diff options
Diffstat (limited to 'R/PELMO_runs.R')
| -rw-r--r-- | R/PELMO_runs.R | 30 |
1 files changed, 26 insertions, 4 deletions
diff --git a/R/PELMO_runs.R b/R/PELMO_runs.R index 3d4f03b..e5a78ff 100644 --- a/R/PELMO_runs.R +++ b/R/PELMO_runs.R @@ -12,7 +12,7 @@ #' run directory, holding the results for all FOCUS periods, equivalent to #' the period.plm file generated by the FOCUS PELMO GUI. #' -#' @return If evaluate is TRUE, a list of lists of data frames holding the +#' @return If evaluate is TRUE, a list of lists of matrices holding the #' PEC data. #' @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, @@ -29,7 +29,31 @@ #' @references PELMO.installeR \url{https://jranke.github.io/PELMO.installeR} #' #' Wine \url{https://winehq.org} +#' +#' PELMO test results \url{http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc} #' @export +#' @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 = 6, overwrite = TRUE) +#' ) +#' print(PECgw_1) +#' # We get exactly the same PECgw values (on Linux, calling PELMO using Wine). +#' print(time_1) +#' +#' # 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) PELMO_runs <- function(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "auto", execute = TRUE, cores = getOption("mc.cores", 2L), evaluate = TRUE, overwrite = FALSE) @@ -142,13 +166,11 @@ 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) + run_PELMO(runs, version = version, PELMO_base = PELMO_base, cores = cores) } if (evaluate) { |