Improve docs, fail with erroneus crop_group arguments

PEC_sw_drift: The argument 'crop_group_focus' was renamed
to 'crop_group_RF' to make it easier to understand the
relation to the 'drift_data' argument.

10 files changed, 73 insertions, 64 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 95ab31e..2757d8b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: pfm
 Type: Package
 Title: Utilities for Pesticide Fate Modelling
-Version: 0.6.2
-Date: 2024-03-06
+Version: 0.6.3
+Date: 2024-04-10
 Authors@R: person("Johannes Ranke", email = "johannes.ranke@agroscope.admin.ch",
                   role = c("aut", "cre"),
                   comment = c(ORCID = "0000-0003-4371-6538"))
diff --git a/R/PEC_sw_drift.R b/R/PEC_sw_drift.R
index 22aa012..c1b24d3 100644
--- a/R/PEC_sw_drift.R
+++ b/R/PEC_sw_drift.R
@@ -14,7 +14,7 @@
 #'   either in the original form or integrated over the width of the water body, depending
 #'   on the 'formula' argument.
 #' @param crop_group_JKI When using the 'JKI' drift data, one of the German names
-#'   as used in [drift_parameters_focus].
+#'   as used in [drift_parameters_focus]. Will only be used if drift_data is 'JKI'.
 #' @param water_depth Depth of the water body in cm
 #' @param rate_units Defaults to g/ha
 #' @param PEC_units Requested units for the calculated PEC. Only µg/L currently supported
@@ -34,13 +34,13 @@
 #' PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF")
 #'
 #' # or consider aerial application
-#' PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF", 
-#'   crop_group_focus = "aerial")
+#' PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF",
+#'   crop_group_RF = "aerial")
 #'
 #' # Using custom drift percentages is also supported
 #' PEC_sw_drift(100, drift_percentages = c(2.77, 0.95, 0.57, 0.48, 0.29, 0.15, 0.06, 0.03))
 #'
-#' # The influence of assuming a 45° angle of the sides of the waterbody and the width of the 
+#' # The influence of assuming a 45° angle of the sides of the waterbody and the width of the
 #' # waterbody can be illustrated
 #' PEC_sw_drift(100)
 #' PEC_sw_drift(100, drift_data = "RF")
@@ -52,10 +52,10 @@ PEC_sw_drift <- function(rate,
   water_depth = 30,
   drift_percentages = NULL,
   drift_data = c("JKI", "RF"),
-  crop_group_JKI = c("Ackerbau", 
+  crop_group_JKI = c("Ackerbau",
     "Obstbau frueh", "Obstbau spaet", "Weinbau frueh", "Weinbau spaet",
     "Hopfenbau", "Flaechenkulturen > 900 l/ha", "Gleisanlagen"),
-  crop_group_focus = c("arable", "hops", "vines, late", "vines, early", 
+  crop_group_RF = c("arable", "hops", "vines, late", "vines, early",
     "fruit, late", "fruit, early", "aerial"),
   distances = c(1, 5, 10, 20),
   formula = c("Rautmann", "FOCUS"),
@@ -68,7 +68,13 @@ PEC_sw_drift <- function(rate,
   PEC_units <- match.arg(PEC_units)
   drift_data <- match.arg(drift_data)
   crop_group_JKI <- match.arg(crop_group_JKI)
-  crop_group_focus <- match.arg(crop_group_focus)
+  crop_group_RF <- match.arg(crop_group_RF)
+  if (drift_data == "JKI" & crop_group_RF != "arable") {
+    stop("Specifying crop_group_RF only makes sense if 'RF' is used for 'drift_data'")
+  }
+  if (drift_data == "RF" & crop_group_JKI != "Ackerbau") {
+    stop("Specifying crop_group_JKI only makes sense if 'JKI' is used for 'drift_data'")
+  }
   formula <- match.arg(formula)
   if (side_angle < 0 | side_angle > 90) stop("The side anglemust be between 0 and 90 degrees")
   mean_water_width <- if (side_angle == 90) water_width
@@ -80,9 +86,9 @@ PEC_sw_drift <- function(rate,
   if (is.null(drift_percentages)) {
     drift_percentages <- switch(drift_data,
       JKI = pfm::drift_data_JKI[[applications]][dist_index, crop_group_JKI],
-      RF =  drift_percentages_rautmann(distances, applications, 
+      RF =  drift_percentages_rautmann(distances, applications,
         formula = formula,
-        crop_group_focus, widths = water_width/100)
+        crop_group_RF, widths = water_width/100)
     )
     names(drift_percentages) <- paste(dist_index, "m")
   } else {
@@ -101,14 +107,14 @@ PEC_sw_drift <- function(rate,
 #' @param distances The distances in m for which to get PEC values
 #' @param widths The widths of the water bodies (only used in the FOCUS formula)
 #' @param applications Number of applications for selection of drift percentile
-#' @param crop_group_focus One of the crop groups as used in [drift_parameters_focus]
+#' @param crop_group_RF One of the crop groups as used in [drift_parameters_focus]
 #' @seealso [drift_parameters_focus], [PEC_sw_drift]
 #' @references FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4).
 #' FOrum for the Co-ordination of pesticde fate models and their USe.
 #' <http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf>
 #' @export
 #' @examples
-#' # Compare JKI data with Rautmann formula
+#' # Compare JKI data with Rautmann and FOCUS formulas for arable crops (default)
 #' # One application on field crops, for 1 m, 3 m and 5 m distance
 #' drift_data_JKI[[1]][as.character(c(1, 3, 5)), "Ackerbau"]
 #' drift_percentages_rautmann(c(1, 3, 5))
@@ -116,31 +122,31 @@ PEC_sw_drift <- function(rate,
 #'
 #' # One application to early or late fruit crops
 #' drift_data_JKI[[1]][as.character(c(3, 5, 20, 50)), "Obstbau frueh"]
-#' drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = "fruit, early")
-#' drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = "fruit, early",
+#' drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = "fruit, early")
+#' drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = "fruit, early",
 #'   formula = "FOCUS")
 #' drift_data_JKI[[1]][as.character(c(3, 5, 20, 50)), "Obstbau spaet"]
-#' drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = "fruit, late")
-#' drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = "fruit, late",
+#' drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = "fruit, late")
+#' drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = "fruit, late",
 #'   formula = "FOCUS")
-#' 
+#'
 #' # We get a continuum if the waterbody covers the hinge distance
 #' # (11.4 m for 1 early app to fruit)
 #' x <- seq(3, 30, by = 0.1)
-#' d <- drift_percentages_rautmann(x, crop_group = "fruit, early", formula = "FOCUS")
+#' d <- drift_percentages_rautmann(x, crop_group_RF = "fruit, early", formula = "FOCUS")
 #' plot(x, d, type = "l",
-#'   xlab = "Distance of near edge [m]", 
+#'   xlab = "Distance of near edge [m]",
 #'   ylab = "Mean drift percentage over waterbody width",
 #'   main = "One application to fruit, early")
 #' abline(v = 11.4, lty = 2)
-drift_percentages_rautmann <- function(distances, applications = 1, 
-  crop_group_focus = c("arable", "hops", "vines, late", "vines, early", "fruit, late",
+drift_percentages_rautmann <- function(distances, applications = 1,
+  crop_group_RF = c("arable", "hops", "vines, late", "vines, early", "fruit, late",
     "fruit, early", "aerial"),
   formula = c("Rautmann", "FOCUS"),
   widths = 1
 )
 {
-  cg <- match.arg(crop_group_focus)
+  cg <- match.arg(crop_group_RF)
   if (!applications %in% 1:8) stop("Only 1 to 8 applications are supported")
   formula <- match.arg(formula)
 
