From a6c13f70f6c6669a8088827a602ac475fdf9b624 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 29 Jan 2017 16:58:53 +0100 Subject: Setting up PELMO runs, execution and evaluation It all works! --- ChangeLog | 29 +++++ DESCRIPTION | 2 +- NAMESPACE | 2 + R/FOCUS_PELMO_data.R | 14 +-- R/PELMO_runs.R | 163 +++++++++++++++++++++---- _pkgdown.yml | 3 + docs/reference/FOCUS_GW_scenarios_2012.html | 10 +- docs/reference/FOCUS_PELMO_crop_sze_names.html | 121 ++++++++++++++++++ docs/reference/FOCUS_PELMO_crops.html | 132 ++++++++++++++++++++ docs/reference/FOCUS_PELMO_location_codes.html | 113 +++++++++++++++++ docs/reference/PELMO_path.html | 112 +++++++++++++++++ docs/reference/PELMO_runs.html | 144 ++++++++++++++++++++++ docs/reference/create_run_list.html | 116 ++++++++++++++++++ docs/reference/evaluate_PELMO.html | 116 ++++++++++++++++++ docs/reference/focus_80th.html | 113 +++++++++++++++++ docs/reference/get_flux.html | 101 +++++++++++++++ docs/reference/get_interval.html | 101 +++++++++++++++ docs/reference/index.html | 11 +- docs/reference/run_PELMO.html | 119 ++++++++++++++++++ docs/reference/sum_periods.html | 101 +++++++++++++++ man/FOCUS_PELMO_crops.Rd | 4 +- man/PELMO_runs.Rd | 17 ++- man/focus_80th.Rd | 19 +++ man/get_flux.Rd | 11 ++ man/get_interval.Rd | 11 ++ man/run_PELMO.Rd | 27 ---- man/sum_periods.Rd | 11 ++ tests/testthat/test_PELMO.R | 74 ++++++++--- 28 files changed, 1717 insertions(+), 80 deletions(-) create mode 100644 docs/reference/FOCUS_PELMO_crop_sze_names.html create mode 100644 docs/reference/FOCUS_PELMO_crops.html create mode 100644 docs/reference/FOCUS_PELMO_location_codes.html create mode 100644 docs/reference/PELMO_path.html create mode 100644 docs/reference/PELMO_runs.html create mode 100644 docs/reference/create_run_list.html create mode 100644 docs/reference/evaluate_PELMO.html create mode 100644 docs/reference/focus_80th.html create mode 100644 docs/reference/get_flux.html create mode 100644 docs/reference/get_interval.html create mode 100644 docs/reference/run_PELMO.html create mode 100644 docs/reference/sum_periods.html create mode 100644 man/focus_80th.Rd create mode 100644 man/get_flux.Rd create mode 100644 man/get_interval.Rd delete mode 100644 man/run_PELMO.Rd create mode 100644 man/sum_periods.Rd diff --git a/ChangeLog b/ChangeLog index 762acf3..38beb77 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,32 @@ +commit 15c1b8c5ddadf938ce13d3dd9da2a09d8749f740 +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 diff --git a/DESCRIPTION b/DESCRIPTION index 81f8df2..97b5962 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling Version: 0.4-2 -Date: 2017-01-27 +Date: 2017-01-29 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph")) Description: Utilities for simple calculations of predicted environmental diff --git a/NAMESPACE b/NAMESPACE index c795c89..feb5ca7 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -26,6 +26,8 @@ export(SFO_actual_twa) export(SSLRC_mobility_classification) export(TOXSWA_cwa) export(endpoint) +export(evaluate_PELMO) +export(focus_80th) export(geomean) export(max_twa) export(one_box) diff --git a/R/FOCUS_PELMO_data.R b/R/FOCUS_PELMO_data.R index 28888e7..89fe5f6 100644 --- a/R/FOCUS_PELMO_data.R +++ b/R/FOCUS_PELMO_data.R @@ -2,10 +2,10 @@ #' #' A named character vector with the crop names used in the PELMO 5.5.3 GUI. #' For the names, three letter codes were constructed by generally taking the -#' first three letters in lower case. Only when there is an expression in -#' parentheses, the first letter of this expression becomes the first letter +#' first three letters in lower case. Only when there is an expression in +#' parentheses, the first letter of this expression becomes the first letter #' in the three letter code, i.e. 