000-10000 5000 0.037 0.159</span> +<span class="r-out co"><span class="r-pr">#></span> >10000-20000 10000 0.031 0.192</span> +<span class="r-out co"><span class="r-pr">#></span> >20000-50000 20000 0.014 0.291</span> +<span class="r-out co"><span class="r-pr">#></span> >50000 50000 0.001 0.451</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + 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</ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Runoff reduction percentages as used in Exposit</h1> @@ -112,80 +43,83 @@ <p>A table of the runoff reduction percentages used in Exposit 3 for different vegetated buffer widths</p> </div> - <pre class="usage"><span class='va'>perc_runoff_reduction_exposit</span></pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">perc_runoff_reduction_exposit</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> <p>A named list of data frames with reduction percentage values for the dissolved fraction and the fraction bound to eroding particles, with vegetated buffer widths as row names. The names of the list items are the Exposit versions -from which the values were taken.</p><dl> - <dt>dissolved</dt><dd><p>The reduction percentage for the dissolved phase</p></dd> - <dt>bound</dt><dd><p>The reduction percentage for the particulate phase</p></dd> - -</dl> +from which the values were taken.</p><dl><dt>dissolved</dt> +<dd><p>The reduction percentage for the dissolved phase</p></dd> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt>bound</dt> +<dd><p>The reduction percentage for the particulate phase</p></dd> + +</dl></div> + <div id="source"> + <h2>Source</h2> <p>Excel 3.02 spreadsheet available from - <a href='https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html'>https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html</a></p> + <a href="https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html" class="external-link">https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html</a></p> <p>Agroscope version 3.01a with additional runoff factors for 3 m and 6 m buffer zones received from Muris Korkaric (not published). The variant 3.01a2 was introduced for consistency with previous calculations performed by Agroscope for a 3 m buffer zone.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>perc_runoff_reduction_exposit</span><span class='op'>)</span> -</div><div class='output co'>#> $`3.02` -#> dissolved bound -#> No buffer 0 0 -#> 5 m 40 40 -#> 10 m 60 85 -#> 20 m 80 95 -#> -#> $`3.01a` -#> dissolved bound -#> No buffer 0 0 -#> 3 m 25 30 -#> 5 m 40 40 -#> 6 m 45 55 -#> 10 m 60 85 -#> 20 m 80 95 -#> -#> $`3.01a2` -#> dissolved bound -#> No buffer 0 0 -#> 3 m 25 25 -#> -#> $`2.0` -#> dissolved bound -#> No buffer 0.0 0.0 -#> 20 m 97.5 97.5 -#> </div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">perc_runoff_reduction_exposit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $`3.02`</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 40 40</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 60 85</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 80 95</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $`3.01a`</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 3 m 25 30</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 40 40</span> +<span class="r-out co"><span class="r-pr">#></span> 6 m 45 55</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 60 85</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 80 95</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $`3.01a2`</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 3 m 25 25</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $`2.0`</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0.0 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 97.5 97.5</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt deleted file mode 100644 index 4618e8b..0000000 --- a/docs/reference/pesticide.txt +++ /dev/null @@ -1,3 +0,0 @@ -Active Substance Compound Comment Mol mass a.i. Mol mass met. Water solubility KOC assessed compound KOC parent compound DT50 Max. in Water Max. in Soil asessed compound App. Rate Number of App. Time between app. App. Type DT50 soil parent compound DT50 soil DT50 water DT50 sediment Region / Season Interception class -Dummy 1 cereals, spring n NA Dummy 1 cereals, spring n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 -M1 cereals, winter n NA M1 cereals, winter n NA 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html index 8d06107..724a1aa 100644 --- a/docs/reference/pfm_degradation.html +++ b/docs/reference/pfm_degradation.html @@ -1,67 +1,12 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -72,35 +17,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate a time course of relative concentrations based on an mkinmod model</h1> @@ -112,80 +43,83 @@ <p>Calculate a time course of relative concentrations based on an mkinmod model</p> </div> - <pre class="usage"><span class='fu'>pfm_degradation</span>( - <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, - <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, - <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span>(<span class='fl'>2</span>)/<span class='no'>DT50</span>), - <span class='kw'>years</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>step_days</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='no'>years</span> * <span class='fl'>365</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='no'>step_days</span>) -)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>model</th> - <td><p>The degradation model to be used. Either a parent only model like -'SFO' or 'FOMC', or an mkinmod object</p></td> - </tr> - <tr> - <th>DT50</th> - <td><p>The half-life. This is only used when simple exponential decline -is calculated (SFO model).</p></td> - </tr> - <tr> - <th>parms</th> - <td><p>The parameters used for the degradation model</p></td> - </tr> - <tr> - <th>years</th> - <td><p>For how many years should the degradation be predicted?</p></td> - </tr> - <tr> - <th>step_days</th> - <td><p>What step size in days should the output have?</p></td> - </tr> - <tr> - <th>times</th> - <td><p>The output times</p></td> - </tr> - </table> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='fu'>pfm_degradation</span>(<span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>10</span>))</div><div class='output co'>#> time parent -#> 0 0 1.0000000 -#> 1 1 0.9330330 -#> 2 2 0.8705506 -#> 3 3 0.8122524 -#> 4 4 0.7578583 -#> 5 5 0.7071068</div></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">pfm_degradation</span><span class="op">(</span></span> +<span> model <span class="op">=</span> <span class="st">"SFO"</span>,</span> +<span> DT50 <span class="op">=</span> <span class="fl">1000</span>,</span> +<span> parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="va">DT50</span><span class="op">)</span>,</span> +<span> years <span class="op">=</span> <span class="fl">1</span>,</span> +<span> step_days <span class="op">=</span> <span class="fl">1</span>,</span> +<span> times <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="va">years</span> <span class="op">*</span> <span class="fl">365</span>, by <span class="op">=</span> <span class="va">step_days</span><span class="op">)</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>model</dt> +<dd><p>The degradation model to be used. Either a parent only model like +'SFO' or 'FOMC', or an mkinmod object</p></dd> + + +<dt>DT50</dt> +<dd><p>The half-life. This is only used when simple exponential decline +is calculated (SFO model).</p></dd> + + +<dt>parms</dt> +<dd><p>The parameters used for the degradation model</p></dd> + + +<dt>years</dt> +<dd><p>For how many years should the degradation be predicted?</p></dd> + + +<dt>step_days</dt> +<dd><p>What step size in days should the output have?</p></dd> + + +<dt>times</dt> +<dd><p>The output times</p></dd> + +</dl></div> + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu">pfm_degradation</span><span class="op">(</span><span class="st">"SFO"</span>, DT50 <span class="op">=</span> <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> time parent</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0 1.0000000</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1 0.9330330</span> +<span class="r-out co"><span class="r-pr">#></span> 2 2 0.8705506</span> +<span class="r-out co"><span class="r-pr">#></span> 3 3 0.8122524</span> +<span class="r-out co"><span class="r-pr">#></span> 4 4 0.7578583</span> +<span class="r-out co"><span class="r-pr">#></span> 5 5 0.7071068</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -70,35 +18,21 @@ segment of a TOXSWA surface water body." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot TOXSWA surface water concentrations</h1> @@ -111,106 +45,112 @@ segment of a TOXSWA surface water body." /> segment of a TOXSWA surface water body.</p> </div> - <pre class="usage"><span class='co'># S3 method for TOXSWA_cwa</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>( - <span class='no'>x</span>, - <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"datetime"</span>, <span class='st'>"t"</span>, <span class='st'>"t_firstjan"</span>, <span class='st'>"t_rel_to_max"</span>), - <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, - <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, - <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>threshold_factor</span> <span class='kw'>=</span> <span class='fl'>1000</span>, - <span class='kw'>thin_low</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>LC_TIME</span> <span class='kw'>=</span> <span class='st'>"C"</span>, - <span class='no'>...</span> -)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>The TOXSWA_cwa object to be plotted.</p></td> - </tr> - <tr> - <th>time_column</th> - <td><p>What should be used for the time axis. If "t_firstjan" is chosen, -the time is given in days relative to the first of January in the first year.</p></td> - </tr> - <tr> - <th>xlab, ylab</th> - <td><p>Labels for x and y axis.</p></td> - </tr> - <tr> - <th>add</th> - <td><p>Should we add to an existing plot?</p></td> - </tr> - <tr> - <th>threshold_factor</th> - <td><p>The factor by which the data have to be lower than the maximum -in order to get thinned for plotting (see next argument).