Use roxygen for functions and methods

1 files changed, 50 insertions, 18 deletions

diff --git a/R/plot.mmkin.R b/R/plot.mmkin.R
index ef80949c..eefafe12 100644
--- a/R/plot.mmkin.R
+++ b/R/plot.mmkin.R
@@ -1,21 +1,53 @@
-# Copyright (C) 2015-2016,2019 Johannes Ranke
-# Contact: jranke@uni-bremen.de
-
-# This file is part of the R package mkin
-
-# mkin is free software: you can redistribute it and/or modify it under the
-# terms of the GNU General Public License as published by the Free Software
-# Foundation, either version 3 of the License, or (at your option) any later
-# version.
-
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-# details.
-
-# You should have received a copy of the GNU General Public License along with
-# this program. If not, see <http://www.gnu.org/licenses/>
-
+#' Plot model fits (observed and fitted) and the residuals for a row or column
+#' of an mmkin object
+#' 
+#' 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.
+#' 
+#' If the current plot device is a \code{\link[tikzDevice]{tikz}} device, then
+#' latex is being used for the formatting of the chi2 error level.
+#' 
+#' @param x An object of class \code{\link{mmkin}}, with either one row or one
+#'   column.
+#' @param main The main title placed on the outer margin of the plot.
+#' @param legends An index for the fits for which legends should be shown.
+#' @param resplot Should the residuals plotted against time, using
+#'   \code{\link{mkinresplot}}, or as squared residuals against predicted
+#'   values, with the error model, using \code{\link{mkinerrplot}}.
+#' @param show_errmin Should the chi2 error level be shown on top of the plots
+#'   to the left?
+#' @param errmin_var The variable for which the FOCUS chi2 error value should
+#'   be shown.
+#' @param errmin_digits The number of significant digits for rounding the FOCUS
+#'   chi2 error percentage.
+#' @param cex Passed to the plot functions and \code{\link{mtext}}.
+#' @param rel.height.middle The relative height of the middle plot, if more
+#'   than two rows of plots are shown.
+#' @param \dots Further arguments passed to \code{\link{plot.mkinfit}} and
+#'   \code{\link{mkinresplot}}.
+#' @return The function is called for its side effect.
+#' @author Johannes Ranke
+#' @examples
+#' 
+#'   \dontrun{
+#'   # Only use one core not to offend CRAN checks
+#'   fits <- mmkin(c("FOMC", "HS"),
+#'                 list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C), # named list for titles
+#'                 cores = 1, quiet = TRUE, error_model = "tc")
+#'   plot(fits[, "FOCUS C"])
+#'   plot(fits["FOMC", ])
+#' 
+#'   # We can also plot a single fit, if we like the way plot.mmkin works, but then the plot
+#'   # height should be smaller than the plot width (this is not possible for the html pages
+#'   # generated by pkgdown, as far as I know).
+#'   plot(fits["FOMC", "FOCUS C"]) # same as plot(fits[1, 2])
+#' 
+#'   # Show the error models
+#'   plot(fits["FOMC", ], resplot = "errmod")
+#'   }
+#' 
+#' @export
 plot.mmkin <- function(x, main = "auto", legends = 1, 
                        resplot = c("time", "errmod"),
                        show_errmin = TRUE,