'Peas (animals)' has the code \code{ape}. -#' +#' #' @docType data #' @export #' @examples @@ -37,13 +37,13 @@ FOCUS_PELMO_crops = c( tom = "Tomatoes", vin = "Vines") -#' FOCUS PELMO crop acronyms used for naming sceneario files +#' FOCUS PELMO crop acronyms used for naming sceneario files #' #' A named character vector with the crop acronyms used in FOCUS PELMO 5.5.3 #' for naming the .sze files located in the FOCUS directory. The crop acronyms #' in the file names are sometimes capitalized, sometimes not. The scenario #' files used for Beans (field) and Beans (vegetable) are the same. -#' +#' #' @docType data #' @export #' @examples @@ -85,6 +85,6 @@ FOCUS_PELMO_crop_sze_names = c( #' @examples #' print(FOCUS_PELMO_location_codes) FOCUS_PELMO_location_codes = c( - Cha = "C", Ham = "H", Jok = "J", - Kre = "K", Oke = "N", Pia = "P", + Cha = "C", Ham = "H", Jok = "J", + Kre = "K", Oke = "N", Pia = "P", Por = "O", Sev = "S", Thi = "T") diff --git a/R/PELMO_runs.R b/R/PELMO_runs.R index f599110..5d401ea 100644 --- a/R/PELMO_runs.R +++ b/R/PELMO_runs.R @@ -1,7 +1,10 @@ #' Set up runs for FOCUS PELMO #' #' Per default, the runs are also executed with FOCUS PELMO, and the results are processed -#' and returned. +#' and returned. Currently, only FOCUS PELMO as installed on Linux (or other Unix systems) +#' using the \code{\link{install_PELMO}} from the \code{PELMO.installeR} package +#' maintained on github is supported. In such installations, FOCUS PELMO is installed into +#' package installation directory of \code{PELMO.installeR} and run with \code{wine}. #' #' @param 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, @@ -15,6 +18,9 @@ #' @param cores The number of cores to execute PELMO runs in parallel #' @param evaluate Should the results be returned? #' @param overwrite Should an existing run directories be overwritten +#' @references PELMO.installeR \url{https://jranke.github.io/PELMO.installeR} +#' +#' Wine \url{https://winehq.org} #' @export PELMO_runs <- function(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "auto", execute = TRUE, cores = getOption("mc.cores", 2L), @@ -80,26 +86,9 @@ PELMO_runs <- function(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "aut add <- function(x) cat(paste0(x, "\r\n"), file = input_file, append = TRUE) - # How many years do we calculate (26, 46 or 66)? - psm <- readLines(psm_file, encoding = "latin1") - number_of_apps_lines <- grep("number of application location", psm) - absolute_apps_line <- grep(location_code, - psm[number_of_apps_lines]) - period <- 1 # application every year - if (length(absolute_apps_line) == 1) { - apps_root <- number_of_apps_lines[absolute_apps_line] - } else { - apps_root <- number_of_apps_lines[1] - } - - number_of_apps <- as.integer(substr(psm[apps_root], 1, 3)) - last_app_line <- psm[apps_root + number_of_apps] - last_app_year <- as.integer(gsub("^.{2,3} .. (..) .*", "\\1", - last_app_line)) - if (last_app_year > 26) period <- 2 - if (last_app_year > 46) period <- 3 + interval <- get_interval(psm_file, location_code) - n_years <- switch(as.character(period), + n_years <- switch(as.character(interval), "1" = 26, "2" = 46, "3" = 66) @@ -145,18 +134,23 @@ PELMO_runs <- function(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "aut # the exe file from this directory file.copy(file.path(PELMO_base, "lf90.eer"), run_dir) } + run_list[[7]] + setup_run(run_list[[7]]) lapply(run_list, setup_run) if (execute) { run_PELMO(runs, version = version, PELMO_base = PELMO_base) } + + if (evaluate) { + evaluate_PELMO(runs, version = version, PELMO_base = PELMO_base) + } } -#' Run PELMO -#' #' @inheritParams PELMO_runs #' @importFrom parallel mclapply +#' @rdname PELMO_runs #' @export run_PELMO <- function(runs, version = "5.5.3", PELMO_base = "auto", cores = getOption("mc.cores", 2L)) @@ -295,3 +289,128 @@ create_run_list <- function(runs, psm_dir = ".", check_psm_files = FALSE) { } return(run_list) } + +#' @rdname PELMO_runs +#' @inheritParams PELMO_runs +#' @importFrom parallel mclapply +#' @export +evaluate_PELMO <- function(runs, version = "5.5.3", PELMO_base = "auto") +{ + + if (PELMO_base[1] == "auto") { + PELMO_base = file.path(system.file(package = "PELMO.installeR"), + paste0("FOCUSPELMO.", gsub("\\.", "", version))) + } + + for (run in runs) { + psm <- run$psm + crops <- setdiff(names(run), "psm") + for (crop in crops) { + for (scenario in run[[crop]]) { + run_dir <- file.path(PELMO_base, "FOCUS", PELMO_path(psm, crop, scenario)) + echo_file <- readLines(file.path(run_dir, "ECHO.PLM"), encoding = "latin1") + parm_lines <- grep("\\*\\*\\* PARAMETERS OF", echo_file, value = TRUE) + acronyms <- gsub(".