</p></td> - </tr> - <tr> - <th>thin_low</th> - <td><p>If an integer greater than 1, the data close to zero (smaller than + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for TOXSWA_cwa</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> time_column <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"datetime"</span>, <span class="st">"t"</span>, <span class="st">"t_firstjan"</span>, <span class="st">"t_rel_to_max"</span><span class="op">)</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"default"</span>,</span> +<span> ylab <span class="op">=</span> <span class="st">"default"</span>,</span> +<span> add <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> threshold_factor <span class="op">=</span> <span class="fl">1000</span>,</span> +<span> thin_low <span class="op">=</span> <span class="fl">1</span>,</span> +<span> total <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> LC_TIME <span class="op">=</span> <span class="st">"C"</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>The TOXSWA_cwa object to be plotted.</p></dd> + + +<dt>time_column</dt> +<dd><p>What should be used for the time axis. If "t_firstjan" is chosen, +the time is given in days relative to the first of January in the first year.</p></dd> + + +<dt>xlab, ylab</dt> +<dd><p>Labels for x and y axis.</p></dd> + + +<dt>add</dt> +<dd><p>Should we add to an existing plot?</p></dd> + + +<dt>threshold_factor</dt> +<dd><p>The factor by which the data have to be lower than the maximum +in order to get thinned for plotting (see next argument).</p></dd> + + +<dt>thin_low</dt> +<dd><p>If an integer greater than 1, the data close to zero (smaller than 1/threshold_factor of the maximum) in the series will be thinned by this factor -in order to decrease the amount of data that is included in the plots</p></td> - </tr> - <tr> - <th>total</th> - <td><p>Should the total concentration in water be plotted, including substance sorbed -to suspended matter?</p></td> - </tr> - <tr> - <th>LC_TIME</th> - <td><p>Specification of the locale used to format dates</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to <code>plot</code> if we are not adding to an existing plot</p></td> - </tr> - </table> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span> <span class='kw'><-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00001p_pa.cwa"</span>, - <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>, - <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/system.file.html'>system.file</a></span>(<span class='st'>"testdata/SwashProjects.zip"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>)) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>H_sw_D4_pond</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_firstjan"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-4.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='no'>H_sw_R1_stream</span> <span class='kw'><-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00003s_pa.cwa"</span>, - <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>, - <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/system.file.html'>system.file</a></span>(<span class='st'>"testdata/SwashProjects.zip"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>)) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>H_sw_R1_stream</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-5.png' alt='' width='700' height='433' /></div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#examples">Examples</a></li> - </ul> +in order to decrease the amount of data that is included in the plots</p></dd> + + +<dt>total</dt> +<dd><p>Should the total concentration in water be plotted, including substance sorbed +to suspended matter?</p></dd> + + +<dt>LC_TIME</dt> +<dd><p>Specification of the locale used to format dates</p></dd> + +<dt>...</dt> +<dd><p>Further arguments passed to <code>plot</code> if we are not adding to an existing plot</p></dd> + +</dl></div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">H_sw_D4_pond</span> <span class="op"><-</span> <span class="fu"><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span><span class="op">(</span><span class="st">"00001p_pa.cwa"</span>,</span></span> +<span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> +<span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>, package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">H_sw_D4_pond</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">H_sw_D4_pond</span>, time_column <span class="op">=</span> <span class="st">"t"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">H_sw_D4_pond</span>, time_column <span class="op">=</span> <span class="st">"t_firstjan"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-3.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">H_sw_D4_pond</span>, time_column <span class="op">=</span> <span class="st">"t_rel_to_max"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-4.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">H_sw_R1_stream</span> <span class="op"><-</span> <span class="fu"><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span><span class="op">(</span><span class="st">"00003s_pa.cwa"</span>,</span></span> +<span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> +<span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>, package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">H_sw_R1_stream</span>, time_column <span class="op">=</span> <span class="st">"t_rel_to_max"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-5.png" alt="" width="700" height="433"></span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - 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navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -69,35 +17,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot time series of decline data</h1> @@ -109,97 +43,101 @@ <p>Plot time series of decline data</p> </div> - <pre class="usage"><span class='co'># S3 method for one_box</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>( - <span class='no'>x</span>, - <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='fu'><a href='https://rdrr.io/r/stats/time.html'>time</a></span>(<span class='no'>x</span>)), - <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>x</span>)), - <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, - <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residue"</span>, - <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/dimnames.html'>dimnames</a></span>(<span class='no'>x</span>)<span class='kw'>[[</span><span class='fl'>2</span>]][<span class='fl'>1</span>], - <span class='no'>...</span> -)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>The object of type <code><a href='one_box.html'>one_box</a></code> to be plotted</p></td> - </tr> - <tr> - <th>xlim</th> - <td><p>Limits for the x axis</p></td> - </tr> - <tr> - <th>ylim</th> - <td><p>Limits for the y axis</p></td> - </tr> - <tr> - <th>xlab</th> - <td><p>Label for the x axis</p></td> - </tr> - <tr> - <th>ylab</th> - <td><p>Label for the y axis</p></td> - </tr> - <tr> - <th>max_twa</th> - <td><p>If a numeric value is given, the maximum time weighted -average concentration(s) is/are shown in the graph.</p></td> - </tr> - <tr> - <th>max_twa_var</th> - <td><p>Variable for which the maximum time weighted average should -be shown if max_twa is not NULL.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to methods</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p><code><a href='sawtooth.html'>sawtooth</a></code></p></div> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>dfop_pred</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='st'>"DFOP"</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k1</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.7</span>)) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>dfop_pred</span>)</div><div class='img'><img src='plot.one_box-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>dfop_pred</span>, <span class='fl'>3</span>, <span class='fl'>7</span>), <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>)</div><div class='img'><img src='plot.one_box-2.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># Use a fitted mkinfit model</span> -<span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>) -<span class='no'>pred_2_saw</span> <span class='kw'><-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='plot.one_box-3.png' alt='' width='700' height='433' /></div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> - </ul> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for one_box</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/time.html" class="external-link">time</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span> +<span> ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"Time"</span>,</span> +<span> ylab <span class="op">=</span> <span class="st">"Residue"</span>,</span> +<span> max_twa <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> max_twa_var <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/dimnames.html" class="external-link">dimnames</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">[[</span><span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>The object of type <code><a href="one_box.html">one_box</a></code> to be plotted</p></dd> + + +<dt>xlim</dt> +<dd><p>Limits for the x axis</p></dd> + + +<dt>ylim</dt> +<dd><p>Limits for the y axis</p></dd> + + +<dt>xlab</dt> +<dd><p>Label for the x axis</p></dd> + +<dt>ylab</dt> +<dd><p>Label for the y axis</p></dd> + + +<dt>max_twa</dt> +<dd><p>If a numeric value is given, the maximum time weighted +average concentration(s) is/are shown in the graph.</p></dd> + + +<dt>max_twa_var</dt> +<dd><p>Variable for which the maximum time weighted average should +be shown if max_twa is not NULL.</p></dd> + + +<dt>...