From 435e07a6f7fd2599d783fd306ee6d9e08acc0c6b Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 27 Sep 2019 10:00:15 +0200 Subject: 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 --- docs/reference/PELMO_runs.html | 282 ----------------------------------------- 1 file changed, 282 deletions(-) delete mode 100644 docs/reference/PELMO_runs.html (limited to 'docs/reference/PELMO_runs.html') diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html deleted file mode 100644 index 2a75191..0000000 --- a/docs/reference/PELMO_runs.html +++ /dev/null @@ -1,282 +0,0 @@ - - - - - - - - -Set up runs for FOCUS PELMO — PELMO_runs • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
- - - -
- -
-
-
-

Set up runs for FOCUS PELMO

- Source: R/PELMO_runs.R - -
- -
- -

Per default, the runs are not only set up but also executed with FOCUS -PELMO, the results are processed and returned. Currently, only FOCUS PELMO -as installed on Linux (or other Unix systems) -using the install_PELMO from the PELMO.installeR package -maintained on github is supported. In such installations, FOCUS PELMO is -installed into the package installation directory of PELMO.installeR -and run using wine.

- -
- - 
PELMO_runs(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "auto",
-  execute = TRUE, cores = getOption("mc.cores", 2L), evaluate = TRUE,
-  overwrite = FALSE)
-
-run_PELMO(runs, version = "5.5.3", PELMO_base = "auto",
-  cores = getOption("mc.cores", 2L))
-
-evaluate_PELMO(runs, version = "5.5.3", PELMO_base = "auto")
- -

Arguments

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
runs

A list of lists. Each inner lists has an element named 'psm' -that holds the psm string, and elements named using three letter crop acronyms, -as used in FOCUS_PELMO_crops, -that hold character vectors of three letter scenario acronyms -as used in FOCUS_GW_scenarios_2012.

psm_dir

The directory where the psm files are located

version

The FOCUS PELMO version

PELMO_base

Where the FOCUS PELMO installation is located

execute

Should PELMO be executed directly?

cores

The number of cores to execute PELMO runs in parallel

evaluate

Should the results be returned?

overwrite

Should existing run directories be overwritten?

- -

Value

- -

If evaluate is TRUE, a list of lists of matrices holding the - PEC data.

- -

Details

- -

As a side effect, an R data file (period_pfm.rda) is generated in each -run directory, holding the results for all FOCUS periods, equivalent to -the period.plm file generated by the FOCUS PELMO GUI.

- -

References

- -

PELMO.installeR https://pkgdown.jrwb.de/PELMO.installeR

-

Wine https://winehq.org

-

PELMO test results http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc

- - -

Examples

- 
# Reproduce the official test results for annual application of Pesticide D
-# to winter cereals at the day before emergence
-runs_1 <- list(
-  list(psm = 'Pesticide_D',
-       win = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi")),
-  list(psm = 'Pesticide_D_1_day_pre_em_every_third_year',
-       pot = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi")))
-time_1 <- system.time(
-  PECgw_1 <- PELMO_runs(runs_1, psm_dir = system.file("testdata", package = "pfm"),
-    cores = 15, overwrite = TRUE)
-)
-print(PECgw_1)
#> $Pesticide_D
-#> $Pesticide_D$win
-#>     FOCUS DUMMY D
-#> Cha         0.025
-#> Ham         1.621
-#> Jok         0.388
-#> Kre         0.467
-#> Oke         1.608
-#> Pia         0.848
-#> Por         2.386
-#> Sev         0.009
-#> Thi         0.030
-#> 
-#> 
-#> $Pesticide_D_1_day_pre_em_every_third_year
-#> $Pesticide_D_1_day_pre_em_every_third_year$pot
-#>     FOCUS DUMMY D
-#> Cha         0.010
-#> Ham         0.014
-#> Jok         0.009
-#> Kre         0.027
-#> Oke         0.085
-#> Pia         0.051
-#> Por         0.021
-#> Sev         0.000
-#> Thi         0.001
-#> 
-#> 
# We get exactly the same PECgw values (on Linux, calling PELMO using Wine).
-print(time_1)
#>        User      System verstrichen 
-#>       0.395       0.093      30.590 
if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) {
-  cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]]))
-}
#> CPU model: AMD Ryzen 7 1700 Eight-Core Processor

-# Demonstrate some results with metabolites.
-runs_2 <- list(list(psm = 'Pesticide_D_1_May_every_other_year_mets',
-                    win = c("Cha", "Ham", "Kre")))
-PECgw_2 <- PELMO_runs(runs_2, psm_dir = system.file("testdata", package = "pfm"),
-  cores = 3, overwrite = TRUE)
-print(PECgw_2)
#> $Pesticide_D_1_May_every_other_year_mets
-#> $Pesticide_D_1_May_every_other_year_mets$win
-#>     FOCUS DUMMY D      M1    M2
-#> Cha         0.001 126.195 0.000
-#> Ham         0.054  82.196 0.001
-#> Kre         0.103  75.494 0.001
-#> 
-#>
-
- -
- - -
- - - - - - -- cgit v1.2.1