*\\((.*)\\).*", "\\1", parm_lines) + met_codes <- gsub(".*METABOLITE (..).*", "\\1", parm_lines) + met_codes[1] <- NA + names(met_codes) <- acronyms + + psm_file <- file.path(run_dir, paste0(psm, ".psm")) + location_code <- FOCUS_PELMO_location_codes[scenario] + interval <- get_interval(psm_file, location_code) + + # Get percolate for each period + wasser <- readLines(file.path(run_dir, "WASSER.PLM")) + percolate_lines <- grep("RECHARGE BELOW ROOT ZONE", wasser, value = TRUE) + percolate <- as.numeric(substr(percolate_lines, 40, 46)) + percolate_period <- sum_periods(percolate, interval) + + # Set up results that should match period.plm generated by the PELMO GUI + results_pfm <- list() + for (acronym in acronyms) { + results_pfm[[acronym]] <- list() + periods <- data.frame( + period = 1:20, + flux = NA, + percolate = 10 * percolate_period, + conc = NA) + + if (is.na(met_codes[acronym])) { + chem_file <- file.path(run_dir, "CHEM.PLM") + } else { + chem_file <- file.path(run_dir, paste0("CHEM_", met_codes[acronym], ".PLM")) + } + + annual_flux <- get_flux(chem_file) + periods$flux <- sum_periods(annual_flux, interval) * 1000 + + periods$conc <- 100 * periods$flux / periods$percolate + + results_pfm[[acronym]]$periods <- periods + results_pfm[[acronym]]$focus <- focus_80th(periods$conc) + } + save(results_pfm, file = file.path(run_dir, "period_pfm.rda")) + } + } + } +} + +#' Get the application interval in years from a psm file +get_interval <- function(psm_file, location_code) { + # How many years do we calculate (26, 46 or 66)? + psm <- readLines(psm_file, encoding = "latin1") + number_of_apps_lines <- grep("number of application location", psm) + absolute_apps_line <- grep(location_code, + psm[number_of_apps_lines]) + interval <- 1 # application every year + if (length(absolute_apps_line) == 1) { + apps_root <- number_of_apps_lines[absolute_apps_line] + } else { + apps_root <- number_of_apps_lines[1] + } + + number_of_apps <- as.integer(substr(psm[apps_root], 1, 3)) + last_app_line <- psm[apps_root + number_of_apps] + last_app_year <- as.integer(gsub("^.{2,3} .. (..) .*", "\\1", + last_app_line)) + if (last_app_year > 26) interval <- 2 + if (last_app_year > 46) interval <- 3 + return(interval) +} + +#' Sum up values according to FOCUS periods +sum_periods <- function(annual, interval) { + n_years <- switch(as.character(interval), + "1" = 26, + "2" = 46, + "3" = 66) + period_start_years <- seq(from = 7, to = n_years, by = interval) + sapply(1:20, function(x) { + years_i <- period_start_years[x] + (0 : (interval - 1)) + sum(annual[years_i]) + }) +} + +#' Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file +get_flux <- function(chem_file) { + chem <- readLines(chem_file) + lowest_focus_comp_lines <- grep("^ . 21 ", chem, value = TRUE) + lowest_focus_comp <- read.table(text = lowest_focus_comp_lines) + return(lowest_focus_comp$V9) +} + +#' Calculate the 80th percentile according to FOCUS guidance +#' +#' This is nowadays defined as the mean of the 16th and the 17th +#' highest value. Previously, the 17th highest values was used (FOCUS 2014, p. +#' 18). NaN values need to be set to zero in order to reproduce the +#' values obtained by PELMO. +#' @param c_period A numeric vector of values to calculate the percentile from +#' @param old Should the old calculation method be used (the 17th highest value)? +#' @export +focus_80th <- function(c_period, old = FALSE) { + c_period <- ifelse(is.na(c_period), 0, c_period) + c_period_sorted <- sort(c_period) + if (old) return(c_period_sorted[17]) + else return(mean(c_period_sorted[c(16, 17)])) +} diff --git a/_pkgdown.yml b/_pkgdown.yml index ff5f43d..829ba48 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -17,6 +17,9 @@ reference: contents: - PEC_soil - soil_scenario_data_EFSA_2015 + - title: Predicted environmental concentrations in groundwater + contents: + - PELMO_runs - title: Predicted environmental concentrations in surface water contents: - PEC_sw_drift diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html index 64b42e9..fbc1649 100644 --- a/docs/reference/FOCUS_GW_scenarios_2012.html +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -70,10 +70,16 @@ -

