diff options
| -rw-r--r-- | R/twa.R | 20 | ||||
| -rw-r--r-- | log/check.log | 7 | ||||
| -rw-r--r-- | man/max_twa.Rd | 4 | ||||
| -rw-r--r-- | man/one_box.Rd | 2 | ||||
| -rw-r--r-- | man/plot.one_box.Rd | 4 | ||||
| -rw-r--r-- | man/sawtooth.Rd | 2 | ||||
| -rw-r--r-- | man/twa.Rd | 2 |
7 files changed, 20 insertions, 21 deletions
@@ -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} @@ -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} } |