commit 539ea37b45ddc41b36dd199f06ffe5936ab13f21 Author: Johannes Ranke Date: 2017-05-17 12:23:38 +0200 Documentation fix commit 62bffd4873bc53fa9cd81336efa716b220c83e0a Author: Johannes Ranke Date: 2017-05-17 09:36:22 +0200 Simplify tests where possible commit d60bb9c0b52c8e0452bfbe507e60d5f651589cc8 Author: Johannes Ranke Date: 2017-05-16 18:57:16 +0200 Update static documentation commit 14fa47b1ea1651fc2cb7bbf0086741a8004d35ee Author: Johannes Ranke Date: 2017-05-16 18:54:34 +0200 Remove external data also from git as their licence is unclear commit 608c4f89a2656f67ba915aab17633d41acc789a7 Author: Johannes Ranke Date: 2017-05-16 18:44:22 +0200 Add build and test logs to the git repo commit 3e26a8ab76a434c3465ea1db1b4a2a2ff3ea8ec8 Author: Johannes Ranke 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 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 Date: 2017-05-15 20:01:28 +0200 Start of an Steps 1/2 calculator in R commit b052bf8d1e090e07bf0853f0aa8b895db8f41a2a Author: Johannes Ranke Date: 2017-03-29 19:24:37 +0200 Make it possible to use expressions in axis labels commit d69fda8d8f854b735394ecdaec9d59fb18c42b00 Author: Johannes Ranke Date: 2017-03-28 10:09:45 +0200 Update Changelog commit 90e5ff0a9fdadd65e179c04c7d43b4db6e301984 Author: Johannes Ranke Date: 2017-03-06 17:59:16 +0100 Move static docs to pkdown.jrwb.de, update them commit 68e36eb0a5f1b611588d47f77e0ef7c3d9ba0beb Author: Johannes Ranke Date: 2017-03-01 11:37:31 +0100 The package is not in subdir `pkg` any more commit f67ea0c4aeb68631e9f93c95e86c14364718477a Author: Johannes Ranke Date: 2017-01-31 07:33:21 +0100 Small documentation fix commit 4e696997516543e29119e94d67283f513be4484d Author: Johannes Ranke Date: 2017-01-30 18:08:50 +0100 Regenerate static documentation commit 03bda75d343402dad99df2aad55611e11279b833 Author: Johannes Ranke Date: 2017-01-30 18:04:53 +0100 Correct psm file in the example with metabolites commit 39d202b0a0f833c756bc98fb4961483de1b15353 Author: Johannes Ranke Date: 2017-01-30 16:14:15 +0100 Ignore windows binary builds in git and in R package commit e6bb9654679f43af6958d6e28cb5206abb91d574 Author: Johannes Ranke 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 Date: 2017-01-30 14:28:23 +0100 PELMO summary files for testing commit 826cf9a2687ff1d7ca5b568882f5686f76f82074 Author: Johannes Ranke 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 Date: 2017-01-30 13:12:24 +0100 Better documentation of PELMO_runs(). commit d78d2effd517ab3c27412ae6f4ae701c456ae590 Author: Johannes Ranke Date: 2017-01-30 12:46:57 +0100 pfm for windows in my drat commit eaf3b558747ff8228e87ded727a6c0e91a6579f8 Author: Johannes Ranke Date: 2017-01-30 12:01:14 +0100 More extreme parameters for metabolites for testing commit a6c13f70f6c6669a8088827a602ac475fdf9b624 Author: Johannes Ranke Date: 2017-01-29 16:58:53 +0100 Setting up PELMO runs, execution and evaluation It all works! commit bc97a35a32c4f47e29364488a3601f94c6e68d45 Author: Johannes Ranke 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 Date: 2017-01-27 18:23:35 +0100 Use all scenarios in the test data commit 3c82d26206e2f2e74600acd71a49c70eaed555c4 Author: Johannes Ranke Date: 2017-01-27 08:17:08 +0100 Also test run with metabolites commit 8fd050e57b7babfbdb1ccfabb468a0398396d466 Author: Johannes Ranke Date: 2017-01-27 07:54:53 +0100 Include a run with metabolites in PELMO test data commit b38055278d4a801598ece9d2c93716a9bf67134a Author: Johannes Ranke 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 Date: 2017-01-26 10:30:32 +0100 Improved test data with 'irrigation' commit 