Currently, only a small subset of the soil definitions are provided.

+

Currently, only scenario names with acronyms and a small subset of the soil definitions are provided. The +soil definitions are from page 46ff. from FOCUS (2012).

+ 
FOCUS_GW_scenarios_2012
+

Format

+ +

An object of class list of length 2.

+

References

FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. @@ -147,6 +153,8 @@

Contents

    +
  • Format
    • +
  • References
  • Examples
    • diff --git a/docs/reference/FOCUS_PELMO_crop_sze_names.html b/docs/reference/FOCUS_PELMO_crop_sze_names.html new file mode 100644 index 0000000..5777868 --- /dev/null +++ b/docs/reference/FOCUS_PELMO_crop_sze_names.html @@ -0,0 +1,121 @@ + + + + + + + + +FOCUS PELMO crop acronyms used for naming sceneario files — FOCUS_PELMO_crop_sze_names • pfm + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    FOCUS PELMO crop acronyms used for naming sceneario files

    +
    + + +

    A named character vector with the crop acronyms used in FOCUS PELMO 5.5.3 +for naming the .sze files located in the FOCUS directory. The crop acronyms +in the file names are sometimes capitalized, sometimes not. The scenario +files used for Beans (field) and Beans (vegetable) are the same.

    + + + 
    FOCUS_PELMO_crop_sze_names
    + +

    Format

    + +

    An object of class character of length 25.

    + + +

    Examples

    + 
    print(FOCUS_PELMO_crop_sze_names)
    #>      app      gra      pot      sug      win      fbe      vbe      bus 
+#> "apples"  "grass" "potato" "sbeets" "wcerea"  "beans"  "beans"  "bushb" 
+#>      cab      car      cit      cot      lin      mai      soi      woi 
+#> "cabbag" "carrot" "citrus" "cotton"  "linse"  "maize" "rapesu" "rapewi" 
+#>      oni      ape      soy      spr      str      sun      tob      tom 
+#> "onions"   "peas"   "soyb" "scerea" "strawb" "sunflo" "tobacc" "tomato" 
+#>      vin 
+#>  "vines"
    +
    + +
    + +
    +
    +

    Developed by Johannes Ranke.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + diff --git a/docs/reference/FOCUS_PELMO_crops.html b/docs/reference/FOCUS_PELMO_crops.html new file mode 100644 index 0000000..d9ad8d2 --- /dev/null +++ b/docs/reference/FOCUS_PELMO_crops.html @@ -0,0 +1,132 @@ + + + + + + + + +FOCUS PELMO crop names — FOCUS_PELMO_crops • pfm + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    FOCUS PELMO crop names

    +
    + + +

    A named character vector with the crop names used in the PELMO 5.5.3 GUI. +For the names, three letter codes were constructed by generally taking the +first three letters in lower case. Only when there is an expression in +parentheses, the first letter of this expression becomes the first letter +in the three letter code, i.e. 'Peas (animals)' has the code ape.

    + + + 
    FOCUS_PELMO_crops
    + +

    Format

    + +

    An object of class character of length 25.

    + + +

    Examples

    + 
    print(FOCUS_PELMO_crops)
    #>                      app                      gra                      pot 
+#>                 "Apples"      "Grass and alfalfa"               "Potatoes" 
+#>                      sug                      win                      fbe 
+#>            "Sugar beets"         "Winter cereals"          "Beans (field)" 
+#>                      vbe                      bus                      cab 
+#>     "Beans (vegetables)"            "Bushberries"                "Cabbage" 
+#>                      car                      cit                      cot 
+#>                "Carrots"                 "Citrus"                 "Cotton" 
+#>                      lin                      mai                      soi 
+#>                "Linseed"                  "Maize" "Oil seed rape (summer)" 
+#>                      woi                      oni                      ape 
+#> "Oil seed rape (winter)"                 "Onions"         "Peas (animals)" 
+#>                      soy                      spr                      str 
+#>               "Soybeans"         "Spring cereals"           "Strawberries" 
+#>                      sun                      tob                      tom 
+#>              "Sunflower"                "Tobacco"               "Tomatoes" 
+#>                      vin 
+#>                  "Vines"
    +
    + +
    + +
    +
    +

