Separate out PELMO utilities into rPELMO

24 files changed, 45 insertions, 285 deletions

diff --git a/man/FOCUS_PELMO_crop_sze_names.Rd b/man/FOCUS_PELMO_crop_sze_names.Rd
deleted file mode 100644
index 180c011..0000000
--- a/man/FOCUS_PELMO_crop_sze_names.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% 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
deleted file mode 100644
index 91a010a..0000000
--- a/man/FOCUS_PELMO_crops.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% 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
deleted file mode 100644
index 961a840..0000000
--- a/man/FOCUS_PELMO_location_codes.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% 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/FOMC_actual_twa.Rd b/man/FOMC_actual_twa.Rd
index 7a1f0fb..2c40048 100644
--- a/man/FOMC_actual_twa.Rd
+++ b/man/FOMC_actual_twa.Rd
@@ -9,8 +9,8 @@ FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
   18 December 2014, p. 251
 }
 \usage{
-FOMC_actual_twa(alpha = 1.0001, beta = 10, times = c(0, 1, 2, 4, 7, 14,
-  21, 28, 42, 50, 100))
+FOMC_actual_twa(alpha = 1.0001, beta = 10, times = c(0, 1, 2, 4, 7,
+  14, 21, 28, 42, 50, 100))
 }
 \arguments{
 \item{alpha}{Parameter of the FOMC model}
diff --git a/man/GUS.Rd b/man/GUS.Rd
index edf61b6..adc1bb3 100644
--- a/man/GUS.Rd
+++ b/man/GUS.Rd
@@ -12,8 +12,9 @@ GUS(...)
 \method{GUS}{numeric}(DT50, Koc, ...)
 
 \method{GUS}{chent}(chent, degradation_value = "DT50ref",
-  lab_field = "laboratory", redox = "aerobic", sorption_value = "Kfoc",
-  degradation_aggregator = geomean, sorption_aggregator = geomean, ...)
+  lab_field = "laboratory", redox = "aerobic",
+  sorption_value = "Kfoc", degradation_aggregator = geomean,
+  sorption_aggregator = geomean, ...)
 
 \method{print}{GUS_result}(x, ..., digits = 1)
 }
diff --git a/man/PEC_soil.Rd b/man/PEC_soil.Rd
index e85f33c..a9e6c49 100644
--- a/man/PEC_soil.Rd
+++ b/man/PEC_soil.Rd
@@ -4,13 +4,14 @@
 \alias{PEC_soil}
 \title{Calculate predicted environmental concentrations in soil}
 \usage{
-PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5,
-  PEC_units = "mg/kg", PEC_pw_units = "mg/L", interval = NA,
-  n_periods = Inf, tillage_depth = 20, leaching_depth = tillage_depth,
-  crop = "annual", cultivation = FALSE, chent = NA, DT50 = NA,
-  FOMC = NA, Koc = NA, Kom = Koc/1.724, t_avg = 0,
-  scenarios = c("default", "EFSA_2017", "EFSA_2015"), leaching = scenarios
-  == "EFSA_2017", porewater = FALSE)
+PEC_soil(rate, rate_units = "g/ha", interception = 0,
+  mixing_depth = 5, PEC_units = "mg/kg", PEC_pw_units = "mg/L",
+  interval = NA, n_periods = Inf, tillage_depth = 20,
+  leaching_depth = tillage_depth, crop = "annual",
+  cultivation = FALSE, chent = NA, DT50 = NA, FOMC = NA,
+  Koc = NA, Kom = Koc/1.724, t_avg = 0, t_act = NULL,
+  scenarios = c("default", "EFSA_2017", "EFSA_2015"),
+  leaching = scenarios == "EFSA_2017", porewater = FALSE)
 }
 \arguments{
 \item{rate}{Application rate in units specified below}
@@ -65,6 +66,8 @@ as Kom here}
 