</dt> +<dd><p>Further arguments passed to methods</p></dd> + +</dl></div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="sawtooth.html">sawtooth</a></code></p></div> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">dfop_pred</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="st">"DFOP"</span>, parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="fl">0.2</span>, k2 <span class="op">=</span> <span class="fl">0.02</span>, g <span class="op">=</span> <span class="fl">0.7</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">dfop_pred</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.one_box-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="va">dfop_pred</span>, <span class="fl">3</span>, <span class="fl">7</span><span class="op">)</span>, max_twa <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.one_box-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Use a fitted mkinfit model</span></span></span> +<span class="r-in"><span><span class="va">m_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="va">m_2</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span><span class="va">pred_2</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="va">fit_2</span>, ini <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">pred_2_saw</span> <span class="op"><-</span> <span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="va">pred_2</span>, <span class="fl">2</span>, <span class="fl">7</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_2_saw</span>, max_twa <span class="op">=</span> <span class="fl">21</span>, max_twa_var <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.one_box-3.png" alt="" width="700" height="433"></span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html index 9c5c2a0..2685c21 100644 --- a/docs/reference/read.TOXSWA_cwa.html +++ b/docs/reference/read.TOXSWA_cwa.html @@ -1,69 +1,17 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Read TOXSWA surface water concentrations — read.TOXSWA_cwa • pfm</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" 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of a TOXSWA surface water body. Per default, the data for the last segment are imported. As TOXSWA 4 reports the values at the end of the hour (ConLiqWatLayCur) in its summary file, we use this value as well instead of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was -renamed to ConLiqWatLay in the out file." /> -<meta name="twitter:card" content="summary" /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +renamed to ConLiqWatLay in the out file."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,35 +22,21 @@ renamed to ConLiqWatLay in the out file." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Read TOXSWA surface water concentrations</h1> @@ -119,103 +53,102 @@ of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was renamed to ConLiqWatLay in the out file.</p> </div> - <pre class="usage"><span class='fu'>read.TOXSWA_cwa</span>( - <span class='no'>filename</span>, - <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"."</span>, - <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>segment</span> <span class='kw'>=</span> <span class='st'>"last"</span>, - <span class='kw'>substance</span> <span class='kw'>=</span> <span class='st'>"parent"</span>, - <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>windows</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>thresholds</span> <span class='kw'>=</span> <span class='kw'>NULL</span> -)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>filename</th> - <td><p>The filename of the cwa file (TOXSWA 2.x.y or similar) or the -out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher.</p></td> - </tr> - <tr> - <th>basedir</th> - <td><p>The path to the directory where the cwa file resides.</p></td> - </tr> - <tr> - <th>zipfile</th> - <td><p>Optional path to a zip file containing the cwa file.</p></td> - </tr> - <tr> - <th>segment</th> - <td><p>The segment for which the data should be read. Either "last", or -the segment number.</p></td> - </tr> - <tr> - <th>substance</th> - <td><p>For .out files, the default value "parent" leads + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">read.TOXSWA_cwa</span><span class="op">(</span></span> +<span> <span class="va">filename</span>,</span> +<span> basedir <span class="op">=</span> <span class="st">"."</span>,</span> +<span> zipfile <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> segment <span class="op">=</span> <span class="st">"last"</span>,</span> +<span> substance <span class="op">=</span> <span class="st">"parent"</span>,</span> +<span> total <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> windows <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> thresholds <span class="op">=</span> <span class="cn">NULL</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>filename</dt> +<dd><p>The filename of the cwa file (TOXSWA 2.x.y or similar) or the +out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher.</p></dd> + + +<dt>basedir</dt> +<dd><p>The path to the directory where the cwa file resides.</p></dd> + + +<dt>zipfile</dt> +<dd><p>Optional path to a zip file containing the cwa file.</p></dd> + + +<dt>segment</dt> +<dd><p>The segment for which the data should be read. Either "last", or +the segment number.</p></dd> + + +<dt>substance</dt> +<dd><p>For .out files, the default value "parent" leads to reading concentrations of the parent compound. Alternatively, the substance -of interested can be selected by its code name.</p></td> - </tr> - <tr> - <th>total</th> - <td><p>Set this to TRUE in order to read total concentrations as well. This is +of interested can be selected by its code name.</p></dd> + + +<dt>total</dt> +<dd><p>Set this to TRUE in order to read total concentrations as well. This is only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa -files. For .cwa files, the total concentration is always read as well.</p></td> - </tr> - <tr> - <th>windows</th> - <td><p>Numeric vector of width of moving windows in days, for calculating -maximum time weighted average concentrations and areas under the curve.</p></td> - </tr> - <tr> - <th>thresholds</th> - <td><p>Numeric vector of threshold concentrations in µg/L for -generating event statistics.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>An instance of an R6 object of class -<code><a href='TOXSWA_cwa.html'>TOXSWA_cwa</a></code>.</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span> <span class='kw'><-</span> <span class='fu'>read.TOXSWA_cwa</span>(<span class='st'>"00001p_pa.cwa"</span>, - <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>, - <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/system.file.html'>system.file</a></span>(<span class='st'>"testdata/SwashProjects.zip"</span>, - <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> - </ul> +files. For .cwa files, the total concentration is always read as well.</p></dd> + + +<dt>windows</dt> +<dd><p>Numeric vector of width of moving windows in days, for calculating +maximum time weighted average concentrations and areas under the curve.</p></dd> + + +<dt>thresholds</dt> +<dd><p>Numeric vector of threshold concentrations in µg/L for +generating event statistics.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + +<p>An instance of an R6 object of class +<code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code>.</p> + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">H_sw_D4_pond</span> <span class="op"><-</span> <span class="fu">read.TOXSWA_cwa</span><span class="op">(</span><span class="st">"00001p_pa.cwa"</span>,</span></span> +<span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> +<span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>,</span></span> +<span class="r-in"><span> package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html new file mode 100644 index 0000000..9b8cb48 --- /dev/null +++ b/docs/reference/reexports.html @@ -0,0 +1,83 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Objects exported from other packages — reexports • pfm</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Objects exported from other packages — reexports"><meta property="og:description" content="These objects are imported from other packages. Follow the links +below to see their documentation. + + mkin +set_nd_nq, set_nd_nq_focus + + +"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Objects exported from other packages</h1> + + <div class="hidden name"><code>reexports.Rd</code></div> + </div> + + <div class="ref-description"> + <p>These objects are imported from other packages. Follow the links +below to see their documentation.</p> +<dl><dt>mkin</dt> +<dd><p><code><a href="https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html" class="external-link">set_nd_nq</a></code>, <code><a href="https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html" class="external-link">set_nd_nq_focus</a></code></p></dd> + + +</dl></div> + + + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/reference/sawtooth-1.png b/docs/reference/sawtooth-1.png Binary files differindex 2952433..062202c 100644 --- a/docs/reference/sawtooth-1.png +++ b/docs/reference/sawtooth-1.png diff --git a/docs/reference/sawtooth-2.png b/docs/reference/sawtooth-2.png Binary files differindex 87da954..cea8b0b 100644 --- a/docs/reference/sawtooth-2.png +++ b/docs/reference/sawtooth-2.png diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html index fea24d4..8e29b9c 100644 --- a/docs/reference/sawtooth.html +++ b/docs/reference/sawtooth.html @@ -1,68 +1,13 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,35 +18,21 @@ n and i are disregarded." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Create decline time series for multiple applications</h1> @@ -114,81 +45,88 @@ n and i are disregarded." /> <code>n</code> and <code>i</code> are disregarded.</p> </div> - <pre class="usage"><span class='fu'>sawtooth</span>( - <span class='no'>x</span>, - <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>365</span>, - <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, (<span class='no'>n</span> - <span class='fl'>1</span>) * <span class='no'>i</span>, <span class='kw'>length.out</span> <span class='kw'>=</span> <span class='no'>n</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fl'>1</span>) -)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>A <code><a href='one_box.html'>one_box</a></code> object</p></td> - </tr> - <tr> - <th>n</th> - <td><p>The number of applications. If <code>applications</code> is specified, <code>n</code> is ignored</p></td> - </tr> - <tr> - <th>i</th> - <td><p>The interval between applications. If <code>applications</code> is specified, <code>i</code> -is ignored</p></td> - </tr> - <tr> - <th>applications</th> - <td><p>A data frame holding the application times in the first column and -the corresponding amounts applied in the second column.</p></td> - </tr> - </table> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>14</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>3</span>)) -<span class='no'>pred</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>) -<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='fu'>sawtooth</span>(<span class='no'>pred</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='no'>applications</span>))</div><div class='img'><img src='sawtooth-1.