Set up FOCUS PELMO runs and run them in parallel

- This works on Linux using wine
- PELMO runs (including pelmo.inp files) are correctly generated
- The PLM files for FOCUS Pesticide_D in the test data archive are
  correctly reproduced
- The data files (including FOCUS groundwater scenario data) are now
  created and documented in R files

8 files changed, 169 insertions, 1 deletions

diff --git a/man/FOCUS_GW_scenarios_2012.Rd b/man/FOCUS_GW_scenarios_2012.Rd
index f2417d9..a19bbe5 100644
--- a/man/FOCUS_GW_scenarios_2012.Rd
+++ b/man/FOCUS_GW_scenarios_2012.Rd
@@ -1,10 +1,16 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/FOCUS_GW_scenarios_2012.R
+\docType{data}
 \name{FOCUS_GW_scenarios_2012}
 \alias{FOCUS_GW_scenarios_2012}
 \title{A very small subset of the FOCUS Groundwater scenario defitions}
+\format{An object of class \code{list} of length 2.}
+\usage{
+FOCUS_GW_scenarios_2012
+}
 \description{
-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).
 }
 \examples{
 FOCUS_GW_scenarios_2012
@@ -14,3 +20,4 @@ FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version
  FOrum for the Co-ordination of pesticde fate models and their USe. 
  http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf
 }
+\keyword{datasets}
diff --git a/man/FOCUS_PELMO_crop_sze_names.Rd b/man/FOCUS_PELMO_crop_sze_names.Rd
new file mode 100644
index 0000000..180c011
--- /dev/null
+++ b/man/FOCUS_PELMO_crop_sze_names.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/FOCUS_PELMO_data.R
+\docType{data}
+\name{FOCUS_PELMO_crop_sze_names}
+\alias{FOCUS_PELMO_crop_sze_names}
+\title{FOCUS PELMO crop acronyms used for naming sceneario files}
+\format{An object of class \code{character} of length 25.}
+\usage{
+FOCUS_PELMO_crop_sze_names
+}
+\description{
+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.
+}
+\examples{
+print(FOCUS_PELMO_crop_sze_names)
+}
+\keyword{datasets}
diff --git a/man/FOCUS_PELMO_crops.Rd b/man/FOCUS_PELMO_crops.Rd
new file mode 100644
index 0000000..f6a41b4
--- /dev/null
+++ b/man/FOCUS_PELMO_crops.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/FOCUS_PELMO_data.R
+\docType{data}
+\name{FOCUS_PELMO_crops}
+\alias{FOCUS_PELMO_crops}
+\title{FOCUS PELMO crop names}
+\format{An object of class \code{character} of length 25.}
+\usage{
+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 
+in the three letter code, i.e. 'Peas (animals)' has the code \code{ape}.
+}
+\examples{
+print(FOCUS_PELMO_crops)
+}
+\keyword{datasets}
diff --git a/man/FOCUS_PELMO_location_codes.Rd b/man/FOCUS_PELMO_location_codes.Rd
new file mode 100644
index 0000000..961a840
--- /dev/null
+++ b/man/FOCUS_PELMO_location_codes.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/FOCUS_PELMO_data.R
+\docType{data}
+\name{FOCUS_PELMO_location_codes}
+\alias{FOCUS_PELMO_location_codes}
+\title{Location codes in FOCUS PELMO}
+\format{An object of class \code{character} of length 9.}
+\usage{
+FOCUS_PELMO_location_codes
+}
+\description{
+A named character vector of one letter location codes used in FOCUS PELMO,
+indexed by three letter acronyms.
+}
+\examples{
+print(FOCUS_PELMO_location_codes)
+}
+\keyword{datasets}
diff --git a/man/PELMO_path.Rd b/man/PELMO_path.Rd
new file mode 100644
index 0000000..e8ca50e
--- /dev/null
+++ b/man/PELMO_path.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PELMO_runs.R
+\name{PELMO_path}
+\alias{PELMO_path}
+\title{Create a path of run directories as the PELMO GUI does}
+\usage{
+PELMO_path(psm, crop, scenario)
+}
+\arguments{
+\item{psm}{The psm identifier}
+
+\item{crop}{The PELMO crop acronym}
+
+\item{scenario}{The scenario}
+}
+\description{
+Create a path of run directories as the PELMO GUI does
+}
diff --git a/man/PELMO_runs.Rd b/man/PELMO_runs.Rd
new file mode 100644
index 0000000..71fe6ef
--- /dev/null
+++ b/man/PELMO_runs.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PELMO_runs.R
+\name{PELMO_runs}
+\alias{PELMO_runs}
+\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)
+}
+\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 an existing run directories be overwritten}
+}
+\description{
+Per default, the runs are also executed with FOCUS PELMO, and the results are processed
+and returned.
+}
diff --git a/man/create_run_list.Rd b/man/create_run_list.Rd
new file mode 100644
index 0000000..3151165
--- /dev/null
+++ b/man/create_run_list.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PELMO_runs.R
+\name{create_run_list}
+\alias{create_run_list}
+\title{Create a list of runs that we can traverse}
+\usage{
+create_run_list(runs, psm_dir = ".", check_psm_files = FALSE)
+}
+\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{check_psm_files}{Should we check if the psm file exists}
+}
+\description{
+Create a list of runs that we can traverse
+}
diff --git a/man/run_PELMO.Rd b/man/run_PELMO.Rd
new file mode 100644
index 0000000..a286c5c
--- /dev/null
+++ b/man/run_PELMO.Rd
@@ -0,0 +1,27 @@
+% 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
+}