@@ -161,7 +167,7 @@ drift_percentages_rautmann <- function(distances, applications = 1,
       ifelse(z2 < hinge,
         # farther edge closer than hinge distance
         A/(widths * (B + 1)) * (z2^(B + 1) - z1^(B + 1)),
-        ifelse(z1 < hinge, 
+        ifelse(z1 < hinge,
           # hinge distance in waterbody (between z1 and z2)
           (A/(B + 1) * (H^(B + 1) - z1^(B + 1)) + C/(D + 1) * (z2^(D + 1) - H^(D + 1)))/widths,
           # z1 >= hinge, i.e. near edge farther than hinge distance
diff --git a/R/PEC_sw_exposit_runoff.R b/R/PEC_sw_exposit_runoff.R
index 8b89cd9..877dd92 100644
--- a/R/PEC_sw_exposit_runoff.R
+++ b/R/PEC_sw_exposit_runoff.R
@@ -137,10 +137,10 @@ PEC_sw_exposit_runoff <- function(rate, interception = 0, Koc, DT50 = Inf, t_run
 #' @param dilution The dilution factor
 #' @return A list containing the following components
 #'   \describe{
-#'     \item{perc_runoff}{The runoff percentages for dissolved and bound substance}
-#'     \item{runoff}{A matrix containing dissolved and bound input for the different distances}
-#'     \item{PEC_sw_runoff}{A matrix containing PEC values for dissolved and bound substance
-#'       for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.}
+#'     \item{perc_drainage_total}{Gesamtaustrag (total fraction of the residue drained)}
+#'     \item{perc_peak}{Stoßbelastung (fraction drained at event)}
+#'     \item{PEC_sw_drainage}{A matrix containing PEC values for the spring and autumn
+#'       scenarios. If the rate was given in g/ha, the PECsw are in microg/L.}
 #'   }
 #' @export
 #' @source Excel 3.02 spreadsheet available from
diff --git a/log/build.log b/log/build.log
index 2c3c139..edca7f6 100644
--- a/log/build.log
+++ b/log/build.log
@@ -3,5 +3,5 @@
 * checking DESCRIPTION meta-information ... OK
 * checking for LF line-endings in source and make files and shell scripts
 * checking for empty or unneeded directories
-* building ‘pfm_0.6.2.tar.gz’
+* building ‘pfm_0.6.3.tar.gz’
 