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>) -<span class='no'>pred_2_saw</span> <span class='kw'><-</span> <span class='fu'>sawtooth</span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>) -<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='sawtooth-2.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred_2_saw</span>)</div><div class='output co'>#> $max -#> parent m1 -#> 0.7834480 0.8617048 -#> -#> $window_start -#> parent m1 -#> 0.00 26.85 -#> -#> $window_end -#> parent m1 -#> 21.00 47.85 -#> </div></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">sawtooth</span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> n <span class="op">=</span> <span class="fl">1</span>,</span> +<span> i <span class="op">=</span> <span class="fl">365</span>,</span> +<span> applications <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="op">(</span><span class="va">n</span> <span class="op">-</span> <span class="fl">1</span><span class="op">)</span> <span class="op">*</span> <span class="va">i</span>, length.out <span class="op">=</span> <span class="va">n</span><span class="op">)</span>, amount <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>A <code><a href="one_box.html">one_box</a></code> object</p></dd> + + +<dt>n</dt> +<dd><p>The number of applications. If <code>applications</code> is specified, <code>n</code> is ignored</p></dd> + + +<dt>i</dt> +<dd><p>The interval between applications. If <code>applications</code> is specified, <code>i</code> +is ignored</p></dd> + + +<dt>applications</dt> +<dd><p>A data frame holding the application times in the first column and +the corresponding amounts applied in the second column.</p></dd> + +</dl></div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">applications</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">14</span>, by <span class="op">=</span> <span class="fl">7</span><span class="op">)</span>, amount <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">pred</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu">sawtooth</span><span class="op">(</span><span class="va">pred</span>, applications <span class="op">=</span> <span class="va">applications</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="sawtooth-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">m_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="va">m_2</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span><span class="va">pred_2</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="va">fit_2</span>, ini <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">pred_2_saw</span> <span class="op"><-</span> <span class="fu">sawtooth</span><span class="op">(</span><span class="va">pred_2</span>, <span class="fl">2</span>, <span class="fl">7</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_2_saw</span>, max_twa <span class="op">=</span> <span class="fl">21</span>, max_twa_var <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="sawtooth-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="max_twa.html">max_twa</a></span><span class="op">(</span><span class="va">pred_2_saw</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $max</span> +<span class="r-out co"><span class="r-pr">#></span> parent m1 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.7834481 0.8617049 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_start</span> +<span class="r-out co"><span class="r-pr">#></span> parent m1 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.00 26.85 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_end</span> +<span class="r-out co"><span class="r-pr">#></span> parent m1 </span> +<span class="r-out co"><span class="r-pr">#></span> 21.00 47.85 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html index cb3cf14..abea480 100644 --- a/docs/reference/soil_scenario_data_EFSA_2015.html +++ b/docs/reference/soil_scenario_data_EFSA_2015.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015 • pfm</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" 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src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015"><meta property="og:description" content="Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the -scenario and model adjustment factors from p. 15 and p. 17 are included." /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +scenario and model adjustment factors from p. 15 and p. 17 are included."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,35 +19,21 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Properties of the predefined scenarios from the EFSA guidance from 2015</h1> @@ -116,81 +47,65 @@ concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the scenario and model adjustment factors from p. 15 and p. 17 are included.</p> </div> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">soil_scenario_data_EFSA_2015</span></span></code></pre></div> + </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div id="format"> + <h2>Format</h2> <p>A data frame with one row for each scenario. Row names are the scenario codes, e.g. CTN for the Northern scenario for the total concentration in soil. Columns are mostly self-explanatory. <code>rho</code> is the dry bulk density of the top soil.</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div id="source"> + <h2>Source</h2> <p>EFSA (European Food Safety Authority) (2015) EFSA guidance document for predicting environmental concentrations of active substances of plant protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093 - doi:10.2903/j.efsa.2015.4093</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - <span class='co'># This is the code that was used to define the data</span> - <span class='no'>soil_scenario_data_EFSA_2015</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>( - <span class='kw'>Zone</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"North"</span>, <span class='st'>"Central"</span>, <span class='st'>"South"</span>), <span class='fl'>2</span>), - <span class='kw'>Country</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Estonia"</span>, <span class='st'>"Germany"</span>, <span class='st'>"France"</span>, <span class='st'>"Denmark"</span>, <span class='st'>"Czech Republik"</span>, <span class='st'>"Spain"</span>), - <span class='kw'>T_arit</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>4.7</span>, <span class='fl'>8.0</span>, <span class='fl'>11.0</span>, <span class='fl'>8.2</span>, <span class='fl'>9.1</span>, <span class='fl'>12.8</span>), - <span class='kw'>T_arr</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>7.0</span>, <span class='fl'>10.1</span>, <span class='fl'>12.3</span>, <span class='fl'>9.8</span>, <span class='fl'>11.2</span>, <span class='fl'>14.7</span>), - <span class='kw'>Texture</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Coarse"</span>, <span class='st'>"Coarse"</span>, <span class='st'>"Medium fine"</span>, <span class='st'>"Medium"</span>, <span class='st'>"Medium"</span>, <span class='st'>"Medium"</span>), - <span class='kw'>f_om</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.118</span>, <span class='fl'>0.086</span>, <span class='fl'>0.048</span>, <span class='fl'>0.023</span>, <span class='fl'>0.018</span>, <span class='fl'>0.011</span>), - <span class='kw'>theta_fc</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.244</span>, <span class='fl'>0.244</span>, <span class='fl'>0.385</span>, <span class='fl'>0.347</span>, <span class='fl'>0.347</span>, <span class='fl'>0.347</span>), - <span class='kw'>rho</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.95</span>, <span class='fl'>1.05</span>, <span class='fl'>1.22</span>, <span class='fl'>1.39</span>, <span class='fl'>1.43</span>, <span class='fl'>1.51</span>), - <span class='kw'>f_sce</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>1.5</span>, <span class='fl'>1.5</span>), - <span class='kw'>f_mod</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>4</span>, <span class='fl'>4</span>), - <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"CTN"</span>, <span class='st'>"CTC"</span>, <span class='st'>"CTS"</span>, <span class='st'>"CLN"</span>, <span class='st'>"CLC"</span>, <span class='st'>"CLS"</span>) - ) - <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>soil_scenario_data_EFSA_2015</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>'../data/soil_scenario_data_EFSA_2015.RData'</span>) -} - -<span class='co'># And this is the resulting dataframe</span> -<span class='no'>soil_scenario_data_EFSA_2015</span></div><div class='output co'>#> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce -#> CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0 -#> CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0 -#> CTS South France 11.0 12.3 Medium fine 0.048 0.385 1.22 2.0 -#> CLN North Denmark 8.2 9.8 Medium 0.023 0.347 1.39 2.0 -#> CLC Central Czech Republik 9.1 11.2 Medium 0.018 0.347 1.43 1.5 -#> CLS South Spain 12.8 14.7 Medium 0.011 0.347 1.51 1.5 -#> f_mod -#> CTN 2 -#> CTC 2 -#> CTS 2 -#> CLN 4 -#> CLC 4 -#> CLS 4</div></pre> + <a href="https://doi.org/10.2903/j.efsa.2015.4093" class="external-link">doi:10.2903/j.efsa.2015.4093</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">soil_scenario_data_EFSA_2015</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce</span> +<span class="r-out co"><span class="r-pr">#></span> CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0</span> +<span class="r-out co"><span class="r-pr">#></span> CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0</span> +<span class="r-out co"><span class="r-pr">#></span> CTS South France 11.0 12.3 Medium fine 0.048 0.385 1.22 2.0</span> +<span class="r-out co"><span class="r-pr">#></span> CLN North Denmark 8.2 9.8 Medium 0.023 0.347 1.39 2.0</span> +<span class="r-out co"><span class="r-pr">#></span> CLC Central Czech Republik 9.1 11.2 Medium 0.018 0.347 1.43 1.5</span> +<span class="r-out co"><span class="r-pr">#></span> CLS South Spain 12.8 14.7 Medium 0.011 0.347 1.51 1.5</span> +<span class="r-out co"><span class="r-pr">#></span> f_mod</span> +<span class="r-out co"><span class="r-pr">#></span> CTN 2</span> +<span class="r-out co"><span class="r-pr">#></span> CTC 2</span> +<span class="r-out co"><span class="r-pr">#></span> CTS 2</span> +<span class="r-out co"><span class="r-pr">#></span> CLN 4</span> +<span class="r-out co"><span class="r-pr">#></span> CLC 4</span> +<span class="r-out co"><span class="r-pr">#></span> CLS 4</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html index 7e8044e..96cdd1b 100644 --- a/docs/reference/soil_scenario_data_EFSA_2017.html +++ b/docs/reference/soil_scenario_data_EFSA_2017.