    Developed by Johannes Ranke.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + diff --git a/docs/reference/FOCUS_PELMO_location_codes.html b/docs/reference/FOCUS_PELMO_location_codes.html new file mode 100644 index 0000000..8051d42 --- /dev/null +++ b/docs/reference/FOCUS_PELMO_location_codes.html @@ -0,0 +1,113 @@ + + + + + + + + +Location codes in FOCUS PELMO — FOCUS_PELMO_location_codes • pfm + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Location codes in FOCUS PELMO

    +
    + + +

    A named character vector of one letter location codes used in FOCUS PELMO, +indexed by three letter acronyms.

    + + + 
    FOCUS_PELMO_location_codes
    + +

    Format

    + +

    An object of class character of length 9.

    + + +

    Examples

    + 
    print(FOCUS_PELMO_location_codes)
    #> Cha Ham Jok Kre Oke Pia Por Sev Thi 
+#> "C" "H" "J" "K" "N" "P" "O" "S" "T"
    +
    + +
    + +
    +
    +

    Developed by Johannes Ranke.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + diff --git a/docs/reference/PELMO_path.html b/docs/reference/PELMO_path.html new file mode 100644 index 0000000..79aa89d --- /dev/null +++ b/docs/reference/PELMO_path.html @@ -0,0 +1,112 @@ + + + + + + + + +Create a path of run directories as the PELMO GUI does — PELMO_path • pfm + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Create a path of run directories as the PELMO GUI does

    +
    + + +

    Create a path of run directories as the PELMO GUI does

    + + + 
    PELMO_path(psm, crop, scenario)
    + +

    Arguments

    +
    +
    psm
    +
    The psm identifier
    +
    crop
    +
    The PELMO crop acronym
    +
    scenario
    +
    The scenario
    +
    + + +
    + +
    + +
    +
    +

    Developed by Johannes Ranke.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html new file mode 100644 index 0000000..e872196 --- /dev/null +++ b/docs/reference/PELMO_runs.html @@ -0,0 +1,144 @@ + + + + + + + + +Set up runs for FOCUS PELMO — PELMO_runs • pfm + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Set up runs for FOCUS PELMO

    +
    + + +

    Per default, the runs are also executed with FOCUS PELMO, and 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 +package installation directory of PELMO.installeR and run with 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 an existing run directories be overwritten
    +
    + +

    References

    + +

    PELMO.installeR https://jranke.github.io/PELMO.installeR

    +

    Wine https://winehq.org

    + + +
    + +
    + +
    +
    +

    Developed by Johannes Ranke.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + diff --git a/docs/reference/create_run_list.html b/docs/reference/create_run_list.html new file mode 100644 index 0000000..b2c9798 --- /dev/null +++ b/docs/reference/create_run_list.html @@ -0,0 +1,116 @@ + + + + + + + + +Create a list of runs that we can traverse — create_run_list • pfm + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Create a list of runs that we can traverse

    +
    + + +

    Create a list of runs that we can traverse

    + + + 
    create_run_list(runs, psm_dir = ".", check_psm_files = FALSE)
    + +

    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
    +
    check_psm_files
    +
    Should we check if the psm file exists
    +
    + + +
    + +
    + +
    +
    +

    Developed by Johannes Ranke.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + diff --git a/docs/reference/evaluate_PELMO.html b/docs/reference/evaluate_PELMO.html new file mode 100644 index 0000000..58e7843 --- /dev/null +++ b/docs/reference/evaluate_PELMO.html @@ -0,0 +1,116 @@ + + + + + + + + +Evaluate PELMO runs — evaluate_PELMO • pfm + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Evaluate PELMO runs

    +
    + + +

    Evaluate PELMO runs

    + + + 
    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.
    +
    version
    +
    The FOCUS PELMO version
    +
    PELMO_base
    +
    Where the FOCUS PELMO installation is located
    +
    + + +
    + +
    + +
    +
    +

    Developed by Johannes Ranke.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + diff --git a/docs/reference/focus_80th.html b/docs/reference/focus_80th.html new file mode 100644 index 0000000..8160746 --- /dev/null +++ b/docs/reference/focus_80th.html @@ -0,0 +1,113 @@ + + + + + + + + +Calculate the 80th percentile according to FOCUS guidance — focus_80th • pfm + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Calculate the 80th percentile according to FOCUS guidance

    +
    + + +

    This is nowadays defined as the mean of the 16th and the 17th +highest value. Previously, the 17th highest values was used (FOCUS 2014, p. +18). NaN values need to be set to zero in order to reproduce the +values obtained by PELMO.

