diff options
Diffstat (limited to 'R/twa.R')
| -rw-r--r-- | R/twa.R | 20 |
1 files changed, 10 insertions, 10 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 \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 |