diff options
| -rw-r--r-- | DESCRIPTION | 4 | ||||
| -rw-r--r-- | R/PEC_sw_drift.R | 50 | ||||
| -rw-r--r-- | R/PEC_sw_exposit_runoff.R | 8 | ||||
| -rw-r--r-- | log/build.log | 2 | ||||
| -rw-r--r-- | log/check.log | 25 | ||||
| -rw-r--r-- | log/test.log | 6 | ||||
| -rw-r--r-- | man/PEC_sw_drift.Rd | 12 | ||||
| -rw-r--r-- | man/PEC_sw_exposit_drainage.Rd | 8 | ||||
| -rw-r--r-- | man/drift_percentages_rautmann.Rd | 18 | ||||
| -rw-r--r-- | tests/testthat/test_PEC_sw_drift.R | 4 |
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")) }) |