 \item{t_avg}{Averaging times for time weighted average concentrations}
 
+\item{t_act}{Time series for actual concentrations}
+
 \item{scenarios}{If this is 'default', the DT50 will be used without correction
 and soil properties as specified in the REACH guidance (R.16, Table
 R.16-9) are used for porewater PEC calculations.  If this is "EFSA_2015",
diff --git a/man/PEC_sw_drainage_UK.Rd b/man/PEC_sw_drainage_UK.Rd
index a968b94..edb239e 100644
--- a/man/PEC_sw_drainage_UK.Rd
+++ b/man/PEC_sw_drainage_UK.Rd
@@ -4,8 +4,9 @@
 \alias{PEC_sw_drainage_UK}
 \title{Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method}
 \usage{
-PEC_sw_drainage_UK(rate, interception = 0, Koc, latest_application = NULL,
-  soil_DT50 = NULL, model = NULL, model_parms = NULL)
+PEC_sw_drainage_UK(rate, interception = 0, Koc,
+  latest_application = NULL, soil_DT50 = NULL, model = NULL,
+  model_parms = NULL)
 }
 \arguments{
 \item{rate}{Application rate in g/ha}
diff --git a/man/PEC_sw_drift.Rd b/man/PEC_sw_drift.Rd
index f74cf67..dfc3f39 100644
--- a/man/PEC_sw_drift.Rd
+++ b/man/PEC_sw_drift.Rd
@@ -6,7 +6,8 @@
 \usage{
 PEC_sw_drift(rate, applications = 1, water_depth = 30,
   drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau",
-  distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")
+  distances = c(1, 5, 10, 20), rate_units = "g/ha",
+  PEC_units = "µg/L")
 }
 \arguments{
 \item{rate}{Application rate in units specified below}
diff --git a/man/PELMO_path.Rd b/man/PELMO_path.Rd
deleted file mode 100644
index 49292c2..0000000
--- a/man/PELMO_path.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% 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 = NA)
-}
-\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
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}
-}
diff --git a/man/SFO_actual_twa.Rd b/man/SFO_actual_twa.Rd
index 720fbc9..30039f2 100644
--- a/man/SFO_actual_twa.Rd
+++ b/man/SFO_actual_twa.Rd
@@ -9,8 +9,8 @@ FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
   18 December 2014, p. 251
 }
 \usage{
-SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50,
-  100))
+SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42,
+  50, 100))
 }
 \arguments{
 \item{DT50}{The half-life.}
diff --git a/man/chent_focus_sw.Rd b/man/chent_focus_sw.Rd
index 8df01ab..9830ade 100644
--- a/man/chent_focus_sw.Rd
+++ b/man/chent_focus_sw.Rd
@@ -4,8 +4,9 @@
 \alias{chent_focus_sw}
 \title{Create a chemical compound object for FOCUS Step 1 calculations}
 \usage{
-chent_focus_sw(name, Koc, DT50_ws = NA, DT50_soil = NA, DT50_water = NA,
-  DT50_sediment = NA, cwsat = 1000, mw = NA, max_soil = 1, max_ws = 1)
+chent_focus_sw(name, Koc, DT50_ws = NA, DT50_soil = NA,
+  DT50_water = NA, DT50_sediment = NA, cwsat = 1000, mw = NA,
+  max_soil = 1, max_ws = 1)
 }
 \arguments{
 \item{name}{Length one character vector containing the name}
diff --git a/man/create_run_list.Rd b/man/create_run_list.Rd
deleted file mode 100644
index 3151165..0000000
--- a/man/create_run_list.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% 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/endpoint.Rd b/man/endpoint.Rd
index 9511083..204905b 100644
--- a/man/endpoint.Rd
+++ b/man/endpoint.Rd
@@ -10,8 +10,8 @@
 \usage{
 endpoint(chent, medium = "soil", type = c("degradation", "sorption"),
   lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic",
-  "anaerobic"), value = c("DT50ref", "Kfoc", "N"), aggregator = geomean,
-  raw = FALSE, signif = 3)
+  "anaerobic"), value = c("DT50ref", "Kfoc", "N"),
+  aggregator = geomean, raw = FALSE, signif = 3)
 
 soil_DT50(chent, aggregator = geomean, signif = 3,
   lab_field = "laboratory", value = "DT50ref", redox = "aerobic",
diff --git a/man/focus_80th.Rd b/man/focus_80th.Rd
deleted file mode 100644
index 8436791..0000000
--- a/man/focus_80th.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% 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
deleted file mode 100644
index c56b891..0000000
--- a/man/get_flux.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% 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)
-}
-\arguments{
-\item{chem_file}{The full path to a CHEM*.PLM 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
deleted file mode 100644
index 519cf36..0000000
--- a/man/get_interval.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% 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)
-}
-\arguments{
-\item{psm_file}{The path to the .psm file}
-
-\item{location_code}{The location code}
-}
-\description{
-Get the application interval in years from a psm file
-}
diff --git a/man/get_vertex.Rd b/man/get_vertex.Rd
index fe2f5c0..519a4e3 100644
--- a/man/get_vertex.Rd
+++ b/man/get_vertex.Rd
@@ -6,6 +6,11 @@
 \usage{
 get_vertex(x, y)
 }
+\arguments{
+\item{x}{Three x coordinates}
+
+\item{y}{Three y coordinates}
+}
 \description{
 This was inspired by an answer on stackoverflow
 https://stackoverflow.com/a/717791
diff --git a/man/one_box.Rd b/man/one_box.Rd
index 89e624c..57d6d77 100644
--- a/man/one_box.Rd
+++ b/man/one_box.Rd
@@ -14,7 +14,8 @@ one_box(x, ini, ..., t_end = 100, res = 0.01)
 \method{one_box}{character}(x, ini = 1, parms, ..., t_end = 100,
   res = 0.01)
 
