From e09f726134ee273b6b191c1ec6465e6f701b082b Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 21 Oct 2019 18:52:24 +0200
Subject: Improve some plotting routines, more tests

Static documentation rebuilt by pkgdown
---
 man/mkinresplot.Rd                 | 32 ++++++++++++++++++++++----------
 man/plot.mkinfit.Rd                | 15 ++++++++++++---
 man/synthetic_data_for_UBA_2014.Rd | 10 ++++++----
 3 files changed, 40 insertions(+), 17 deletions(-)

(limited to 'man')

diff --git a/man/mkinresplot.Rd b/man/mkinresplot.Rd
index cdcfbd37..e788d836 100644
--- a/man/mkinresplot.Rd
+++ b/man/mkinresplot.Rd
@@ -14,38 +14,50 @@
     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", ...)
+    maxabs = "auto", legend = TRUE, lpos = "topright", 
+    col_obs = "auto", pch_obs = "auto",
+    frame = TRUE,
+    ...)
 }
 \arguments{
   \item{object}{
     A fit represented in an \code{\link{mkinfit}} object.
-}
+  }
   \item{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
-}
+  }
   \item{xlim}{
     plot range in x direction.
   }
   \item{xlab}{
     Label for the x axis. Defaults to "Time [days]".
-}
+  }
   \item{ylab}{
     Label for the y axis. Defaults to "Residual [\% of applied radioactivity]".
-}
+  }
   \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{lpos}{ 
     Where should the legend be placed? Default is "topright". Will be passed on to
-		\code{\link{legend}}. }
+    \code{\link{legend}}. }
+  \item{col_obs}{
+    Colors for the observed variables.
+  }
+  \item{pch_obs}{
+    Symbols to be used for the observed variables.
+  }
+  \item{frame}{
+    Should a frame be drawn around the plots?
+  }
   \item{\dots}{
-   further arguments passed to \code{\link{plot}}.
-}
+    further arguments passed to \code{\link{plot}}.
+  }
 }
 \value{
   Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index a4f47073..e7b456a1 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -1,6 +1,8 @@
 \name{plot.mkinfit}
 \alias{plot.mkinfit}
 \alias{plot_sep}
+\alias{plot_res}
+\alias{plot_err}
 \title{
   Plot the observed data and the fitted model of an mkinfit object
 }
@@ -26,9 +28,12 @@
   show_errplot = FALSE,
   maxabs = "auto",
   sep_obs = FALSE, rel.height.middle = 0.9,
+  row_layout = FALSE,
   lpos = "topright", inset = c(0.05, 0.05),
   show_errmin = FALSE, errmin_digits = 3, frame = TRUE, \dots)
-plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, \dots)
+plot_sep(fit, show_errmin = TRUE, \dots)
+plot_res(fit, sep_obs = FALSE, show_errmin = sep_obs, \dots)
+plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, \dots)
 }
 \arguments{
   \item{x}{
@@ -92,6 +97,10 @@ plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, \dots)
   \item{rel.height.middle}{
     The relative height of the middle plot, if more than two rows of plots are shown.
   }
+  \item{row_layout}{
+    Should we use a row layout where the residual plot or the error model plot is shown
+    to the right?
+  }
   \item{lpos}{
     Position(s) of the legend(s). Passed to \code{\link{legend}} as the first argument.
     If not length one, this should be of the same length as the obs_var argument.
@@ -123,8 +132,8 @@ SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"),
                    m1 = mkinsub("SFO", full = "Metabolite M1" ))
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = "tc")
 plot(fit)
-plot(fit, show_residuals = TRUE)
-plot(fit, show_errplot = TRUE)
+plot_res(fit)
+plot_err(fit)
 
 # Show the observed variables separately
 plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright"))
diff --git a/man/synthetic_data_for_UBA_2014.Rd b/man/synthetic_data_for_UBA_2014.Rd
index cfab5622..d68f45d4 100644
--- a/man/synthetic_data_for_UBA_2014.Rd
+++ b/man/synthetic_data_for_UBA_2014.Rd
@@ -138,9 +138,11 @@ d_synth_err_names = c(
 
 # This is just one example of an evaluation using the kinetic model used for
 # the generation of the data
-fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data,
-               quiet = TRUE)
-plot_sep(fit)
-summary(fit)
+\dontrun{
+  fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data,
+                 quiet = TRUE)
+  plot_sep(fit)
+  summary(fit)
+}
 }
 \keyword{datasets}
-- 
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