    + + + 
    focus_80th(c_period, old = FALSE)
    + +

    Arguments

    +
    +
    c_period
    +
    A numeric vector of values to calculate the percentile from
    +
    old
    +
    Should the old calculation method be used (the 17th highest value)?
    +
    + + +
    + +
    + +
    +
    +

    Developed by Johannes Ranke.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + diff --git a/docs/reference/get_flux.html b/docs/reference/get_flux.html new file mode 100644 index 0000000..64ea25e --- /dev/null +++ b/docs/reference/get_flux.html @@ -0,0 +1,101 @@ + + + + + + + + +Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file — get_flux • pfm + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file

    +
    + + +

    Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file

    + + + 
    get_flux(chem_file)
    + + +
    + +
    + +
    +
    +

    Developed by Johannes Ranke.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + diff --git a/docs/reference/get_interval.html b/docs/reference/get_interval.html new file mode 100644 index 0000000..13171c1 --- /dev/null +++ b/docs/reference/get_interval.html @@ -0,0 +1,101 @@ + + + + + + + + +Get the application interval in years from a psm file — get_interval • pfm + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Get the application interval in years from a psm file

    +
    + + +

    Get the application interval in years from a psm file

    + + + 
    get_interval(psm_file, location_code)
    + + +
    + +
    + +
    +
    +

    Developed by Johannes Ranke.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 8f57cd2..33713b6 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -67,7 +67,7 @@

    Function reference

    -

    version 0.4-1

    +

    version 0.4-2

    @@ -116,6 +116,14 @@

    Properties of the predefined scenarios from the EFSA guidance from 2015

    +

    Predicted environmental concentrations in groundwater

    +

    + + +

    Set up runs for FOCUS PELMO

    +

    Predicted environmental concentrations in surface water

    @@ -173,6 +181,7 @@ diff --git a/docs/reference/run_PELMO.html b/docs/reference/run_PELMO.html new file mode 100644 index 0000000..067d3c1 --- /dev/null +++ b/docs/reference/run_PELMO.html @@ -0,0 +1,119 @@ + + + + + + + + +Run PELMO — run_PELMO • pfm + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Run PELMO

    +
    + + +

    Run PELMO

    + + + 
    run_PELMO(runs, version = "5.5.3", PELMO_base = "auto",
+  cores = getOption("mc.cores", 2L))
    + +

    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.
    +
    version
    +
    The FOCUS PELMO version
    +
    PELMO_base
    +
    Where the FOCUS PELMO installation is located
    +
    cores
    +
    The number of cores to execute PELMO runs in parallel
    +
    + + +
    + +
    + +
    +
    +

    Developed by Johannes Ranke.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + diff --git a/docs/reference/sum_periods.html b/docs/reference/sum_periods.html new file mode 100644 index 0000000..66466ac --- /dev/null +++ b/docs/reference/sum_periods.html @@ -0,0 +1,101 @@ + + + + + + + + +Sum up values according to FOCUS periods — sum_periods • pfm + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Sum up values according to FOCUS periods

