Add dots argument to plot.one_boxHEADmain

Also, use markdown for some links that R CMD check complained about.

11 files changed, 37 insertions, 38 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 084818b..047d427 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: pfm
 Type: Package
 Title: Utilities for Pesticide Fate Modelling
 Version: 0.6.4
-Date: 2025-06-24
+Date: 2026-01-05
 Authors@R: c(
   person("Johannes Ranke", email = "johannes.ranke@agroscope.admin.ch",
     role = c("aut", "cre"),
@@ -37,4 +37,4 @@ LazyData: true
 Encoding: UTF-8
 URL: https://pkgdown.jrwb.de/pfm, https://github.com/jranke/pfm, http://jranke.github.io/pfm/
 Roxygen: list(markdown = TRUE, r6 = TRUE)
-RoxygenNote: 7.3.2.9000
+RoxygenNote: 7.3.3
diff --git a/R/TOXSWA_cwa.R b/R/TOXSWA_cwa.R
index 310029e..b132beb 100644
--- a/R/TOXSWA_cwa.R
+++ b/R/TOXSWA_cwa.R
@@ -150,7 +150,7 @@ plot.TOXSWA_cwa <- function(x, time_column = c("datetime", "t", "t_firstjan", "t
 #' by \code{\link{read.TOXSWA_cwa}}.
 #'
 #' @export
-#' @format An \code{\link{R6Class}} generator object.
+#' @format An [R6::R6Class] generator object.
 #' @field filename Length one character vector holding the filename.
 #' @field basedir Length one character vector holding the directory where the file came from.
 #' @field zipfile If not null, giving the path to the zip file from which the file was read.
diff --git a/R/twa.R b/R/twa.R
index 2018dfa..0506334 100644
--- a/R/twa.R
+++ b/R/twa.R
@@ -3,9 +3,9 @@
 #' @param x When numeric, this is the half-life to be used for an exponential
 #'   decline. When a character string specifying a parent decline model is given
 #'   e.g. \code{FOMC}, \code{parms} must contain the corresponding parameters.
-#'   If x is an \code{\link{mkinfit}} object, the decline is calculated from this
+#'   If x is an [mkinfit] object, the decline is calculated from this
 #'   object.
-#' @param ini The initial amount. If x is an \code{\link{mkinfit}} object, and
+#' @param ini The initial amount. If x is an [mkinfit] object, and
 #'   ini is 'model', the fitted initial concentrations are used. Otherwise, ini
 #'   must be numeric. If it has length one, it is used for the parent and
 #'   initial values of metabolites are zero, otherwise, it must give values for
@@ -13,7 +13,7 @@
 #' @param t_end End of the time series
 #' @param res Resolution of the time series
 #' @param ... Further arguments passed to methods
-#' @return An object of class \code{one_box}, inheriting from \code{\link{ts}}.
+#' @return An object of class \code{one_box}, inheriting from [ts].
 #' @importFrom stats filter frequency time ts
 #' @export
 #' @examples
@@ -108,7 +108,7 @@ one_box.mkinfit <- function(x, ini = "model", ..., t_end = 100, res = 0.01) {
 
 #' Plot time series of decline data
 #'
-#' @param x The object of type \code{\link{one_box}} to be plotted
+#' @param x The object of type [one_box] to be plotted
 #' @param xlim Limits for the x axis
 #' @param ylim Limits for the y axis
 #' @param xlab Label for the x axis
@@ -119,7 +119,7 @@ one_box.mkinfit <- function(x, ini = "model", ..., t_end = 100, res = 0.01) {
 #'   be shown if max_twa is not NULL.
 #' @param ... Further arguments passed to methods
 #' @importFrom stats plot.ts
-#' @seealso \code{\link{sawtooth}}
+#' @seealso [sawtooth]
 #' @export
 #' @examples
 #' dfop_pred <- one_box("DFOP", parms = c(k1 = 0.2, k2 = 0.02, g = 0.7))
@@ -141,7 +141,7 @@ plot.one_box <- function(x,
   obs_vars <- dimnames(x)[[2]]
   plot.ts(x, plot.type = "single", xlab = xlab, ylab = ylab,
           lty = 1:length(obs_vars), col = 1:length(obs_vars),
-          las = 1, xlim = xlim, ylim = ylim)
+          las = 1, xlim = xlim, ylim = ylim, ...)
   if (!is.null(max_twa)) {
     x_twa <- max_twa(x, window = max_twa)
     value <- x_twa$max[max_twa_var]
@@ -151,7 +151,7 @@ plot.one_box <- function(x,
     # Plot a second time to cover the grey rectangle
     plot.ts(x, plot.type = "single", xlab = xlab, ylab = ylab,
             lty = 1:length(obs_vars), col = 1:length(obs_vars),
-            las = 1, xlim = xlim, ylim = ylim)
+            las = 1, xlim = xlim, ylim = ylim, ...)
   }
 }
 
