From 4c69847346a9c254e4e803b6987a63e3fd9c14ae Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 26 Jun 2015 08:50:13 +0200
Subject: Subsetting and plotting for mmkin objects

Including documentation and documentation improvements for mmkin().
---
 man/Extract.mmkin.Rd | 36 ++++++++++++++++++++++++++++++++++++
 man/mmkin.Rd         |  6 +++---
 man/plot.mmkin.Rd    | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 89 insertions(+), 3 deletions(-)
 create mode 100644 man/Extract.mmkin.Rd
 create mode 100644 man/plot.mmkin.Rd

(limited to 'man')

diff --git a/man/Extract.mmkin.Rd b/man/Extract.mmkin.Rd
new file mode 100644
index 00000000..769f2f5a
--- /dev/null
+++ b/man/Extract.mmkin.Rd
@@ -0,0 +1,36 @@
+\name{[.mmkin}
+\alias{[.mmkin}
+\title{Subsetting method for mmkin objects}
+\usage{
+\method{[}{mmkin}(x, i, j, ..., drop = FALSE)
+}
+\description{
+ Subsetting method for mmkin objects. 
+}
+\arguments{
+\item{x}{An \code{\link{mmkin} object}}
+
+\item{i}{Row index selecting the fits for specific models}
+
+\item{j}{Column index selecting the fits to specific datasets}
+
+\item{...}{Not used, only there to satisfy the generic method definition}
+
+\item{drop}{If FALSE, the method always returns an mmkin object, otherwise either 
+  a list of mkinfit objects or a single mkinfit object.}
+}
+\value{
+  An object of class \code{\link{mmkin}}.
+}
+\author{
+  Johannes Ranke
+}
+\examples{
+  fits <- mmkin(c("SFO", "FOMC"), list(B = FOCUS_2006_B, C = FOCUS_2006_C))
+  fits["FOMC", ]
+  fits[, "B"]
+  fits[, "B", drop = TRUE]$FOMC
+  fits["SFO", "B"]
+  fits[["SFO", "B"]] # This is equivalent to
+  fits["SFO", "B", drop = TRUE]
+}
diff --git a/man/mmkin.Rd b/man/mmkin.Rd
index 0b35738a..4859d658 100644
--- a/man/mmkin.Rd
+++ b/man/mmkin.Rd
@@ -4,8 +4,8 @@
   Fit one or more kinetic models with one or more state variables to one or more datasets
 }
 \description{
-  This code calls \code{\link{mkinfit}} on each combination of model and dataset
-  given in its first two arguments.
+  This function calls \code{\link{mkinfit}} on all combinations of models and datasets
+  specified in its first two arguments.
 }
 \usage{
 mmkin(models, datasets,
@@ -26,7 +26,7 @@ mmkin(models, datasets,
     used when the \code{cluster} argument is \code{NULL}.
   }
   \item{cluster}{
-    A cluster as returned by \code{link{makeCluster}} to be used for parallel 
+    A cluster as returned by \code{\link{makeCluster}} to be used for parallel 
     execution.
   }
   \item{\dots}{
diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd
new file mode 100644
index 00000000..4f78de2c
--- /dev/null
+++ b/man/plot.mmkin.Rd
@@ -0,0 +1,50 @@
+\name{plot.mmkin}
+\alias{plot.mmkin}
+\title{
+  Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object.
+}
+\description{
+  When x is a row selected from an mmkin object (\code{\link{[.mmkin}}), the same model
+  fitted for at least one dataset is shown. When it is a column, the fit of at least one model 
+  to the same dataset is shown.
+}
+\usage{
+\method{plot}{mmkin}(x, main = "auto", legends = 1, errmin_var = "All data", errmin_digits = 2, 
+           cex = 0.7, rel.height.middle = 0.9, ...)
+}
+\arguments{
+  \item{x}{
+    An object of class \{code{\link{mmkin}}, with either one row or one column.
+}
+  \item{main}{
+    The main title placed on the outer margin of the plot.
+}
+  \item{legends}{
+    An index for the fits for which legends should be shown.
+}
+  \item{errmin_var}{
+    The variable for which the FOCUS chi2 error value should be shown.
+}
+  \item{errmin_digits}{
+    The number of digits for rounding the FOCUS chi2 error percentage.
+}
+  \item{cex}{
+    Passed to the plot functions and \code{\link{mtext}}.
+}
+  \item{rel.height.middle}{
+    The relative height of the middle plot.
+}
+  \item{\dots}{
+    Further arguments passed to \code{\link{plot.mkinfit}} and \code{\link{mkinresplot}}.
+}
+}
+\value{
+  The function is called for its side effect.
+}
+\author{
+  Johannes Ranke
+}
+\examples{
+  fits <- mmkin(c("SFO", "FOMC"), list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C))
+  plot(fits[, "FOCUS C"])
+}
-- 
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