Setting up PELMO runs, execution and evaluation

It all works!

7 files changed, 70 insertions, 30 deletions

diff --git a/man/FOCUS_PELMO_crops.Rd b/man/FOCUS_PELMO_crops.Rd
index f6a41b4..91a010a 100644
--- a/man/FOCUS_PELMO_crops.Rd
+++ b/man/FOCUS_PELMO_crops.Rd
@@ -11,8 +11,8 @@ 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 
+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{
diff --git a/man/PELMO_runs.Rd b/man/PELMO_runs.Rd
index 71fe6ef..1d81e6d 100644
--- a/man/PELMO_runs.Rd
+++ b/man/PELMO_runs.Rd
@@ -2,11 +2,18 @@
 % 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'
@@ -31,5 +38,13 @@ as used in \code{\link{FOCUS_GW_scenarios_2012}}.}
 }
 \description{
 Per default, the runs are also executed with FOCUS PELMO, and the results are processed
-and returned.
+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
+maintained on github is supported. In such installations, FOCUS PELMO is installed into
+package installation directory of \code{PELMO.installeR} and run with \code{wine}.
+}
+\references{
+PELMO.installeR \url{https://jranke.github.io/PELMO.installeR}
+
+Wine \url{https://winehq.org}
 }
diff --git a/man/focus_80th.Rd b/man/focus_80th.Rd
new file mode 100644
index 0000000..8436791
--- /dev/null
+++ b/man/focus_80th.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PELMO_runs.R
+\name{focus_80th}
+\alias{focus_80th}
+\title{Calculate the 80th percentile according to FOCUS guidance}
+\usage{
+focus_80th(c_period, old = FALSE)
+}
+\arguments{
+\item{c_period}{A numeric vector of values to calculate the percentile from}
+
+\item{old}{Should the old calculation method be used (the 17th highest value)?}
+}
+\description{
+This is nowadays defined as the mean of the 16th and the 17th
+highest value. Previously, the 17th highest values was used (FOCUS 2014, p.
+18). NaN values need to be set to zero in order to reproduce the
+values obtained by PELMO.
+}
diff --git a/man/get_flux.Rd b/man/get_flux.Rd
new file mode 100644
index 0000000..93778cb
--- /dev/null
+++ b/man/get_flux.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PELMO_runs.R
+\name{get_flux}
+\alias{get_flux}
+\title{Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file}
+\usage{
+get_flux(chem_file)
+}
+\description{
+Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file
+}
diff --git a/man/get_interval.Rd b/man/get_interval.Rd
new file mode 100644
index 0000000..a751996
--- /dev/null
+++ b/man/get_interval.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PELMO_runs.R
+\name{get_interval}
+\alias{get_interval}
+\title{Get the application interval in years from a psm file}
+\usage{
+get_interval(psm_file, location_code)
+}
+\description{
+Get the application interval in years from a psm file
+}
diff --git a/man/run_PELMO.Rd b/man/run_PELMO.Rd
deleted file mode 100644
index a286c5c..0000000
--- a/man/run_PELMO.Rd
+++ /dev/null
@@ -1,27 +0,0 @@
-% 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
-}
diff --git a/man/sum_periods.Rd b/man/sum_periods.Rd
new file mode 100644
index 0000000..5051af4
--- /dev/null
+++ b/man/sum_periods.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PELMO_runs.R
+\name{sum_periods}
+\alias{sum_periods}
+\title{Sum up values according to FOCUS periods}
+\usage{
+sum_periods(annual, interval)
+}
+\description{
+Sum up values according to FOCUS periods
+}