diff --git a/log/check.log b/log/check.log
index 93948df..f6d14ce 100644
--- a/log/check.log
+++ b/log/check.log
@@ -1,22 +1,24 @@
-* using log directory ‘/home/agsad.admin.ch/f80868656/projects/pfm/pfm.Rcheck’
+* using log directory ‘/home/jranke/git/pfm/pfm.Rcheck’
 * using R version 4.3.3 (2024-02-29)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
-    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
-    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
-* running under: Ubuntu 22.04.4 LTS
+    gcc (Debian 12.2.0-14) 12.2.0
+    GNU Fortran (Debian 12.2.0-14) 12.2.0
+* running under: Debian GNU/Linux 12 (bookworm)
 * using session charset: UTF-8
 * using options ‘--no-tests --as-cran’
 * checking for file ‘pfm/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘pfm’ version ‘0.6.2’
+* this is package ‘pfm’ version ‘0.6.3’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... [2s/14s] NOTE
+* checking CRAN incoming feasibility ... [1s/103s] NOTE
 Maintainer: ‘Johannes Ranke <johannes.ranke@agroscope.admin.ch>’
 
-Size of tarball: 8530336 bytes
+Size of tarball: 8530180 bytes
 * checking package namespace information ... OK
-* checking package dependencies ... OK
+* checking package dependencies ...Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
+  cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
+ OK
 * checking if this is a source package ... OK
 * checking if there is a namespace ... OK
 * checking for executable files ... OK
@@ -29,7 +31,8 @@ Size of tarball: 8530336 bytes
   sub-directories of 1Mb or more:
     testdata   9.9Mb
 * checking package directory ... OK
-* checking for future file timestamps ... OK
+* checking for future file timestamps ... NOTE
+unable to verify current time
 * checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
@@ -72,9 +75,9 @@ Skipping checking HTML validation: no command 'tidy' found
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 3 NOTEs
+Status: 4 NOTEs
 See
-  ‘/home/agsad.admin.ch/f80868656/projects/pfm/pfm.Rcheck/00check.log’
+  ‘/home/jranke/git/pfm/pfm.Rcheck/00check.log’
 for details.
 