228ab628b407af4812a48f20693a9a3a6bba8af4 Author: Johannes Ranke Date: 2017-01-25 16:45:24 +0100 More variable selection of test data commit bf6634b7d9a5033a217f04060f77e0c7d5b3046a Author: Johannes Ranke Date: 2017-01-25 15:27:05 +0100 Use tar.bz2 to correctly transfer file names commit 476d556cb6a490b138e47d487dd732f298aa6c3d Author: Johannes Ranke Date: 2017-01-25 14:29:41 +0100 Add FOCUS PELMO 5.5.3 output for dummy pesticide D commit 9f16be247e851c948edb30ac756550d89ba0af52 Author: Johannes Ranke Date: 2017-01-19 11:44:22 +0100 Another correction of the docs commit 2ab822d51c4c7e29d62076336d7a3f02a46e41a5 Author: Johannes Ranke Date: 2017-01-19 11:41:19 +0100 Corrections in the documentation commit 46883a0c3a3c00127a563a7befa0af440573baaa Author: Johannes Ranke Date: 2017-01-19 11:22:08 +0100 Correct default y axis label for plot.one_box commit 3947731a5a8c3598271b26f5201dea4bcb13ef6d Author: Johannes Ranke Date: 2017-01-19 10:47:09 +0100 Fix one_box for ini = 1, use in sawtooth examples commit dd30f0d0ff1d8d0cc46aaef6e0917c51fe798f52 Author: Johannes Ranke 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 Date: 2017-01-19 09:42:21 +0100 Make max_twa() a bit safer commit 74ed85b07f09ea99476208749cd274a476ba4536 Author: Johannes Ranke Date: 2017-01-19 09:27:36 +0100 Documentation updates commit a6d61c06d573574cf574ed893cc13808a9e8b785 Author: Johannes Ranke Date: 2017-01-19 09:20:22 +0100 Fix order of arguments to one_box, correct docs commit b8ac1393b9e1bef8c48b26b790cf5759ccd69fed Author: Johannes Ranke Date: 2017-01-19 09:10:37 +0100 Predict parent decline without fitting for non-SFO models commit 3d4f6f8c582c19c38587ead305a1229ff069da63 Author: Johannes Ranke 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 Date: 2017-01-18 23:02:14 +0100 Point to the github.io documentation site commit cff68edc1ac113ac9e159dfdf7cfcbb6721ff2a7 Author: Johannes Ranke Date: 2017-01-18 22:58:51 +0100 Make README.md simple, and point to the reference commit a76221d87485029444c8e684022ca606a0c7e68d Author: Johannes Ranke 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 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 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 Date: 2016-12-14 18:26:14 +0100 Changelog update and roxygen run commit 5a04ad3061c1484b45703e44149f49ec97cfbf15 Author: Johannes Ranke 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 Date: 2016-12-12 21:24:24 +0100 Fix reading .out for acronyms containing numbers commit 9124e0f7d673c65584c1b2f838a3b944ea89c31d Author: Johannes Ranke Date: 2016-10-13 17:49:18 +0200 Add drat target, remove unmaintained usage hints commit 12a31f4c130c551f82232d9ef7dfb608bd52c53f Author: Johannes Ranke Date: 2016-09-27 23:00:48 +0200 Reorganise repository using standard package layout commit 0d958ab6f84b569b5437f231c56004890c4ae23b Author: Johannes Ranke Date: 2016-09-27 17:50:34 +0200 Make the chents package optional commit 399383adcdb37c4a3e32f1a2133a2fa3663618d0 Author: Johannes Ranke 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 Date: 2016-09-23 18:16:51 +0200 Slightly update the README commit 2f618da8cfbeb0379f4d38af6f608a69c6d54bd5 Author: Johannes Ranke Date: 2016-07-30 11:29:09 +0200 Update static documentation commit 3b8730a58f7846b5261922ec90e582e0158a54c7 Author: Johannes Ranke Date: 2016-07-30 11:09:47 +0200 Add 'methods' to dependecies commit 3260b0e875b7af24f2aef7bc2464418525a192df Author: Johannes Ranke 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 Date: 2016-07-30 11:06:53 +0200 Import 'is' from methods commit 1ceb226d999d56276c9e361f359368287a0749c4 Author: Johannes Ranke 