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-% Generated by roxygen2: do not edit by hand
-% 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'
-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{execute}{Should PELMO be executed directly?}
-
-\item{cores}{The number of cores to execute PELMO runs in parallel}
-
-\item{evaluate}{Should the results be returned?}
-
-\item{overwrite}{Should existing run directories be overwritten?}
-}
-\value{
-If evaluate is TRUE, a list of lists of matrices holding the
-  PEC data.
-}
-\description{
-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 \code{install_PELMO} from the \code{PELMO.installeR} package
-maintained on github is supported. In such installations, FOCUS PELMO is
-installed into the package installation directory of \code{PELMO.installeR}
-and run using \code{wine}.
-}
-\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.
-}
-\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)
-# We get exactly the same PECgw values (on Linux, calling PELMO using Wine).
-print(time_1)
-if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) {
-  cat(gsub("model name\\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[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)
-}
-\references{
-PELMO.installeR \url{https://pkgdown.jrwb.de/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}
-}