 
diff --git a/log/test.log b/log/test.log
index 71834bd..8393cf9 100644
--- a/log/test.log
+++ b/log/test.log
@@ -2,17 +2,17 @@
 ✔ | F W  S  OK | Context
 ✔ |          7 | Exposit calculations
 ✔ |          6 | Geometric mean calculation
-✔ |          1 | Check max_twa for parent mkinfit models against analytical solutions [1.1s]
+✔ |          1 | Check max_twa for parent mkinfit models against analytical solutions
 ✔ |          1 | Simple PEC sediment calculations
 ✔ |         17 | Simple PEC soil calculations
 ✔ |          7 | Simple PEC surface water calculations with drift entry
 ✔ |          1 | Actual and time weighted average concentrations for SFO kinetics
 ✔ |          9 | FOCUS Step 1 calculations
 ✔ |          8 | FOCUS Steps 12 input files
-✔ |          7 | Read and analyse TOXSWA cwa files [4.7s]
+✔ |          7 | Read and analyse TOXSWA cwa files [4.2s]
 ✔ |         12 | UK drainage PEC calculations
 
 ══ Results ═════════════════════════════════════════════════════════════════════════════════════════
-Duration: 6.4 s
+Duration: 5.5 s
 
 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 76 ]
diff --git a/man/PEC_sw_drift.Rd b/man/PEC_sw_drift.Rd
index c576753..a24b783 100644
--- a/man/PEC_sw_drift.Rd
+++ b/man/PEC_sw_drift.Rd
@@ -12,7 +12,7 @@ PEC_sw_drift(
   drift_data = c("JKI", "RF"),
   crop_group_JKI = c("Ackerbau", "Obstbau frueh", "Obstbau spaet", "Weinbau frueh",
     "Weinbau spaet", "Hopfenbau", "Flaechenkulturen > 900 l/ha", "Gleisanlagen"),
-  crop_group_focus = c("arable", "hops", "vines, late", "vines, early", "fruit, late",
+  crop_group_RF = c("arable", "hops", "vines, late", "vines, early", "fruit, late",
     "fruit, early", "aerial"),
   distances = c(1, 5, 10, 20),
   formula = c("Rautmann", "FOCUS"),
@@ -38,9 +38,9 @@ either in the original form or integrated over the width of the water body, depe
 on the 'formula' argument.}
 
 \item{crop_group_JKI}{When using the 'JKI' drift data, one of the German names
-as used in \link{drift_parameters_focus}.}
+as used in \link{drift_parameters_focus}. Will only be used if drift_data is 'JKI'.}
 
-\item{crop_group_focus}{One of the crop groups as used in \link{drift_parameters_focus}}
+\item{crop_group_RF}{One of the crop groups as used in \link{drift_parameters_focus}}
 
 \item{distances}{The distances in m for which to get PEC values}
 
@@ -75,13 +75,13 @@ PEC_sw_drift(100, drift_data = "RF")
 PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF")
 
 # or consider aerial application
-PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF", 
-  crop_group_focus = "aerial")
+PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF",
+  crop_group_RF = "aerial")
 
 # Using custom drift percentages is also supported
 PEC_sw_drift(100, drift_percentages = c(2.77, 0.95, 0.57, 0.48, 0.29, 0.15, 0.06, 0.03))
 
-# The influence of assuming a 45° angle of the sides of the waterbody and the width of the 
+# The influence of assuming a 45° angle of the sides of the waterbody and the width of the
 # waterbody can be illustrated
 PEC_sw_drift(100)
 PEC_sw_drift(100, drift_data = "RF")
diff --git a/man/PEC_sw_exposit_drainage.Rd b/man/PEC_sw_exposit_drainage.Rd
index c809e08..b145d5c 100644
--- a/man/PEC_sw_exposit_drainage.Rd
+++ b/man/PEC_sw_exposit_drainage.Rd
@@ -44,10 +44,10 @@ autumn/winter/early spring.}
 \value{
 A list containing the following components
 \describe{
-\item{perc_runoff}{The runoff percentages for dissolved and bound substance}
-\item{runoff}{A matrix containing dissolved and bound input for the different distances}
-\item{PEC_sw_runoff}{A matrix containing PEC values for dissolved and bound substance
-for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.}
+\item{perc_drainage_total}{Gesamtaustrag (total fraction of the residue drained)}
+\item{perc_peak}{Stoßbelastung (fraction drained at event)}
+\item{PEC_sw_drainage}{A matrix containing PEC values for the spring and autumn
+scenarios. If the rate was given in g/ha, the PECsw are in microg/L.}
 }
 }
 \description{
diff --git a/man/drift_percentages_rautmann.Rd b/man/drift_percentages_rautmann.Rd
index 5fb2586..e2a50d1 100644
--- a/man/drift_percentages_rautmann.Rd
+++ b/man/drift_percentages_rautmann.Rd
@@ -7,7 +7,7 @@
 drift_percentages_rautmann(
   distances,
   applications = 1,
-  crop_group_focus = c("arable", "hops", "vines, late", "vines, early", "fruit, late",
+  crop_group_RF = c("arable", "hops", "vines, late", "vines, early", "fruit, late",
     "fruit, early", "aerial"),
   formula = c("Rautmann", "FOCUS"),
   widths = 1
@@ -18,7 +18,7 @@ drift_percentages_rautmann(
 