    +
    + + +

    Sum up values according to FOCUS periods

    + + + 
    sum_periods(annual, interval)
    + + +
    + +
    + + +
    + + + diff --git a/man/FOCUS_PELMO_crops.Rd b/man/FOCUS_PELMO_crops.Rd index f6a41b4..91a010a 100644 --- a/man/FOCUS_PELMO_crops.Rd +++ b/man/FOCUS_PELMO_crops.Rd @@ -11,8 +11,8 @@ FOCUS_PELMO_crops \description{ A named character vector with the crop names used in the PELMO 5.5.3 GUI. For the names, three letter codes were constructed by generally taking the -first three letters in lower case. Only when there is an expression in -parentheses, the first letter of this expression becomes the first letter +first three letters in lower case. Only when there is an expression in +parentheses, the first letter of this expression becomes the first letter in the three letter code, i.e. 'Peas (animals)' has the code \code{ape}. } \examples{ diff --git a/man/PELMO_runs.Rd b/man/PELMO_runs.Rd index 71fe6ef..1d81e6d 100644 --- a/man/PELMO_runs.Rd +++ b/man/PELMO_runs.Rd @@ -2,11 +2,18 @@ % Please edit documentation in R/PELMO_runs.R \name{PELMO_runs} \alias{PELMO_runs} +\alias{run_PELMO} +\alias{evaluate_PELMO} \title{Set up runs for FOCUS PELMO} \usage{ 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{ \item{runs}{A list of lists. Each inner lists has an element named 'psm' @@ -31,5 +38,13 @@ as used in \code{\link{FOCUS_GW_scenarios_2012}}.} } \description{ Per default, the runs are also executed with FOCUS PELMO, and the results are processed -and returned. +and returned. Currently, only FOCUS PELMO as installed on Linux (or other Unix systems) +using the \code{\link{install_PELMO}} from the \code{PELMO.installeR} package +maintained on github is supported. In such installations, FOCUS PELMO is installed into +package installation directory of \code{PELMO.installeR} and run with \code{wine}. +} +\references{ +PELMO.installeR \url{https://jranke.github.io/PELMO.installeR} + +Wine \url{https://winehq.org} } diff --git a/man/focus_80th.Rd b/man/focus_80th.Rd new file mode 100644 index 0000000..8436791 --- /dev/null +++ b/man/focus_80th.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/PELMO_runs.R +\name{focus_80th} +\alias{focus_80th} +\title{Calculate the 80th percentile according to FOCUS guidance} +\usage{ +focus_80th(c_period, old = FALSE) +} +\arguments{ +\item{c_period}{A numeric vector of values to calculate the percentile from} + +\item{old}{Should the old calculation method be used (the 17th highest value)?} +} +\description{ +This is nowadays defined as the mean of the 16th and the 17th +highest value. Previously, the 17th highest values was used (FOCUS 2014, p. +18). NaN values need to be set to zero in order to reproduce the +values obtained by PELMO. +} diff --git a/man/get_flux.Rd b/man/get_flux.Rd new file mode 100644 index 0000000..93778cb --- /dev/null +++ b/man/get_flux.Rd @@ -0,0 +1,11 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/PELMO_runs.R +\name{get_flux} +\alias{get_flux} +\title{Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file} +\usage{ +get_flux(chem_file) +} +\description{ +Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file +} diff --git a/man/get_interval.Rd b/man/get_interval.Rd new file mode 100644 index 0000000..a751996 --- /dev/null +++ b/man/get_interval.Rd @@ -0,0 +1,11 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/PELMO_runs.R +\name{get_interval} +\alias{get_interval} +\title{Get the application interval in years from a psm file} +\usage{ +get_interval(psm_file, location_code) +} +\description{ +Get the application interval in years from a psm file +} diff --git a/man/run_PELMO.Rd b/man/run_PELMO.Rd deleted file mode 100644 index a286c5c..0000000 --- a/man/run_PELMO.Rd +++ /dev/null @@ -1,27 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/PELMO_runs.R -\name{run_PELMO} -\alias{run_PELMO} -\title{Run PELMO} -\usage{ -run_PELMO(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "auto", - cores = getOption("mc.cores", 2L)) -} -\arguments{ -\item{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 \code{\link{FOCUS_PELMO_crops}}, -that hold character vectors of three letter scenario acronyms -as used in \code{\link{FOCUS_GW_scenarios_2012}}.