diff options
Diffstat (limited to 'R/PELMO_runs.R')
| -rw-r--r-- | R/PELMO_runs.R | 13 |
1 files changed, 12 insertions, 1 deletions
diff --git a/R/PELMO_runs.R b/R/PELMO_runs.R index 0f134e0..b152b4d 100644 --- a/R/PELMO_runs.R +++ b/R/PELMO_runs.R @@ -3,7 +3,7 @@ #' 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{\link{install_PELMO}} from the \code{PELMO.installeR} package +#' 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}. @@ -33,6 +33,8 @@ #' 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 +#' # At the moment I can not run the examples, as my wine installation is not working +#' \dontrun{ #' # Reproduce the official test results for annual application of Pesticide D #' # to winter cereals at the day before emergence #' runs_1 <- list( @@ -54,6 +56,7 @@ #' 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) @@ -410,6 +413,9 @@ evaluate_PELMO <- function(runs, version = "5.5.3", PELMO_base = "auto") } #' Get the application interval in years from a psm file +#' +#' @param psm_file The path to the .psm file +#' @param location_code The location code get_interval <- function(psm_file, location_code) { # How many years do we calculate (26, 46 or 66)? psm <- readLines(psm_file, encoding = "latin1") @@ -433,6 +439,9 @@ get_interval <- function(psm_file, location_code) { } #' Sum up values according to FOCUS periods +#' +#' @param annual The annual flux as obtained by \code{get_flux} +#' @param interval The interval in years sum_periods <- function(annual, interval) { n_years <- switch(as.character(interval), "1" = 26, @@ -446,6 +455,8 @@ sum_periods <- function(annual, interval) { } #' Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file +#' +#' @param chem_file The full path to a CHEM*.PLM file get_flux <- function(chem_file) { chem <- readLines(chem_file) lowest_focus_comp_lines <- grep("^ . 21 ", chem, value = TRUE) |