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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Also, the -scenario and model adjustment factors from p. 16 and p. 18 are included." /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +scenario and model adjustment factors from p. 16 and p. 18 are included."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,35 +19,21 @@ scenario and model adjustment factors from p. 16 and p. 18 are included." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Properties of the predefined scenarios from the EFSA guidance from 2017</h1> @@ -116,61 +47,98 @@ concentration in soil as given in the EFSA guidance (2017, p. 14/15). Also, the scenario and model adjustment factors from p. 16 and p. 18 are included.</p> </div> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">soil_scenario_data_EFSA_2017</span></span></code></pre></div> + </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div id="format"> + <h2>Format</h2> <p>A data frame with one row for each scenario. Row names are the scenario codes, e.g. CTN for the Northern scenario for the total concentration in soil. Columns are mostly self-explanatory. <code>rho</code> is the dry bulk density of the top soil.</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div id="source"> + <h2>Source</h2> <p>EFSA (European Food Safety Authority) (2017) EFSA guidance document for predicting environmental concentrations of active substances of plant protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>15</b>(10) 4982 - doi:10.2903/j.efsa.2017.4982</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>soil_scenario_data_EFSA_2017</span></div><div class='output co'>#> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce f_mod -#> CTN North Estonia 5.7 7.6 Coarse 0.220 0.244 0.707 1.4 3 -#> CTC Central Poland 7.4 9.3 Coarse 0.122 0.244 0.934 1.4 3 -#> CTS South France 10.2 11.7 Medium 0.070 0.349 1.117 1.4 3 -#> CLN North Denmark 8.0 9.2 Medium 0.025 0.349 1.371 1.6 4 -#> CLC Central Austria 9.3 11.3 Medium 0.018 0.349 1.432 1.6 4 -#> CLS South Spain 15.4 16.7 Medium 0.010 0.349 1.521 1.6 4 -#> FOCUS_zone prec -#> CTN Hamburg 639 -#> CTC Hamburg 617 -#> CTS Hamburg 667 -#> CLN Hamburg 602 -#> CLC Châteaudun 589 -#> CLS Sevilla 526</div></pre> + <a href="https://doi.org/10.2903/j.efsa.2017.4982" class="external-link">doi:10.2903/j.efsa.2017.4982</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">soil_scenario_data_EFSA_2017</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce f_mod</span> +<span class="r-out co"><span class="r-pr">#></span> CTN North Estonia 5.7 7.6 Coarse 0.220 0.244 0.707 1.4 3</span> +<span class="r-out co"><span class="r-pr">#></span> CTC Central Poland 7.4 9.3 Coarse 0.122 0.244 0.934 1.4 3</span> +<span class="r-out co"><span class="r-pr">#></span> CTS South France 10.2 11.7 Medium 0.070 0.349 1.117 1.4 3</span> +<span class="r-out co"><span class="r-pr">#></span> CLN North Denmark 8.0 9.2 Medium 0.025 0.349 1.371 1.6 4</span> +<span class="r-out co"><span class="r-pr">#></span> CLC Central Austria 9.3 11.3 Medium 0.018 0.349 1.432 1.6 4</span> +<span class="r-out co"><span class="r-pr">#></span> CLS South Spain 15.4 16.7 Medium 0.010 0.349 1.521 1.6 4</span> +<span class="r-out co"><span class="r-pr">#></span> FOCUS_zone prec</span> +<span class="r-out co"><span class="r-pr">#></span> CTN Hamburg 639</span> +<span class="r-out co"><span class="r-pr">#></span> CTC Hamburg 617</span> +<span class="r-out co"><span class="r-pr">#></span> CTS Hamburg 667</span> +<span class="r-out co"><span class="r-pr">#></span> CLN Hamburg 602</span> +<span class="r-out co"><span class="r-pr">#></span> CLC Châteaudun 589</span> +<span class="r-out co"><span class="r-pr">#></span> CLS Sevilla 526</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu">waldo</span><span class="fu">::</span><span class="fu"><a href="https://waldo.r-lib.org/reference/compare.html" class="external-link">compare</a></span><span class="op">(</span><span class="va">soil_scenario_data_EFSA_2017</span>, <span class="va">soil_scenario_data_EFSA_2015</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> `old` is length 12</span> +<span class="r-out co"><span class="r-pr">#></span> `new` is length 10</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `names(old)[8:12]`: <span style="color: #555555;">"rho"</span> <span style="color: #555555;">"f_sce"</span> <span style="color: #555555;">"f_mod"</span> <span style="color: #BBBB00;">"FOCUS_zone"</span> <span style="color: #BBBB00;">"prec"</span></span> +<span class="r-out co"><span class="r-pr">#></span> `names(new)[8:10]`: <span style="color: #555555;">"rho"</span> <span style="color: #555555;">"f_sce"</span> <span style="color: #555555;">"f_mod"</span> </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$Country`: <span style="color: #555555;">"Estonia"</span> <span style="color: #00BB00;">"Poland"</span> <span style="color: #555555;">"France"</span> <span style="color: #555555;">"Denmark"</span> <span style="color: #00BB00;">"Austria"</span> <span style="color: #555555;">"Spain"</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$Country`: <span style="color: #555555;">"Estonia"</span> <span style="color: #00BB00;">"Germany"</span> <span style="color: #555555;">"France"</span> <span style="color: #555555;">"Denmark"</span> <span style="color: #00BB00;">"Czech Republik"</span> <span style="color: #555555;">"Spain"</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$T_arit`: <span style="color: #00BB00;">5.7</span> <span style="color: #00BB00;">7.4</span> <span style="color: #00BB00;">10.2</span> <span style="color: #00BB00;">8.0</span> <span style="color: #00BB00;">9.3</span> <span style="color: #00BB00;">15.4</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$T_arit`: <span style="color: #00BB00;">4.7</span> <span style="color: #00BB00;">8.0</span> <span style="color: #00BB00;">11.0</span> <span style="color: #00BB00;">8.2</span> <span style="color: #00BB00;">9.1</span> <span style="color: #00BB00;">12.8</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$T_arr`: <span style="color: #00BB00;">7.6</span> <span style="color: #00BB00;">9.3</span> <span style="color: #00BB00;">11.7</span> <span style="color: #00BB00;">9.2</span> <span style="color: #00BB00;">11.3</span> <span style="color: #00BB00;">16.7</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$T_arr`: <span style="color: #00BB00;">7.0</span> <span style="color: #00BB00;">10.1</span> <span style="color: #00BB00;">12.3</span> <span style="color: #00BB00;">9.8</span> <span style="color: #00BB00;">11.2</span> <span style="color: #00BB00;">14.7</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$Texture`: <span style="color: #555555;">"Coarse"</span> <span style="color: #555555;">"Coarse"</span> <span style="color: #00BB00;">"Medium"</span> <span style="color: #555555;">"Medium"</span> <span style="color: #555555;">"Medium"</span> <span style="color: #555555;">"Medium"</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$Texture`: <span style="color: #555555;">"Coarse"</span> <span style="color: #555555;">"Coarse"</span> <span style="color: #00BB00;">"Medium fine"</span> <span style="color: #555555;">"Medium"</span> <span style="color: #555555;">"Medium"</span> <span style="color: #555555;">"Medium"</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$f_om`: <span style="color: #00BB00;">0.220</span> <span style="color: #00BB00;">0.122</span> <span style="color: #00BB00;">0.070</span> <span style="color: #00BB00;">0.025</span> <span style="color: #555555;">0.018</span> <span style="color: #00BB00;">0.010</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$f_om`: <span style="color: #00BB00;">0.118</span> <span style="color: #00BB00;">0.086</span> <span style="color: #00BB00;">0.048</span> <span style="color: #00BB00;">0.023</span> <span style="color: #555555;">0.018</span> <span style="color: #00BB00;">0.011</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$theta_fc`: <span style="color: #555555;">0.244</span> <span style="color: #555555;">0.244</span> <span style="color: #00BB00;">0.349</span> <span style="color: #00BB00;">0.349</span> <span style="color: #00BB00;">0.349</span> <span style="color: #00BB00;">0.349</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$theta_fc`: <span style="color: #555555;">0.244</span> <span style="color: #555555;">0.244</span> <span style="color: #00BB00;">0.385</span> <span style="color: #00BB00;">0.347</span> <span style="color: #00BB00;">0.347</span> <span style="color: #00BB00;">0.347</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$rho`: <span style="color: #00BB00;">0.707</span> <span style="color: #00BB00;">0.934</span> <span style="color: #00BB00;">1.117</span> <span style="color: #00BB00;">1.371</span> <span style="color: #00BB00;">1.432</span> <span style="color: #00BB00;">1.521</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$rho`: <span style="color: #00BB00;">0.950</span> <span style="color: #00BB00;">1.050</span> <span style="color: #00BB00;">1.220</span> <span style="color: #00BB00;">1.390</span> <span style="color: #00BB00;">1.430</span> <span style="color: #00BB00;">1.510</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$f_sce`: <span style="color: #00BB00;">1.4</span> <span style="color: #00BB00;">1.4</span> <span style="color: #00BB00;">1.4</span> <span style="color: #00BB00;">1.6</span> <span style="color: #00BB00;">1.6</span> <span style="color: #00BB00;">1.6</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$f_sce`: <span style="color: #00BB00;">3.0</span> <span style="color: #00BB00;">2.0</span> <span style="color: #00BB00;">2.0</span> <span style="color: #00BB00;">2.0</span> <span style="color: #00BB00;">1.5</span> <span style="color: #00BB00;">1.5</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> And 3 more differences ...