} - -\item{psm_dir}{The directory where the psm files are located} - -\item{version}{The FOCUS PELMO version} - -\item{PELMO_base}{Where the FOCUS PELMO installation is located} - -\item{cores}{The number of cores to execute PELMO runs in parallel} -} -\description{ -Run PELMO -} diff --git a/man/sum_periods.Rd b/man/sum_periods.Rd new file mode 100644 index 0000000..5051af4 --- /dev/null +++ b/man/sum_periods.Rd @@ -0,0 +1,11 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/PELMO_runs.R +\name{sum_periods} +\alias{sum_periods} +\title{Sum up values according to FOCUS periods} +\usage{ +sum_periods(annual, interval) +} +\description{ +Sum up values according to FOCUS periods +} diff --git a/tests/testthat/test_PELMO.R b/tests/testthat/test_PELMO.R index 7b7e2b6..ab0e37a 100644 --- a/tests/testthat/test_PELMO.R +++ b/tests/testthat/test_PELMO.R @@ -17,40 +17,33 @@ runs <- list( pot = c("Cha", "Ham")), list( psm = "Pesticide_D_1_May_every_other_year_mets", - mai = c("Cha"))) - + win = names(FOCUS_GW_scenarios_2012$names))) test_that("PELMO paths are correctly created", { psm_paths = c( PELMO_path(runs[[1]]$psm, "fbe", "Por"), PELMO_path(runs[[2]]$psm, "pot", "Ham"), - PELMO_path(runs[[3]]$psm, "mai", "Cha")) + PELMO_path(runs[[3]]$psm, "win", "Cha")) - # Check for psm files and put them into PELMO_base - psm_new_locations <- character(0) for (i in seq_along(psm_paths)) { psm_file <- file.path(test_dir, psm_paths[i], paste0(runs[[i]]$psm, ".psm")) expect_true(file.exists(psm_file)) psm_new_location <- file.path(PELMO_base, basename(psm_file)) - psm_new_locations[i] <- psm_new_location - file.copy(psm_file, psm_new_location) + file.copy(psm_file, psm_new_location, overwrite = TRUE) } }) test_that("PELMO runs are correctly set up", { # Prepare runs in analogy to the test archive - PELMO_runs(runs, psm_dir = PELMO_base, execute = FALSE, overwrite = TRUE) + PELMO_runs(runs, psm_dir = PELMO_base, execute = FALSE, evaluate = FALSE, overwrite = TRUE) # Check that input files are correctly generated in the right location for (run in runs) { psm <- run$psm - # message(psm) crops <- setdiff(names(run), "psm") for (crop in crops) { - # message(crop) for (scenario in run[[crop]]) { - # message(scenario) pp <- PELMO_path(psm, crop, scenario) input_new <- readLines(file.path(PELMO_base, "FOCUS", pp, "pelmo.inp")) @@ -64,7 +57,7 @@ test_that("PELMO runs are correctly set up", { }) test_that("PELMO runs can be run and give the expected result files", { - run_PELMO(runs, cores = 5) + run_PELMO(runs, cores = 7) plm_files <- c("CHEM.PLM", "ECHO.PLM", "KONZCHEM.PLM", "KONZC_A1", "KONZC_B1", @@ -75,9 +68,7 @@ test_that("PELMO runs can be run and give the expected result files", { psm <- run$psm crops <- setdiff(names(run), "psm") for (crop in crops) { - # message(crop) for (scenario in run[[crop]]) { - # message(scenario) pp <- PELMO_path(psm, crop, scenario) for (plm in plm_files) { @@ -95,10 +86,57 @@ test_that("PELMO runs can be run and give the expected result files", { }) test_that("PELMO runs are correctly evaluated", { - evaluate_PELMO(runs, psm_dir = PELMO_base) + results <- evaluate_PELMO(runs) + # Check that if output is the same as in the test archive + for (run in runs) { + psm <- run$psm + crops <- setdiff(names(run), "psm") + for (crop in crops) { + for (scenario in run[[crop]]) { + pp <- PELMO_path(psm, crop, scenario) -}) + period_file <- readLines(file.path(test_dir, pp, "period.plm"), encoding = "latin1") + + result_lines <- grep("^\tResults for.*in the percolate at 1 m soil depth$", period_file) + acronyms <- gsub(".*\\((.*)\\).*", "\\1", period_file[result_lines]) + names(result_lines) <- acronyms + + results <- list() + for (acronym in acronyms) { + results[[acronym]] <- list() + conc_lines <- result_lines[acronym] + 5:24 + tmp <- read.table(text = period_file[conc_lines], sep = "\t") + results[[acronym]]$periods <- data.frame( + period = as.integer(tmp$V2), + flux = tmp$V3, + percolate = tmp$V4, + conc = tmp$V5) + tmp80 <- read.table(text = period_file[result_lines[acronym] + 27], sep = "\t") + results[[acronym]]$focus <- tmp80[[1, "V5"]] + } -# Clean up -unlink(psm_new_locations) + period_pfm_file <- file.path(PELMO_base, "FOCUS", pp, "period_pfm.rda") + load(period_pfm_file) + + # Test for equality of all the components separately, + # as we need to adapt the tolerance + for (acronym in acronyms) { + p_pelmo <- results[[acronym]]$periods + p_test <- results_pfm[[acronym]]$periods + expect_equal(p_test$flux, p_pelmo$flux, tol = 1e-6, scale = 1) + expect_equal(p_test$percolate, p_pelmo$percolate) + # PELMO sets the concentration to 0 when the percolate is zero. + # We get NaN, which is more reasonable, but we need to + # take this into account for testing + p_test$conc <- ifelse(is.na(p_test$conc), 0, p_test$conc) + expect_equal(p_test$conc, p_pelmo$conc, tol = 1e-3, scale = 1) + + # FOCUS PEC + expect_equal(results_pfm[[acronym]]$focus, results[[acronym]]$focus, + tol = 1e-3, scale = 1) + } + } + } + } +}) -- cgit v1.2.1