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 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 Date: 2016-06-08 08:36:48 +0200 Clean up remainders of NL drift calculation function commit 234a20018fe9fe9824bcfaae2c391e59d09f9871 Author: Johannes Ranke 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 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 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 Date: 2016-03-10 05:17:45 +0100 Add NL specific drift calculations commit 1ab6d4c9f186fb7ea9bb8b968e47a9f1eab64583 Author: Johannes Ranke Date: 2016-03-02 17:51:21 +0100 Fix the name of the Chateadun scenario commit d14923ae1ac023c8f8f5ae8b5c0884f4247f764b Author: Johannes Ranke Date: 2016-02-04 18:06:15 +0100 Test reading .out files and close connections commit 98a706373107188496a1df295697e739e51d6b06 Author: Johannes Ranke Date: 2016-02-04 17:45:02 +0100 Improve reading spead for new TOXSWA format commit 057ba40426d49e09c06db26fb7d4072741b4cb8d Author: Johannes Ranke Date: 2016-02-04 12:21:02 +0100 Read cwa data from TOXSWA 4.4.2 .out files commit e7f8a0e82b24d28b74681dafc97f1cf8a4662b51 Author: Johannes Ranke Date: 2015-12-27 12:30:20 +0100 Fix rounding of endpoint retrieval functions commit f9373e361dde232b08fe7431e85bf367a1cfc269 Author: Johannes Ranke Date: 2015-12-27 12:29:37 +0100 Another useless variant to avoid warnings in staticdoc plots commit 3a579d87820ccbec514f1be5eb090e874fd87eec Author: Johannes Ranke Date: 2015-12-22 19:32:54 +0100 EFSA 2015 tier 1 PEC soil, clean up, add static docs commit 9851a97ec915ddbfc8357f1a7e2cabae56c89f7d Author: Johannes Ranke Date: 2015-12-18 14:45:24 +0100 Documentation fixes, chents is currently a hard dependency commit 6b4e342b240baaf18150360986d15895fc80a937 Author: Johannes Ranke Date: 2015-10-15 14:41:26 +0200 Add endpoint and GUS functions, roxygenize commit c43b4947007b3c26bc56260499af51c41b8cd702 Author: Johannes Ranke Date: 2015-10-01 14:42:14 +0200 Add some soil data for FOCUS groundwater scenarios commit 697e0554bf89a63f23b9ab5548e31f218bc483e9 Author: Johannes Ranke 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 Date: 2015-09-10 16:18:17 +0200 Add PEC soil for product with serveral ais commit 1ec3ee4a03d4e47fdd3be1bcbe754e478353410b Author: Johannes Ranke Date: 2015-08-22 12:10:06 +0200 Updates of DESCRIPTION and NAMESPACE commit 51aa1a77c9b9b9a6becdb2a5a85213946719b051 Author: Johannes Ranke Date: 2015-08-22 12:06:37 +0200 Add README.html for cgit on jrwb.de commit 83c8575e2abde12208584b9c80935d4a873689fd Author: Johannes Ranke Date: 2015-08-22 12:01:57 +0200 Small documentation updates commit 5038ba57fef6cc386566ec30f3d5dd67e62decff Author: Johannes Ranke Date: 2015-08-21 15:10:42 +0200 Adapt the description to R CMD check requirements commit 4477e69b46e88c196f354463190753650157ea0d Author: Johannes Ranke Date: 2015-08-21 15:01:10 +0200 Updates to pass checks and tests commit ad4cd5d9a1f8c3976d08048a441129b1fb49a62b Author: Johannes Ranke Date: 2015-07-02 16:05:59 +0200 Changes to pass R CMD check --as-cran, roxygen run commit fef0bb7fe916f91dcff089c17aa3290c0ea1ab1f Author: Johannes Ranke Date: 2015-06-12 02:19:38 +0200 Add sediment PEC calculations using the percentage method commit 5b32c30549bfa3cb42ffde7e13f75608b98c79c2 Author: Johannes Ranke Date: 2015-06-12 02:19:01 +0200 Make UK drainage with non-SFO soil degradation work commit 9b8e5cb80ba4a89578d979bee134f8342ca0a527 Author: Johannes Ranke Date: 2015-06-11 17:38:01 +0200 Now we pass R CMD check commit dd803b191062925eda830543236836e7822fd884 Author: Johannes Ranke Date: 2015-06-11 16:57:43 +0200 Add UK tier 1 