-\method{one_box}{mkinfit}(x, ini = "model", ..., t_end = 100, res = 0.01)
+\method{one_box}{mkinfit}(x, ini = "model", ..., t_end = 100,
+  res = 0.01)
 }
 \arguments{
 \item{x}{When numeric, this is the half-life to be used for an exponential
diff --git a/man/pfm_degradation.Rd b/man/pfm_degradation.Rd
index 0f3cc79..fdc99fe 100644
--- a/man/pfm_degradation.Rd
+++ b/man/pfm_degradation.Rd
@@ -5,8 +5,8 @@
 \title{Calculate a time course of relative concentrations based on an mkinmod model}
 \usage{
 pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink =
-  log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by =
-  step_days))
+  log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365,
+  by = step_days))
 }
 \arguments{
 \item{model}{The degradation model to be used. Either a parent only model like
diff --git a/man/plot.TOXSWA_cwa.Rd b/man/plot.TOXSWA_cwa.Rd
index 88e1f37..f06d3c7 100644
--- a/man/plot.TOXSWA_cwa.Rd
+++ b/man/plot.TOXSWA_cwa.Rd
@@ -4,10 +4,10 @@
 \alias{plot.TOXSWA_cwa}
 \title{Plot TOXSWA surface water concentrations}
 \usage{
-\method{plot}{TOXSWA_cwa}(x, time_column = c("datetime", "t", "t_firstjan",
-  "t_rel_to_max"), xlab = "default", ylab = "default", add = FALSE,
-  threshold_factor = 1000, thin_low = 1, total = FALSE, LC_TIME = "C",
-  ...)
+\method{plot}{TOXSWA_cwa}(x, time_column = c("datetime", "t",
+  "t_firstjan", "t_rel_to_max"), xlab = "default", ylab = "default",
+  add = FALSE, threshold_factor = 1000, thin_low = 1,
+  total = FALSE, LC_TIME = "C", ...)
 }
 \arguments{
 \item{x}{The TOXSWA_cwa object to be plotted.}
diff --git a/man/read.TOXSWA_cwa.Rd b/man/read.TOXSWA_cwa.Rd
index c76fdbd..ccd403a 100644
--- a/man/read.TOXSWA_cwa.Rd
+++ b/man/read.TOXSWA_cwa.Rd
@@ -4,9 +4,9 @@
 \alias{read.TOXSWA_cwa}
 \title{Read TOXSWA surface water concentrations}
 \usage{
-read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last",
-  substance = "parent", total = FALSE, windows = NULL,
-  thresholds = NULL)
+read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL,
+  segment = "last", substance = "parent", total = FALSE,
+  windows = NULL, thresholds = NULL)
 }
 \arguments{
 \item{filename}{The filename of the cwa file (TOXSWA 2.x.y  or similar) or the
diff --git a/man/sawtooth.Rd b/man/sawtooth.Rd
index aba3428..22ad103 100644
--- a/man/sawtooth.Rd
+++ b/man/sawtooth.Rd
@@ -4,8 +4,8 @@
 \alias{sawtooth}
 \title{Create decline time series for multiple applications}
 \usage{
-sawtooth(x, n = 1, i = 365, applications = data.frame(time = seq(0, (n -
-  1) * i, length.out = n), amount = 1))
+sawtooth(x, n = 1, i = 365, applications = data.frame(time = seq(0,
+  (n - 1) * i, length.out = n), amount = 1))
 }
 \arguments{
 \item{x}{A \code{\link{one_box}} object}
diff --git a/man/sum_periods.Rd b/man/sum_periods.Rd
deleted file mode 100644
index 21bd2c9..0000000
--- a/man/sum_periods.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% 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)
-}
-\arguments{
-\item{annual}{The annual flux as obtained by \code{get_flux}}
-
-\item{interval}{The interval in years}
-}
-\description{
-Sum up values according to FOCUS periods
-}