Improve some plotting routines, more tests

Static documentation rebuilt by pkgdown

3 files changed, 40 insertions, 17 deletions

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}