diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/mkinresplot.R | 38 | ||||
| -rw-r--r-- | R/plot.mkinfit.R | 35 |
2 files changed, 50 insertions, 23 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]) } diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R index 16415a3b..e0b3ad13 100644 --- a/R/plot.mkinfit.R +++ b/R/plot.mkinfit.R @@ -30,7 +30,10 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "variable", "obse #' @param show_residuals Should residuals be shown? If only one plot of the #' fits is shown, the residual plot is in the lower third of the plot. #' Otherwise, i.e. if "sep_obs" is given, the residual plots will be located -#' to the right of the plots of the fitted curves. +#' to the right of the plots of the fitted curves. If this is set to +#' 'standardized', a plot of the residuals divided by the standard deviation +#' given by the fitted error model will be shown. +#' @param standardized For #' @param show_errplot Should squared residuals and the error model be shown? #' If only one plot of the fits is shown, this plot is in the lower third of #' the plot. Otherwise, i.e. if "sep_obs" is given, the residual plots will @@ -68,6 +71,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "variable", "obse #' fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = "tc") #' plot(fit) #' plot_res(fit) +#' plot_res(fit, standardized = FALSE) #' plot_err(fit) #' #' # Show the observed variables separately, with residuals @@ -101,11 +105,19 @@ plot.mkinfit <- function(x, fit = x, show_errmin = FALSE, errmin_digits = 3, frame = TRUE, ...) { + if (identical(show_residuals, "standardized")) { + show_residuals <- TRUE + standardized <- TRUE + } else { + standardized <- FALSE + } + if (add && show_residuals) stop("If adding to an existing plot we can not show residuals") if (add && show_errplot) stop("If adding to an existing plot we can not show the error model plot") if (show_residuals && show_errplot) stop("We can either show residuals over time or the error model plot, not both") if (add && sep_obs) stop("If adding to an existing plot we can not show observed variables separately") + solution_type = fit$solution_type parms.all <- c(fit$bparms.optim, fit$bparms.fixed) @@ -260,14 +272,16 @@ plot.mkinfit <- function(x, fit = x, # Show residuals if requested if (show_residuals) { - mkinresplot(fit, obs_vars = row_obs_vars, pch_obs = pch_obs[row_obs_vars], col_obs = col_obs[row_obs_vars], - legend = FALSE, frame = frame) + mkinresplot(fit, obs_vars = row_obs_vars, standardized = standardized, + pch_obs = pch_obs[row_obs_vars], col_obs = col_obs[row_obs_vars], + legend = FALSE, frame = frame) } # Show error model plot if requested if (show_errplot) { - mkinerrplot(fit, obs_vars = row_obs_vars, pch_obs = pch_obs[row_obs_vars], col_obs = col_obs[row_obs_vars], - legend = FALSE, frame = frame) + mkinerrplot(fit, obs_vars = row_obs_vars, + pch_obs = pch_obs[row_obs_vars], col_obs = col_obs[row_obs_vars], + legend = FALSE, frame = frame) } } if (do_layout) par(oldpar, no.readonly = TRUE) @@ -275,16 +289,19 @@ plot.mkinfit <- function(x, fit = x, #' @rdname plot.mkinfit #' @export -plot_sep <- function(fit, show_errmin = TRUE, ...) { - plot.mkinfit(fit, sep_obs = TRUE, show_residuals = TRUE, +plot_sep <- function(fit, show_errmin = TRUE, + show_residuals = ifelse(identical(fit$err_mod, "const"), TRUE, "standardized"), ...) { + plot.mkinfit(fit, sep_obs = TRUE, show_residuals = show_residuals, show_errmin = show_errmin, ...) } #' @rdname plot.mkinfit #' @export -plot_res <- function(fit, sep_obs = FALSE, show_errmin = sep_obs, ...) { +plot_res <- function(fit, sep_obs = FALSE, show_errmin = sep_obs, + show_residuals = ifelse(identical(fit$err_mod, "const"), TRUE, "standardized"), ...) +{ plot.mkinfit(fit, sep_obs = sep_obs, show_errmin = show_errmin, - show_residuals = TRUE, row_layout = TRUE, ...) + show_residuals = show_residuals, row_layout = TRUE, ...) } #' @rdname plot.mkinfit |