diff options
Diffstat (limited to 'R/mkinresplot.R')
| -rw-r--r-- | R/mkinresplot.R | 38 |
1 files changed, 24 insertions, 14 deletions
diff --git a/R/mkinresplot.R b/R/mkinresplot.R index 5377dbf2..0bfdd02f 100644 --- a/R/mkinresplot.R +++ b/R/mkinresplot.R @@ -1,23 +1,25 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("variable", "residual")) #' Function to plot residuals stored in an mkin object -#' +#' #' This function plots the residuals for the specified subset of the observed #' variables from an mkinfit object. A combined plot of the fitted model and #' the residuals can be obtained using \code{\link{plot.mkinfit}} using the #' argument \code{show_residuals = TRUE}. -#' +#' +#' @importFrom stats residuals #' @param object A fit represented in an \code{\link{mkinfit}} object. #' @param obs_vars A character vector of names of the observed variables for #' which residuals should be plotted. Defaults to all observed variables in #' the model #' @param xlim plot range in x direction. -#' @param xlab Label for the x axis. Defaults to "Time [days]". -#' @param ylab Label for the y axis. Defaults to "Residual [\% of applied -#' radioactivity]". +#' @param xlab Label for the x axis. +#' @param standardized Should the residuals be standardized by dividing by the +#' standard deviation given by the error model of the fit? +#' @param ylab Label for the y axis. #' @param maxabs Maximum absolute value of the residuals. This is used for the #' scaling of the y axis and defaults to "auto". -#' @param legend Should a legend be plotted? Defaults to "TRUE". +#' @param legend Should a legend be plotted? #' @param lpos Where should the legend be placed? Default is "topright". Will #' be passed on to \code{\link{legend}}. #' @param col_obs Colors for the observed variables. @@ -28,19 +30,21 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("variable", "residual")) #' effect, namely to produce a plot. #' @author Johannes Ranke #' @seealso \code{\link{mkinplot}}, for a way to plot the data and the fitted -#' lines of the mkinfit object. +#' lines of the mkinfit object, and \code{\link{plot_res}} for a function +#' combining the plot of the fit and the residual plot. #' @examples -#' +#' #' model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) #' fit <- mkinfit(model, FOCUS_2006_D, quiet = TRUE) #' mkinresplot(fit, "m1") -#' +#' #' @export mkinresplot <- function (object, obs_vars = names(object$mkinmod$map), xlim = c(0, 1.1 * max(object$data$time)), - xlab = "Time", ylab = "Residual", - maxabs = "auto", legend= TRUE, lpos = "topright", + standardized = FALSE, + xlab = "Time", ylab = ifelse(standardized, "Standardized residual", "Residual"), + maxabs = "auto", legend = TRUE, lpos = "topright", col_obs = "auto", pch_obs = "auto", frame = TRUE, ...) @@ -51,9 +55,15 @@ mkinresplot <- function (object, obs_vars <- intersect(obs_vars_all, obs_vars) } else obs_vars <- obs_vars_all - residuals <- subset(object$data, variable %in% obs_vars, residual) + if (standardized) { + res_col <- "standardized" + object$data[[res_col]] <- residuals(object, standardized = TRUE) + } else { + res_col <- "residual" + } + res <- subset(object$data, variable %in% obs_vars)[res_col] - if (maxabs == "auto") maxabs = max(abs(residuals), na.rm = TRUE) + if (maxabs == "auto") maxabs = max(abs(res), na.rm = TRUE) # Set colors and symbols if (col_obs[1] == "auto") { @@ -71,7 +81,7 @@ mkinresplot <- function (object, ylim = c(-1.2 * maxabs, 1.2 * maxabs), ...) for(obs_var in obs_vars){ - residuals_plot <- subset(object$data, variable == obs_var, c("time", "residual")) + residuals_plot <- subset(object$data, variable == obs_var, c("time", res_col)) points(residuals_plot, pch = pch_obs[obs_var], col = col_obs[obs_var]) } |