 \item{applications}{Number of applications for selection of drift percentile}
 
-\item{crop_group_focus}{One of the crop groups as used in \link{drift_parameters_focus}}
+\item{crop_group_RF}{One of the crop groups as used in \link{drift_parameters_focus}}
 
 \item{formula}{By default, the original Rautmann formula is used. If you
 specify "FOCUS", mean drift input over the width of the water body is
@@ -30,7 +30,7 @@ calculated as described in Chapter 5.4.5 of the FOCUS surface water guidance}
 Calculate drift percentages based on Rautmann data
 }
 \examples{
-# Compare JKI data with Rautmann formula
+# Compare JKI data with Rautmann and FOCUS formulas for arable crops (default)
 # One application on field crops, for 1 m, 3 m and 5 m distance
 drift_data_JKI[[1]][as.character(c(1, 3, 5)), "Ackerbau"]
 drift_percentages_rautmann(c(1, 3, 5))
@@ -38,20 +38,20 @@ drift_percentages_rautmann(c(1, 3, 5), formula = "FOCUS")
 
 # One application to early or late fruit crops
 drift_data_JKI[[1]][as.character(c(3, 5, 20, 50)), "Obstbau frueh"]
-drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = "fruit, early")
-drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = "fruit, early",
+drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = "fruit, early")
+drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = "fruit, early",
   formula = "FOCUS")
 drift_data_JKI[[1]][as.character(c(3, 5, 20, 50)), "Obstbau spaet"]
-drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = "fruit, late")
-drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = "fruit, late",
+drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = "fruit, late")
+drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = "fruit, late",
   formula = "FOCUS")
 
 # We get a continuum if the waterbody covers the hinge distance
 # (11.4 m for 1 early app to fruit)
 x <- seq(3, 30, by = 0.1)
-d <- drift_percentages_rautmann(x, crop_group = "fruit, early", formula = "FOCUS")
+d <- drift_percentages_rautmann(x, crop_group_RF = "fruit, early", formula = "FOCUS")
 plot(x, d, type = "l",
-  xlab = "Distance of near edge [m]", 
+  xlab = "Distance of near edge [m]",
   ylab = "Mean drift percentage over waterbody width",
   main = "One application to fruit, early")
 abline(v = 11.4, lty = 2)
diff --git a/tests/testthat/test_PEC_sw_drift.R b/tests/testthat/test_PEC_sw_drift.R
index a0972eb..7e3b965 100644
--- a/tests/testthat/test_PEC_sw_drift.R
+++ b/tests/testthat/test_PEC_sw_drift.R
@@ -25,7 +25,7 @@ test_that("The Rautmann formula is correctly implemented", {
   expect_equal(pfm_jki, pfm_rf, tolerance = 0.01)
 
   expect_error(PEC_sw_drift(100, drift_data = "RF", applications = 10), "Only 1 to 8 applications")
-  expect_error(PEC_sw_drift(100, drift_data = "RF", applications = 1, crop_group_focus = "Obstbau spaet"),
+  expect_error(PEC_sw_drift(100, drift_data = "RF", applications = 1, crop_group_RF = "Obstbau spaet"),
     "should be one of")
-  expect_silent(PEC_sw_drift(100, drift_data = "RF", applications = 1, crop_group_focus = "fruit, late"))
+  expect_silent(PEC_sw_drift(100, drift_data = "RF", applications = 1, crop_group_RF = "fruit, late"))
 })