@@ -159,7 +159,7 @@ plot.one_box <- function(x,
 #'
 #' If the application pattern is specified in \code{applications},
 #' \code{n} and \code{i} are disregarded.
-#' @param x A \code{\link{one_box}} object
+#' @param x A [one_box] object
 #' @param n The number of applications. If \code{applications} is specified, \code{n} is ignored
 #' @param i The interval between applications. If \code{applications} is specified, \code{i}
 #'   is ignored
@@ -210,7 +210,7 @@ sawtooth <- function(x, n = 1, i = 365,
 #' the earliest possible time for the maximum in the time series returned
 #' is after one window has passed.
 #'
-#' @param x An object of type \code{\link{one_box}}
+#' @param x An object of type [one_box]
 #' @param window The size of the moving window
 #' @seealso \code{\link{max_twa}}
 #' @importFrom stats start end
@@ -246,7 +246,7 @@ twa.one_box <- function(x, window = 21)
 #' \code{\link{plot.one_box}} using the window size for the argument
 #' \code{max_twa}.
 #'
-#' The method working directly on fitted \code{\link{mkinfit}} objects uses the
+#' The method working directly on fitted [mkinfit] objects uses the
 #' equations given in the PEC soil section of the FOCUS guidance and is restricted
 #' SFO, FOMC and DFOP models and to the parent compound
 #' @references FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and
diff --git a/log/build.log b/log/build.log
index 5b3f7ee..e6b9b08 100644
--- a/log/build.log
+++ b/log/build.log
@@ -3,9 +3,6 @@
 * checking DESCRIPTION meta-information ... OK
 * checking for LF line-endings in source and make files and shell scripts
 * checking for empty or unneeded directories
-Removed empty directory ‘pfm/inst/testdata/SwashProjects/Project_1/MACRO’
-Removed empty directory ‘pfm/inst/testdata/SwashProjects/Project_1’
-Removed empty directory ‘pfm/inst/testdata/SwashProjects’
 * re-saving image files
 * building ‘pfm_0.6.4.tar.gz’
 
diff --git a/log/check.log b/log/check.log
index bd2b822..4e23c07 100644
--- a/log/check.log
+++ b/log/check.log
@@ -1,10 +1,10 @@
-* using log directory ‘/home/jranke/git/pfm/pfm.Rcheck’
-* using R version 4.4.2 (2024-10-31)
+* using log directory ‘/home/agsad.admin.ch/f80868656/projects/pfm/pfm.Rcheck’
+* using R version 4.5.2 (2025-10-31)
 * using platform: x86_64-pc-linux-gnu
 * R was compiled by
-    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)
+    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
+    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
+* running under: Ubuntu 24.04.3 LTS
 * using session charset: UTF-8
 * using options ‘--no-tests --as-cran’
 * checking for file ‘pfm/DESCRIPTION’ ... OK
@@ -14,7 +14,7 @@
 * checking CRAN incoming feasibility ... NOTE
 Maintainer: ‘Johannes Ranke <johannes.ranke@agroscope.admin.ch>’
 
-Size of tarball: 8532625 bytes
+Size of tarball: 8534480 bytes
 * checking package namespace information ... OK
 * checking package dependencies ... OK
 * checking if this is a source package ... OK
@@ -24,13 +24,12 @@ Size of tarball: 8532625 bytes
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
 * checking whether package ‘pfm’ can be installed ... OK
-* checking installed package size ... NOTE
+* checking installed package size ... INFO
   installed size is 10.3Mb
   sub-directories of 1Mb or more:
     testdata   9.9Mb
 * checking package directory ... OK
-* checking for future file timestamps ... NOTE
-unable to verify current time
+* checking for future file timestamps ... OK
 * checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
@@ -67,13 +66,16 @@ unable to verify current time
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ... SKIPPED
 * checking PDF version of manual ... OK
-* checking HTML version of manual ... OK
+* checking HTML version of manual ... NOTE
+Skipping checking HTML validation: no command 'tidy' found.
+Please obtain a recent version of HTML Tidy by downloading a binary
+release or compiling the source code from <https://www.html-tidy.org/>.
 * checking for non-standard things in the check directory ... OK
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 3 NOTEs
+Status: 2 NOTEs
 See
-  ‘/home/jranke/git/pfm/pfm.Rcheck/00check.log’
+  ‘/home/agsad.admin.ch/f80868656/projects/pfm/pfm.Rcheck/00check.log’
 for details.
 
diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd
index 0923f10..0e8a953 100644
--- a/man/TOXSWA_cwa.Rd
+++ b/man/TOXSWA_cwa.Rd
@@ -4,7 +4,7 @@
 \alias{TOXSWA_cwa}
 \title{R6 class for holding TOXSWA water concentration data and associated statistics}
 \format{
-An \code{\link{R6Class}} generator object.
+An \link[R6:R6Class]{R6::R6Class} generator object.
 }
 \description{
 An R6 class for holding TOXSWA water concentration (cwa) data
diff --git a/man/max_twa.Rd b/man/max_twa.Rd
index 43ad50e..2bba22f 100644
--- a/man/max_twa.Rd
+++ b/man/max_twa.Rd
@@ -7,7 +7,7 @@
 max_twa(x, window = 21)
 }
 \arguments{
-\item{x}{An object of type \code{\link{one_box}}}
+\item{x}{An object of type \link{one_box}}
 
 \item{window}{The size of the moving window}
 }
@@ -19,7 +19,7 @@ for finding the maximum. It is therefore recommended to check this using
 \code{max_twa}.
 }
 \details{
-The method working directly on fitted \code{\link{mkinfit}} objects uses the
+The method working directly on fitted \link[mkin:mkinfit]{mkin::mkinfit} objects uses the
 equations given in the PEC soil section of the FOCUS guidance and is restricted
 SFO, FOMC and DFOP models and to the parent compound
 }
diff --git a/man/one_box.Rd b/man/one_box.Rd
index a60aa39..83a9fe0 100644
--- a/man/one_box.Rd
+++ b/man/one_box.Rd
@@ -19,10 +19,10 @@ one_box(x, ini, ..., t_end = 100, res = 0.01)
 \item{x}{When numeric, this is the half-life to be used for an exponential
 decline. When a character string specifying a parent decline model is given
 e.g. \code{FOMC}, \code{parms} must contain the corresponding parameters.
-If x is an \code{\link{mkinfit}} object, the decline is calculated from this
+If x is an \link[mkin:mkinfit]{mkin::mkinfit} object, the decline is calculated from this
 object.}
 
-\item{ini}{The initial amount. If x is an \code{\link{mkinfit}} object, and
+\item{ini}{The initial amount. If x is an \link[mkin:mkinfit]{mkin::mkinfit} object, and
 ini is 'model', the fitted initial concentrations are used. Otherwise, ini
 must be numeric. If it has length one, it is used for the parent and
 initial values of metabolites are zero, otherwise, it must give values for
@@ -37,7 +37,7 @@ all observed variables.}
 \item{parms}{A named numeric vector containing the model parameters}
 }
 \value{
-An object of class \code{one_box}, inheriting from \code{\link{ts}}.
+An object of class \code{one_box}, inheriting from \link{ts}.
 }
 \description{
 Create a time series of decline data
diff --git a/man/plot.one_box.Rd b/man/plot.one_box.Rd
index 443be99..91fddf0 100644
--- a/man/plot.one_box.Rd
+++ b/man/plot.one_box.Rd
@@ -16,7 +16,7 @@
 )
 }
 \arguments{
-\item{x}{The object of type \code{\link{one_box}} to be plotted}
+\item{x}{The object of type \link{one_box} to be plotted}
 
 \item{xlim}{Limits for the x axis}
 
@@ -51,5 +51,5 @@ plot(pred_2_saw)
 plot(pred_2_saw, max_twa = 21, max_twa_var = "m1")
 }
 \seealso{
-\code{\link{sawtooth}}
+\link{sawtooth}
 }
diff --git a/man/sawtooth.Rd b/man/sawtooth.Rd
index 0850ded..d85b161 100644
--- a/man/sawtooth.Rd
+++ b/man/sawtooth.Rd
@@ -12,7 +12,7 @@ sawtooth(
 )
 }
 \arguments{
-\item{x}{A \code{\link{one_box}} object}
+\item{x}{A \link{one_box} object}
 
 \item{n}{The number of applications. If \code{applications} is specified, \code{n} is ignored}
 
diff --git a/man/twa.Rd b/man/twa.Rd
index a3509cd..da66257 100644
--- a/man/twa.Rd
+++ b/man/twa.Rd
@@ -10,7 +10,7 @@ twa(x, window = 21)
 \method{twa}{one_box}(x, window = 21)
 }
 \arguments{
-\item{x}{An object of type \code{\link{one_box}}}
+\item{x}{An object of type \link{one_box}}
 
 \item{window}{The size of the moving window}
 }