drainage PEC calculations commit 09cf970942706cfab43753d298b42e8d85216d80 Author: Johannes Ranke Date: 2015-06-11 15:25:22 +0200 Now there is enough content to warrant 0.2-x commit 3aa5fb86772c28402047c7ebd07841061dbcdbba Author: Johannes Ranke Date: 2015-06-11 15:23:22 +0200 Add facilities to calculate decline curves commit d3daa7b73fa5d0508ff51a843247d126c2a11691 Author: Johannes Ranke Date: 2015-06-11 13:17:13 +0200 Generate README.md with current pfm version commit cb0d72e2c2d431bd32ffb129b62ea1a522cbdfeb Author: Johannes Ranke Date: 2015-06-11 13:09:10 +0200 Rename PEC_sw_drift() to PEC_sw_drift_ini() commit ea9b75183bcf41fcdd6f61ec6060e94c4bc321a2 Author: Johannes Ranke 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 Date: 2015-06-11 12:12:40 +0200 Use devtools for roxygenizing, improve logging commit 6e4a152925011528c21937f12bc53042a53f72de Author: Johannes Ranke Date: 2015-06-11 10:13:18 +0200 JKI drift percentage data for field crops and pome/stone fruit commit 53099978c971ee8e5c94e67bf972f51629d67fd3 Author: Johannes Ranke Date: 2015-06-11 10:04:22 +0200 and the incomplete documentation commit 372ab2f2f59f0baaee759ce966a705f9f754cf6d Author: Johannes Ranke Date: 2015-06-11 10:03:32 +0200 Intermediate stage for pfm_chent commit 586b248f5d249f4ebaad2175c9f78fcae8646636 Author: Johannes Ranke Date: 2015-06-11 09:54:57 +0200 Formatting commit fd1609aafd2f40266c1e29d8dfdf5e08e8838d35 Author: Johannes Ranke Date: 2015-05-24 03:52:28 +0200 Start of a pfm_chent data object commit e2b1d510e921f7721647b0df6602c2618937c1da Author: Johannes Ranke Date: 2015-05-08 08:47:11 +0200 Update the Figure in the README commit 8021c7cb9aac06e961227a3c0e0b013ec2d2d501 Author: Johannes Ranke Date: 2015-05-07 16:15:23 +0200 Bugfix: Reset maximum event concentration for each event commit 508d883f7689d617d15915dbd26a27f1613bb857 Author: Johannes Ranke Date: 2015-05-07 12:04:28 +0200 Make quarterly labels for plot.TOXSWA_cwa commit c6e57ab29170266b3038b01c54bf161ab361d440 Author: Johannes Ranke Date: 2015-04-24 02:22:21 +0200 Do not test the path to the zip file commit 7d2096855edcc196629c1c7a9983a56ec6addd1e Author: Johannes Ranke Date: 2015-04-24 02:21:04 +0200 Add a geometric mean function commit bcfe0af7970efe36c3aa661e89953fbe3689c310 Author: Johannes Ranke Date: 2015-04-24 02:20:21 +0200 Clean the Makefile a bit commit 768a043848dd84b9e699916657d0a23b2f3b9e83 Author: Johannes Ranke Date: 2015-04-22 13:48:42 +0200 Fix header formatting commit 04502ca0c658a6c929debd61aee87be8c7eceb04 Author: Johannes Ranke Date: 2015-04-22 13:46:32 +0200 Update markdown version of README commit ec79637749d300ab4ca170805c673905e52d67dd Author: Johannes Ranke Date: 2015-04-22 13:42:10 +0200 Add simplest PEC soil calcs, use testthat commit 8ffbc49b3f01deac6f9e83aaa6d318d4e2f8552b Author: Johannes Ranke Date: 2015-01-23 16:44:04 +0100 Add option to plot relative to maximum commit 8975dc148d0a6f222174980eb60314054be9b6cf Author: Johannes Ranke Date: 2015-01-13 14:54:58 +0100 Fix warning in README commit 891af5d0f1ee8d45cd4403af43293463d23ba96b Author: Johannes Ranke Date: 2015-01-13 14:05:31 +0100 README.rmd with example, fix reading unzipped files commit 4d74570f1ca4a94d894c6c5169684a8246d0a51c Author: Johannes Ranke Date: 2015-01-13 12:58:26 +0100 Correctly initialize R6 fields, read from zip files commit ee070c11f7c7faff2f573d27cf32aafab78971a8 Author: Johannes Ranke Date: 2015-01-07 23:56:54 +0100 Pass ... parameters to added cwa lines commit 92d97ba99d7b90d95a67796cb5e68f28f752b70b Author: Johannes Ranke Date: 2014-12-17 21:39:42 +0100 Initial commit: R6 class for TOXSWA cwa files