Merge branch 'main' into UK_drainage_with_units

7 files changed, 20 insertions, 21 deletions

diff --git a/R/twa.R b/R/twa.R
index c756f58..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 [mkin::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 [mkin::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 [mkin::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/check.log b/log/check.log
index 9ed80ce..5deae11 100644
--- a/log/check.log
+++ b/log/check.log
@@ -14,7 +14,7 @@
 * checking CRAN incoming feasibility ... NOTE
 Maintainer: ‘Johannes Ranke <johannes.ranke@agroscope.admin.ch>’
 
-Size of tarball: 8533567 bytes
+Size of tarball: 8533512 bytes
 * checking package namespace information ... OK
 * checking package dependencies ... OK
 * checking if this is a source package ... OK
@@ -29,8 +29,7 @@ Size of tarball: 8533567 bytes
   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
@@ -72,7 +71,7 @@ unable to verify current time
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 2 NOTEs
+Status: 1 NOTE
 See
   ‘/home/jranke/git/pfm/pfm.Rcheck/00check.log’
 for details.
diff --git a/man/max_twa.Rd b/man/max_twa.Rd
index 0fb5c93..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 \link[mkin:mkinfit]{mkin::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 afa6e10..83a9fe0 100644
--- a/man/one_box.Rd
+++ b/man/one_box.Rd
@@ -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}
 }