</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git 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possible time for the maximum in the time series returned -is after one window has passed." /> -<meta name="twitter:card" content="summary" /> - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +is after one window has passed."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -68,36 +19,21 @@ is after one window has passed." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate a time weighted average concentration</h1> @@ -106,82 +42,73 @@ is after one window has passed." /> </div> <div class="ref-description"> - <p>The moving average is built only using the values in the past, so the earliest possible time for the maximum in the time series returned is after one window has passed.</p> - </div> - <pre class="usage"><span class='fu'>twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</span>) + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">twa</span><span class="op">(</span><span class="va">x</span>, window <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for one_box</span></span> +<span><span class="fu">twa</span><span class="op">(</span><span class="va">x</span>, window <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span></code></pre></div> + </div> -<span class='co'># S3 method for one_box</span> -<span class='fu'>twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</span>)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>An object of type <code><a href='one_box.html'>one_box</a></code></p></td> - </tr> - <tr> - <th>window</th> - <td><p>The size of the moving window</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>An object of type <code><a href="one_box.html">one_box</a></code></p></dd> - <div class='dont-index'><p><code><a href='max_twa.html'>max_twa</a></code></p></div> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>pred</span> <span class='kw'><-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>), - <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>1</span>))) -<span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred</span>)</div><div class='output co'>#> $max -#> parent -#> 0.9537545 -#> -#> $window_start -#> parent -#> 0 -#> -#> $window_end -#> parent -#> 21 -#> </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - - <li><a href="#see-also">See also</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> +<dt>window</dt> +<dd><p>The size of the moving window</p></dd> +</dl></div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="max_twa.html">max_twa</a></code></p></div> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">pred</span> <span class="op"><-</span> <span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> applications <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">7</span><span class="op">)</span>, amount <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="max_twa.html">max_twa</a></span><span class="op">(</span><span class="va">pred</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $max</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 0.9537545 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_start</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 0 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_end</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 21 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 0c507b6..6ba511d 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -1,6 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9"> <url> + <loc>https://pkgdown.jrwb.de/pfm/404.html</loc> + </url> + <url> + <loc>https://pkgdown.jrwb.de/pfm/authors.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/pfm/index.html</loc> </url> <url> @@ -76,6 +82,9 @@ <loc>https://pkgdown.jrwb.de/pfm/reference/get_vertex.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/pfm/reference/index.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/pfm/reference/max_twa.html</loc> </url> <url> @@ -100,6 +109,9 @@ <loc>https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/pfm/reference/reexports.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/pfm/reference/sawtooth.html</loc> </url> <url> diff --git a/inst/data_generation/EFSA_GW_interception.R b/inst/data_generation/EFSA_GW_interception.R new file mode 100644 index 0000000..353b676 --- /dev/null +++ b/inst/data_generation/EFSA_GW_interception.R @@ -0,0 +1,29 @@ +library(here) + +bbch <- paste0(0:9, "x") +crops <- c( + "Beans (field + vegetable)", + "Peas", + "Summer oilseed rape", "Winter oilseed rape", + "Tomatoes", + "Spring cereals", "Winter cereals") +EFSA_GW_interception_2014 <- matrix(NA, length(crops), length(bbch), + dimnames = list(Crop = crops, BBCH = bbch)) +EFSA_GW_interception_2014["Beans (field + vegetable)", ] <- + c(0, 0.25, rep(0.4, 2), rep(0.7, 5), 0.8) +EFSA_GW_interception_2014["Peas", ] <- + c(0, 0.35, rep(0.55, 2), rep(0.85, 5), 0.85) +EFSA_GW_interception_2014["Summer oilseed rape", ] <- + c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9) +EFSA_GW_interception_2014["Winter oilseed rape", ] <- + c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9) +EFSA_GW_interception_2014["Tomatoes", ] <- + c(0, 0.5, rep(0.7, 2), rep(0.8, 5), 0.5) +EFSA_GW_interception_2014["Spring cereals", ] <- + c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8) +EFSA_GW_interception_2014["Winter cereals", ] <- + c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8) + +save(EFSA_GW_interception_2014, + file = here("data/EFSA_GW_interception_2014.RData")) + diff --git a/inst/data_generation/EFSA_washoff_2017.R b/inst/data_generation/EFSA_washoff_2017.R new file mode 100644 index 0000000..cbe43c6 --- /dev/null +++ b/inst/data_generation/EFSA_washoff_2017.R @@ -0,0 +1,29 @@ +library(here) + +bbch <- paste0(0:9, "x") +crops <- c( + "Beans (field + vegetable)", + "Peas", + "Summer oilseed rape", "Winter oilseed rape", + "Tomatoes", + "Spring cereals", "Winter cereals") +EFSA_washoff_2017 <- matrix(NA, length(crops), length(bbch), + dimnames = list(Crop = crops, BBCH = bbch)) +EFSA_washoff_2017["Beans (field + vegetable)", ] <- + c(NA, 0.6, rep(0.75, 2), rep(0.8, 5), 0.35) +EFSA_washoff_2017["Peas", ] <- + c(NA, 0.4, rep(0.6, 2), rep(0.65, 5), 0.35) +EFSA_washoff_2017["Summer oilseed rape", ] <- + c(NA, 0.4, rep(0.5, 2), rep(0.6, 5), 0.5) +EFSA_washoff_2017["Winter oilseed rape", ] <- + c(NA, 0.1, rep(0.4, 2), rep(0.55, 5), 0.3) +EFSA_washoff_2017["Tomatoes", ] <- + c(NA, 0.55, rep(0.75, 2), rep(0.7, 5), 0.35) +EFSA_washoff_2017["Spring cereals", ] <- + c(NA, 0.4, 0.5, 0.5, rep(0.65, 3), rep(0.65, 2), 0.55) +EFSA_washoff_2017["Winter cereals", ] <- + c(NA, 0.1, 0.4, 0.6, rep(0.55, 3), rep(0.6, 2), 0.4) + +save(EFSA_washoff_2017, + file = here("data/EFSA_washoff_2017.RData")) + diff --git a/inst/extdata/FOCUS_GW_scenarios_2012.R b/inst/data_generation/FOCUS_GW_scenarios_2012.R index 3715325..1358b8d 100644 --- a/inst/extdata/FOCUS_GW_scenarios_2012.R +++ b/inst/data_generation/FOCUS_GW_scenarios_2012.R @@ -1,3 +1,5 @@ +library(here) + # FOCUS 2012 p. 46 ff FOCUS_GW_scenarios_2012 = list() @@ -56,4 +58,6 @@ FOCUS_GW_scenarios_2012$soils <- data.frame( 1, 0.5, 0.3, 0, 1, 1, 0.5, 0.3, 0, 0, 1, 0.5, 0.5, 0.3, 0.3, 0)) -save(FOCUS_GW_scenarios_2012, file = "../../data/FOCUS_GW_scenarios_2012.RData") + +save(FOCUS_GW_scenarios_2012, + file = here("data/FOCUS_GW_scenarios_2012.RData")) diff --git a/inst/data_generation/PEC_sw_exposit.R b/inst/data_generation/PEC_sw_exposit.R new file mode 100644 index 0000000..f7d9737 --- /dev/null +++ b/inst/data_generation/PEC_sw_exposit.R @@ -0,0 +1,34 @@ +library(here) + +# Runoff percentages +Koc_breaks <- c(0, 20, 50, 100, 200, 500, 1000, 2000, 5000, 10000, 20000, 50000, Inf) +tmp <- paste(Koc_breaks[1:11], Koc_breaks[2:12], sep = "-") +Koc_classes <- c(tmp[1], paste0(">", tmp[2:11]), ">50000") +perc_runoff_exposit <- data.frame( + Koc_lower_bound = Koc_breaks[1:12], + dissolved = c(0.11, 0.151, 0.197, 0.248, 0.224, 0.184, 0.133, 0.084, 0.037, 0.031, 0.014, 0.001), + bound = c(0, 0, 0, 0.001, 0.004, 0.020, 0.042, 0.091, 0.159, 0.192, 0.291, 0.451)) +rownames(perc_runoff_exposit) <- Koc_classes + +# Runoff reduction percentages +perc_runoff_reduction_exposit <- list( + "3.02" = data.frame( + dissolved = c(0, 40, 60, 80), + bound = c(0, 40, 85, 95), + row.names = c("No buffer", paste(c(5, 10, 20), "m"))), + "3.01a" = data.frame( + dissolved = c(0, 25, 40, 45, 60, 80), + bound = c(0, 30, 40, 55, 85, 95), + row.names = c("No buffer", paste(c(3, 5, 6, 10, 20), "m"))), + "3.01a2" = data.frame( + dissolved = c(0, 25), + bound = c(0, 25), + row.names = c("No buffer", paste(c(3), "m"))), + "2.0" = data.frame( + dissolved = c(0, 97.5), + bound = c(0, 97.5), + row.names = c("No buffer", "20 m")) +) + +save(perc_runoff_exposit, perc_runoff_reduction_exposit, + file = here("data/perc_runoff.RData")) diff --git a/inst/data_generation/drift_data_JKI.R b/inst/data_generation/drift_data_JKI.R new file mode 100644 index 0000000..d28409c --- /dev/null +++ b/inst/data_generation/drift_data_JKI.R @@ -0,0 +1,47 @@ +library(here) + +# The following code was in the example code of the help page of the data object up to pfm version 0.6.0 +# It was not executed after migrating it to this directory (inst/data_generation), because +# the spreadsheet is not available at the JKI website any more. +library(readxl) +abdrift_path <- here("inst/extdata/Tabelle der Abdrifteckwerte.xls") +JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet", "Weinbau frueh", "Weinbau spaet", + "Hopfenbau", "Flaechenkulturen > 900 l/ha", "Gleisanlagen") +names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late", + "Vines early", "Vines late", "Hops", "Areic cultures > 900 L/ha", "Railroad tracks") +drift_data_JKI <- list() + +for (n in 1:8) { + drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2) + drift_data <- matrix(NA, nrow = 9, ncol = length(JKI_crops)) + dimnames(drift_data) <- list(distance = drift_data_raw[[1]][1:9], + crop = JKI_crops) + if (n == 1) { # Values for railroad tracks only present for one application + drift_data[, c(1:3, 5:8)] <- as.matrix(drift_data_raw[c(2:7, 11)][1:9, ]) + } else { + drift_data[, c(1:3, 5:7)] <- as.matrix(drift_data_raw[c(2:7)][1:9, ]) + } + drift_data_JKI[[n]] <- drift_data +} + +# Manual data entry from the Rautmann paper +drift_data_JKI[[1]]["3", "Ackerbau"] <- 0.95 +drift_data_JKI[[1]][, "Weinbau frueh"] <- c(NA, 2.7, 1.18, 0.39, 0.2, 0.13, 0.07, 0.04, 0.03) +drift_data_JKI[[2]]["3", "Ackerbau"] <- 0.79 +drift_data_JKI[[2]][, "Weinbau frueh"] <- c(NA, 2.53, 1.09, 0.35, 0.18, 0.11, 0.06, 0.03, 0.02) +drift_data_JKI[[3]]["3", "Ackerbau"] <- 0.68 +drift_data_JKI[[3]][, "Weinbau frueh"] <- c(NA, 2.49, 1.04, 0.32, 0.16, 0.10, 0.05, 0.03, 0.02) +drift_data_JKI[[4]]["3", "Ackerbau"] <- 0.62 +drift_data_JKI[[4]][, "Weinbau frueh"] <- c(NA, 2.44, 1.02, 0.31, 0.16, 0.10, 0.05, 0.03, 0.02) +drift_data_JKI[[5]]["3", "Ackerbau"] <- 0.59 +drift_data_JKI[[5]][, "Weinbau frueh"] <- c(NA, 2.37, 1.00, 0.31, 0.15, 0.09, 0.05, 0.03, 0.02) +drift_data_JKI[[6]]["3", "Ackerbau"] <- 0.56 +drift_data_JKI[[6]][, "Weinbau frueh"] <- c(NA, 2.29, 0.97, 0.30, 0.15, 0.09, 0.05, 0.03, 0.02) +drift_data_JKI[[7]]["3", "Ackerbau"] <- 0.55 +drift_data_JKI[[7]][, "Weinbau frueh"] <- c(NA, 2.24, 0.94, 0.29, 0.15, 0.09, 0.05, 0.03, 0.02) +drift_data_JKI[[8]]["3", "Ackerbau"] <- 0.52 +drift_data_JKI[[8]][, "Weinbau frueh"] <- c(NA, 2.16, 0.91, 0.28, 0.14, 0.09, 0.04, 0.03, 0.02) + +# Save the data +save(drift_data_JKI, + file = here("data/drift_data_JKI.RData")) diff --git a/inst/data_generation/drift_parameters_Rautmann.R b/inst/data_generation/drift_parameters_Rautmann.R new file mode 100644 index 0000000..2dea272 --- /dev/null +++ b/inst/data_generation/drift_parameters_Rautmann.R @@ -0,0 +1,5 @@ +library(here) + +save(drift_parameters_Rautmann, + file = "../data/drift_parameters_Rautmann.RData") + diff --git a/inst/data_generation/soil_scenario_data_EFSA.R b/inst/data_generation/soil_scenario_data_EFSA.R new file mode 100644 index 0000000..80b5ce2 --- /dev/null +++ b/inst/data_generation/soil_scenario_data_EFSA.R @@ -0,0 +1,40 @@ +library(here) + +# Data from 2015 +soil_scenario_data_EFSA_2015 <- data.frame( + Zone = rep(c("North", "Central", "South"), 2), + Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"), + T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8), + T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7), + Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"), + f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011), + theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347), + rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51), + f_sce = c(3, 2, 2, 2, 1.5, 1.5), + f_mod = c(2, 2, 2, 4, 4, 4), + stringsAsFactors = FALSE, + row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS") +) +save(soil_scenario_data_EFSA_2015, + file = here('data/soil_scenario_data_EFSA_2015.RData')) + +# Data from 2017 +soil_scenario_data_EFSA_2017 <- data.frame( + Zone = rep(c("North", "Central", "South"), 2), + Country = c("Estonia", "Poland", "France", "Denmark", "Austria", "Spain"), + T_arit = c(5.7, 7.4, 10.2, 8.0, 9.3, 15.4), + T_arr = c(7.6, 9.3, 11.7, 9.2, 11.3, 16.7), + Texture = c("Coarse", "Coarse", "Medium", "Medium", "Medium", "Medium"), + f_om = c(0.220, 0.122, 0.070, 0.025, 0.018, 0.010), + theta_fc = c(0.244, 0.244, 0.349, 0.349, 0.349, 0.349), + rho = c(0.707, 0.934, 1.117, 1.371, 1.432, 1.521), + f_sce = rep(c(1.4, 1.6), each = 3), + f_mod = rep(c(3, 4), each = 3), + FOCUS_zone = c("Hamburg", "Hamburg", "Hamburg", "Hamburg", "Ch\u00e2teaudun", "Sevilla"), + prec = c(639, 617, 667, 602, 589, 526), + stringsAsFactors = FALSE, + row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS") +) + +save(soil_scenario_data_EFSA_2017, + file = here('data/soil_scenario_data_EFSA_2017.RData')) diff --git a/log/build.log b/log/build.log new file mode 100644 index 0000000..63a1cd1 --- /dev/null +++ b/log/build.log @@ -0,0 +1,7 @@ +* checking for file ‘./DESCRIPTION’ ... OK +* preparing ‘pfm’: +* checking DESCRIPTION meta-information ... OK +* checking for LF line-endings in source and make files and shell scripts +* checking for empty or unneeded directories +* building ‘pfm_0.6.1.tar.gz’ + diff --git a/log/check.log b/log/check.log new file mode 100644 index 0000000..b08d8dc --- /dev/null +++ b/log/check.log @@ -0,0 +1,80 @@ +* using log directory ‘/home/agsad.admin.ch/f80868656/projects/pfm/pfm.Rcheck’ +* using R version 4.3.2 (2023-10-31) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.3 LTS +* using session charset: UTF-8 +* using options ‘--no-tests --as-cran’ +* checking for file ‘pfm/DESCRIPTION’ ... OK +* checking extension type ... Package +* this is package ‘pfm’ version ‘0.6.1’ +* package encoding: UTF-8 +* checking CRAN incoming feasibility ... NOTE +Maintainer: ‘Johannes Ranke <johannes.ranke@agroscope.admin.ch>’ + +Size of tarball: 8487405 bytes +* checking package namespace information ... OK +* checking package dependencies ... OK +* checking if this is a source package ... OK +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘pfm’ can be installed ... OK +* checking installed package size ... NOTE + installed size is 10.2Mb + sub-directories of 1Mb or more: + testdata 9.9Mb +* checking package directory ... OK +* checking for future file timestamps ... OK +* checking DESCRIPTION meta-information ... OK +* checking top-level files ... OK +* checking for left-over files ... OK +* checking index information ... OK +* checking package subdirectories ... OK +* checking R files for non-ASCII characters ... OK +* checking R files for syntax errors ... OK +* checking whether the package can be loaded ... OK +* checking whether the package can be loaded with stated dependencies ... OK +* checking whether the package can be unloaded cleanly ... OK +* checking whether the namespace can be loaded with stated dependencies ... OK +* checking whether the namespace can be unloaded cleanly ... OK +* checking loading without being on the library search path ... OK +* checking use of S3 registration ... OK +* checking dependencies in R code ... OK +* checking S3 generic/method consistency ... OK +* checking replacement functions ... OK +* checking foreign function calls ... OK +* checking R code for possible problems ... OK +* checking Rd files ... OK +* checking Rd metadata ... OK +* checking Rd line widths ... OK +* checking Rd cross-references ... OK +* checking for missing documentation entries ... OK +* checking for code/documentation mismatches ... OK +* checking Rd \usage sections ... OK +* checking Rd contents ... OK +* checking for unstated dependencies in examples ... OK +* checking contents of ‘data’ directory ... OK +* checking data for non-ASCII characters ... OK +* checking LazyData ... OK +* checking data for ASCII and uncompressed saves ... OK +* checking examples ... OK +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... SKIPPED +* checking PDF version of manual ... OK +* checking HTML version of manual ... NOTE +Skipping checking HTML validation: no command 'tidy' found +* checking for non-standard things in the check directory ... OK +* checking for detritus in the temp directory ... OK +* DONE + +Status: 3 NOTEs +See + ‘/home/agsad.admin.ch/f80868656/projects/pfm/pfm.Rcheck/00check.log’ +for details. + + diff --git a/man/EFSA_GW_interception_2014.Rd b/man/EFSA_GW_interception_2014.Rd index 2334d7f..ed29454 100644 --- a/man/EFSA_GW_interception_2014.Rd +++ b/man/EFSA_GW_interception_2014.Rd @@ -14,37 +14,13 @@ of active substances of plant protection products and transformation products of these active substances in soil. \emph{EFSA Journal} \bold{12}(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662 } +\usage{ +EFSA_GW_interception_2014 +} \description{ Subset of EFSA crop interception default values for groundwater modelling } \examples{ -\dontrun{ - # This is the code that was used to define the data - bbch <- paste0(0:9, "x") - crops <- c( - "Beans (field + vegetable)", - "Peas", - "Summer oilseed rape", "Winter oilseed rape", - "Tomatoes", - "Spring cereals", "Winter cereals") - EFSA_GW_interception_2014 <- matrix(NA, length(crops), length(bbch), - dimnames = list(Crop = crops, BBCH = bbch)) - EFSA_GW_interception_2014["Beans (field + vegetable)", ] <- - c(0, 0.25, rep(0.4, 2), rep(0.7, 5), 0.8) - EFSA_GW_interception_2014["Peas", ] <- - c(0, 0.35, rep(0.55, 2), rep(0.85, 5), 0.85) - EFSA_GW_interception_2014["Summer oilseed rape", ] <- - c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9) - EFSA_GW_interception_2014["Winter oilseed rape", ] <- - c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9) - EFSA_GW_interception_2014["Tomatoes", ] <- - c(0, 0.5, rep(0.7, 2), rep(0.8, 5), 0.5) - EFSA_GW_interception_2014["Spring cereals", ] <- - c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8) - EFSA_GW_interception_2014["Winter cereals", ] <- - c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8) - save(EFSA_GW_interception_2014, - file = "../data/EFSA_GW_interception_2014.RData") -} EFSA_GW_interception_2014 } +\keyword{datasets} diff --git a/man/EFSA_washoff_2017.Rd b/man/EFSA_washoff_2017.Rd index e153fbe..28c50df 100644 --- a/man/EFSA_washoff_2017.Rd +++ b/man/EFSA_washoff_2017.Rd @@ -14,37 +14,13 @@ European Food Safety Authority (2017) EFSA guidance document for in soil. \emph{EFSA Journal} \bold{15}(10) 4982 doi:10.2903/j.efsa.2017.4982 } +\usage{ +EFSA_washoff_2017 +} \description{ Subset of EFSA crop washoff default values } \examples{ -\dontrun{ - # This is the code that was used to define the data - bbch <- paste0(0:9, "x") - crops <- c( - "Beans (field + vegetable)", - "Peas", - "Summer oilseed rape", "Winter oilseed rape", - "Tomatoes", - "Spring cereals", "Winter cereals") - EFSA_washoff_2017 <- matrix(NA, length(crops), length(bbch), - dimnames = list(Crop = crops, BBCH = bbch)) - EFSA_washoff_2017["Beans (field + vegetable)", ] <- - c(NA, 0.6, rep(0.75, 2), rep(0.8, 5), 0.35) - EFSA_washoff_2017["Peas", ] <- - c(NA, 0.4, rep(0.6, 2), rep(0.65, 5), 0.35) - EFSA_washoff_2017["Summer oilseed rape", ] <- - c(NA, 0.4, rep(0.5, 2), rep(0.6, 5), 0.5) - EFSA_washoff_2017["Winter oilseed rape", ] <- - c(NA, 0.1, rep(0.4, 2), rep(0.55, 5), 0.3) - EFSA_washoff_2017["Tomatoes", ] <- - c(NA, 0.55, rep(0.75, 2), rep(0.7, 5), 0.35) - EFSA_washoff_2017["Spring cereals", ] <- - c(NA, 0.4, 0.5, 0.5, rep(0.65, 3), rep(0.65, 2), 0.55) - EFSA_washoff_2017["Winter cereals", ] <- - c(NA, 0.1, 0.4, 0.6, rep(0.55, 3), rep(0.6, 2), 0.4) - save(EFSA_washoff_2017, - file = "../data/EFSA_washoff_2017.RData") -} EFSA_washoff_2017 } +\keyword{datasets} diff --git a/man/PEC_sw_exposit_drainage.Rd b/man/PEC_sw_exposit_drainage.Rd index 5a543c8..6f7f41a 100644 --- a/man/PEC_sw_exposit_drainage.Rd +++ b/man/PEC_sw_exposit_drainage.Rd @@ -5,7 +5,7 @@ \title{Calculate PEC surface water due to drainage as in Exposit 3} \source{ Excel 3.02 spreadsheet available from - \url{https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3} + \url{https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html} } \usage{ PEC_sw_exposit_drainage( diff --git a/man/PEC_sw_exposit_runoff.Rd b/man/PEC_sw_exposit_runoff.Rd index a415a63..4b6efba 100644 --- a/man/PEC_sw_exposit_runoff.Rd +++ b/man/PEC_sw_exposit_runoff.Rd @@ -5,7 +5,7 @@ \title{Calculate PEC surface water due to runoff and erosion as in Exposit 3} \source{ Excel 3.02 spreadsheet available from - \url{https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3} + \url{https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html} } \usage{ PEC_sw_exposit_runoff( diff --git a/man/PEC_sw_focus.Rd b/man/PEC_sw_focus.Rd index f23423b..362c432 100644 --- a/man/PEC_sw_focus.Rd +++ b/man/PEC_sw_focus.Rd @@ -21,7 +21,7 @@ PEC_sw_focus( met_form_water = TRUE, txt_file = "pesticide.txt", overwrite = FALSE, - append = TRUE + append = FALSE ) } \arguments{ @@ -73,7 +73,7 @@ should be written} \item{overwrite}{Should an existing file a the location specified in \code{txt_file} be overwritten? Only takes effect if append is FALSE.