From b935273d651301b271e0cb66bf36c2bbc1d15b32 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 31 Jan 2019 01:40:24 +0100 Subject: Separate out PELMO utilities into rPELMO --- man/PELMO_runs.Rd | 89 ------------------------------------------------------- 1 file changed, 89 deletions(-) delete mode 100644 man/PELMO_runs.Rd (limited to 'man/PELMO_runs.Rd') diff --git a/man/PELMO_runs.Rd b/man/PELMO_runs.Rd deleted file mode 100644 index 6021613..0000000 --- a/man/PELMO_runs.Rd +++ /dev/null @@ -1,89 +0,0 @@ -% 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} -} -- cgit v1.2.1