From 3410513f55b3f8b5c4331f4fb4487613d3a28208 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 4 Nov 2019 23:48:20 +0100
Subject: Scaled residual plots

---
 man/mkinresplot.Rd  | 16 ++++++++++------
 man/plot.mkinfit.Rd | 15 ++++++++++++---
 2 files changed, 22 insertions(+), 9 deletions(-)

(limited to 'man')

diff --git a/man/mkinresplot.Rd b/man/mkinresplot.Rd
index 27e1322f..465b3038 100644
--- a/man/mkinresplot.Rd
+++ b/man/mkinresplot.Rd
@@ -5,7 +5,8 @@
 \title{Function to plot residuals stored in an mkin object}
 \usage{
 mkinresplot(object, obs_vars = names(object$mkinmod$map), xlim = c(0,
-  1.1 * max(object$data$time)), xlab = "Time", ylab = "Residual",
+  1.1 * max(object$data$time)), standardized = FALSE, xlab = "Time",
+  ylab = ifelse(standardized, "Standardized residual", "Residual"),
   maxabs = "auto", legend = TRUE, lpos = "topright",
   col_obs = "auto", pch_obs = "auto", frame = TRUE, ...)
 }
@@ -18,15 +19,17 @@ the model}
 
 \item{xlim}{plot range in x direction.}
 
-\item{xlab}{Label for the x axis. Defaults to "Time [days]".}
+\item{standardized}{Should the residuals be standardized by dividing by the
+standard deviation given by the error model of the fit?}
 
-\item{ylab}{Label for the y axis. Defaults to "Residual [\% of applied
-radioactivity]".}
+\item{xlab}{Label for the x axis.}
+
+\item{ylab}{Label for the y axis.}
 
 \item{maxabs}{Maximum absolute value of the residuals. This is used for the
 scaling of the y axis and defaults to "auto".}
 
-\item{legend}{Should a legend be plotted? Defaults to "TRUE".}
+\item{legend}{Should a legend be plotted?}
 
 \item{lpos}{Where should the legend be placed? Default is "topright". Will
 be passed on to \code{\link{legend}}.}
@@ -58,7 +61,8 @@ mkinresplot(fit, "m1")
 }
 \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.
 }
 \author{
 Johannes Ranke
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index 3834eaf5..6824f8a5 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -16,9 +16,13 @@
   lpos = "topright", inset = c(0.05, 0.05), show_errmin = FALSE,
   errmin_digits = 3, frame = TRUE, ...)
 
-plot_sep(fit, show_errmin = TRUE, ...)
+plot_sep(fit, show_errmin = TRUE,
+  show_residuals = ifelse(identical(fit$err_mod, "const"), TRUE,
+  "standardized"), ...)
 
-plot_res(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)
+plot_res(fit, sep_obs = FALSE, show_errmin = sep_obs,
+  show_residuals = ifelse(identical(fit$err_mod, "const"), TRUE,
+  "standardized"), ...)
 
 plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)
 }
@@ -54,7 +58,9 @@ corresponding model prediction lines.}
 \item{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.}
 
 \item{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
@@ -89,6 +95,8 @@ chi2 error percentage.}
 \item{frame}{Should a frame be drawn around the plots?}
 
 \item{\dots}{Further arguments passed to \code{\link{plot}}.}
+
+\item{standardized}{For}
 }
 \value{
 The function is called for its side effect.
@@ -113,6 +121,7 @@ SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"),
 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
-- 
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