} -\item{append}{Should the input text file be appended?} +\item{append}{Should the input text file be appended, if it exists?} } \description{ This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2, @@ -81,8 +81,8 @@ authored by Michael Klein, in R. Note that results for multiple applications should be compared to the corresponding results for a single application. At current, this is not done automatically in this implementation. Only Step 1 PECs are calculated. However, -input files are generated that are suitable as input also for Step 2 -to be used with the FOCUS calculator. +input files can be generated that are suitable as input for +the FOCUS calculator. } \note{ The formulas for input to the waterbody via runoff/drainage of the @@ -97,7 +97,7 @@ Step 2 is not implemented. \examples{ # Parent only dummy_1 <- chent_focus_sw("Dummy 1", cwsat = 6000, DT50_ws = 6, Koc = 344.8) -PEC_sw_focus(dummy_1, 3000, f_drift = 0, overwrite = TRUE, append = FALSE) +PEC_sw_focus(dummy_1, 3000, f_drift = 0) # Metabolite new_dummy <- chent_focus_sw("New Dummy", mw = 250, Koc = 100) diff --git a/man/drift_data_JKI.Rd b/man/drift_data_JKI.Rd index bde9aad..49b7552 100644 --- a/man/drift_data_JKI.Rd +++ b/man/drift_data_JKI.Rd @@ -14,7 +14,7 @@ data for field crops (Ackerbau), and Pome/stone fruit, early and late JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved from http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html -on 2015-06-11 +on 2015-06-11, not present any more 2024-01-31 Rautmann, D., Streloke, M and Winkler, R (2001) New basic drift values in the authorization procedure for plant protection products Mitt. Biol. @@ -43,53 +43,6 @@ Values for non-professional use listed in the JKI spreadsheet were not included. } \examples{ - -\dontrun{ - # This is the code that was used to extract the data - library(readxl) - abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls" - JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet", "Weinbau frueh", "Weinbau spaet", - "Hopfenbau", "Flaechenkulturen > 900 l/ha", "Gleisanlagen") - names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late", - "Vines early", "Vines late", "Hops", "Areic cultures > 900 L/ha", "Railroad tracks") - drift_data_JKI <- list() - - for (n in 1:8) { - drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2) - drift_data <- matrix(NA, nrow = 9, ncol = length(JKI_crops)) - dimnames(drift_data) <- list(distance = drift_data_raw[[1]][1:9], - crop = JKI_crops) - if (n == 1) { # Values for railroad tracks only present for one application - drift_data[, c(1:3, 5:8)] <- as.matrix(drift_data_raw[c(2:7, 11)][1:9, ]) - } else { - drift_data[, c(1:3, 5:7)] <- as.matrix(drift_data_raw[c(2:7)][1:9, ]) - } - drift_data_JKI[[n]] <- drift_data - } - - # Manual data entry from the Rautmann paper - drift_data_JKI[[1]]["3", "Ackerbau"] <- 0.95 - drift_data_JKI[[1]][, "Weinbau frueh"] <- c(NA, 2.7, 1.18, 0.39, 0.2, 0.13, 0.07, 0.04, 0.03) - drift_data_JKI[[2]]["3", "Ackerbau"] <- 0.79 - drift_data_JKI[[2]][, "Weinbau frueh"] <- c(NA, 2.53, 1.09, 0.35, 0.18, 0.11, 0.06, 0.03, 0.02) - drift_data_JKI[[3]]["3", "Ackerbau"] <- 0.68 - drift_data_JKI[[3]][, "Weinbau frueh"] <- c(NA, 2.49, 1.04, 0.32, 0.16, 0.10, 0.05, 0.03, 0.02) - drift_data_JKI[[4]]["3", "Ackerbau"] <- 0.62 - drift_data_JKI[[4]][, "Weinbau frueh"] <- c(NA, 2.44, 1.02, 0.31, 0.16, 0.10, 0.05, 0.03, 0.02) - drift_data_JKI[[5]]["3", "Ackerbau"] <- 0.59 - drift_data_JKI[[5]][, "Weinbau frueh"] <- c(NA, 2.37, 1.00, 0.31, 0.15, 0.09, 0.05, 0.03, 0.02) - drift_data_JKI[[6]]["3", "Ackerbau"] <- 0.56 - drift_data_JKI[[6]][, "Weinbau frueh"] <- c(NA, 2.29, 0.97, 0.30, 0.15, 0.09, 0.05, 0.03, 0.02) - drift_data_JKI[[7]]["3", "Ackerbau"] <- 0.55 - drift_data_JKI[[7]][, "Weinbau frueh"] <- c(NA, 2.24, 0.94, 0.29, 0.15, 0.09, 0.05, 0.03, 0.02) - drift_data_JKI[[8]]["3", "Ackerbau"] <- 0.52 - drift_data_JKI[[8]][, "Weinbau frueh"] <- c(NA, 2.16, 0.91, 0.28, 0.14, 0.09, 0.04, 0.03, 0.02) - - # Save the data - save(drift_data_JKI, file = "data/drift_data_JKI.RData") -} - -# And these are the resulting data drift_data_JKI } \keyword{datasets} diff --git a/man/perc_runoff_exposit.Rd b/man/perc_runoff_exposit.Rd index 0bd2827..5b92ab3 100644 --- a/man/perc_runoff_exposit.Rd +++ b/man/perc_runoff_exposit.Rd @@ -1,5 +1,6 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/PEC_sw_exposit_runoff.R +\docType{data} \name{perc_runoff_exposit} \alias{perc_runoff_exposit} \title{Runoff loss percentages as used in Exposit 3} @@ -16,7 +17,10 @@ A data frame with percentage values for the dissolved fraction and the fraction } \source{ Excel 3.02 spreadsheet available from - \url{https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html} + \url{https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html} +} +\usage{ +perc_runoff_exposit } \description{ A table of the loss percentages used in Exposit 3 for the twelve different Koc classes @@ -24,3 +28,4 @@ A table of the loss percentages used in Exposit 3 for the twelve different Koc c \examples{ print(perc_runoff_exposit) } +\keyword{datasets} diff --git a/man/perc_runoff_reduction_exposit.Rd b/man/perc_runoff_reduction_exposit.Rd index 93016b7..0157e48 100644 --- a/man/perc_runoff_reduction_exposit.Rd +++ b/man/perc_runoff_reduction_exposit.Rd @@ -16,7 +16,7 @@ from which the values were taken. } \source{ Excel 3.02 spreadsheet available from - \url{https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html} + \url{https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html} Agroscope version 3.01a with additional runoff factors for 3 m and 6 m buffer zones received from Muris Korkaric (not published). The variant 3.01a2 was introduced for consistency with previous calculations performed by Agroscope for a 3 m buffer zone. diff --git a/man/soil_scenario_data_EFSA_2015.Rd b/man/soil_scenario_data_EFSA_2015.Rd index dfad4aa..4d625f8 100644 --- a/man/soil_scenario_data_EFSA_2015.Rd +++ b/man/soil_scenario_data_EFSA_2015.Rd @@ -14,7 +14,10 @@ EFSA (European Food Safety Authority) (2015) EFSA guidance document for predicting environmental concentrations of active substances of plant protection products and transformation products of these active substances in soil. \emph{EFSA Journal} \bold{13}(4) 4093 - doi:10.2903/j.efsa.2015.4093 + \doi{10.2903/j.efsa.2015.4093} +} +\usage{ +soil_scenario_data_EFSA_2015 } \description{ Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the @@ -22,26 +25,6 @@ concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the scenario and model adjustment factors from p. 15 and p. 17 are included. } \examples{ -\dontrun{ - # This is the code that was used to define the data - soil_scenario_data_EFSA_2015 <- data.frame( - Zone = rep(c("North", "Central", "South"), 2), - Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"), - T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8), - T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7), - Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"), - f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011), - theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347), - rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51), - f_sce = c(3, 2, 2, 2, 1.5, 1.5), - f_mod = c(2, 2, 2, 4, 4, 4), - stringsAsFactors = FALSE, - row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS") - ) - save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData') -} - -# And this is the resulting dataframe soil_scenario_data_EFSA_2015 } \keyword{datasets} diff --git a/man/soil_scenario_data_EFSA_2017.Rd b/man/soil_scenario_data_EFSA_2017.Rd index f6de290..c43a5b7 100644 --- a/man/soil_scenario_data_EFSA_2017.Rd +++ b/man/soil_scenario_data_EFSA_2017.Rd @@ -14,7 +14,10 @@ EFSA (European Food Safety Authority) (2017) EFSA guidance document for predicting environmental concentrations of active substances of plant protection products and transformation products of these active substances in soil. \emph{EFSA Journal} \bold{15}(10) 4982 - doi:10.2903/j.efsa.2017.4982 + \doi{10.2903/j.efsa.2017.4982} +} +\usage{ +soil_scenario_data_EFSA_2017 } \description{ Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the @@ -23,5 +26,7 @@ scenario and model adjustment factors from p. 16 and p. 18 are included. } \examples{ soil_scenario_data_EFSA_2017 + +waldo::compare(soil_scenario_data_EFSA_2017, soil_scenario_data_EFSA_2015) } \keyword{datasets} diff --git a/test.log b/test.log deleted file mode 100644 index 0938948..0000000 --- a/test.log +++ /dev/null @@ -1,18 +0,0 @@ -ℹ Testing pfm -✔ | F W S OK | Context -✔ | 7 | Exposit calculations [0.1s] -✔ | 6 | Geometric mean calculation -✔ | 1 | Check max_twa for parent mkinfit models against analytical solutions [0.9s] -✔ | 1 | Simple PEC sediment calculations -✔ | 17 | Simple PEC soil calculations [0.2s] -✔ | 6 | Simple PEC surface water calculations with drift entry -✔ | 1 | Actual and time weighted average concentrations for SFO kinetics -✔ | 9 | FOCUS Step 1 calculations [0.2s] -✔ | 8 | FOCUS Steps 12 input files -✔ | 7 | Read and analyse TOXSWA cwa files [6.1s] -✔ | 12 | UK drainage PEC calculations - -══ Results ═════════════════════════════════════════════════════════════════════════════════════════ -Duration: 7.6 s - -[ FAIL 0 | WARN 0 | SKIP 0 | PASS 75 ] |
