From 161ec8fb10e1b60a97d294bdd4f21ed2230c236d Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 2 May 2014 12:16:11 +0200
Subject: Add missing files for plotting confindence intervals

---
 R/mkinparplot.R    | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 man/mkinparplot.Rd | 35 +++++++++++++++++++++++++++++++++++
 2 files changed, 88 insertions(+)
 create mode 100644 R/mkinparplot.R
 create mode 100644 man/mkinparplot.Rd

diff --git a/R/mkinparplot.R b/R/mkinparplot.R
new file mode 100644
index 0000000..8e8de02
--- /dev/null
+++ b/R/mkinparplot.R
@@ -0,0 +1,53 @@
+# Copyright (C) 2014 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/>
+mkinparplot <- function(object) {
+  state.optim = rownames(subset(object$start, type == "state"))
+  deparms.optim = rownames(subset(object$start, type == "deparm"))
+  fractions.optim = grep("^f_", deparms.optim, value = TRUE)
+  if ("g" %in% deparms.optim) fractions.optim <- c("g", fractions.optim)
+  rates.optim = setdiff(deparms.optim, fractions.optim)
+  n.plot <- c(state.optim = length(state.optim), 
+              rates.optim = length(rates.optim), 
+              fractions.optim = length(fractions.optim))
+  n.plot <- n.plot[n.plot > 0]
+
+  layout(matrix(1:length(n.plot), ncol = 1), heights = n.plot + 1)
+
+  s <- summary(object)
+  bpar <- data.frame(t(s$bpar))
+  oldpars <- par(no.readonly = TRUE)
+  par(mar = c(2.1, 2.1, 0.1, 2.1))
+  for (type in names(n.plot)) {
+    parnames <- get(type)
+    values <- bpar[parnames]
+    xlim = switch(type,
+                  state.optim = range(c(0, unlist(values)), 
+                                      na.rm = TRUE, finite = TRUE),
+                  rates.optim = range(unlist(values), 
+                                      na.rm = TRUE, finite = TRUE),
+                  fractions.optim = range(c(0, 1, unlist(values)), 
+                                          na.rm = TRUE, finite = TRUE))
+    stripchart(bpar[get(type)], xlim = xlim,
+               yaxt = "n", ylim = c(0.5, length(get(type)) + 0.5))
+    text(mean(xlim), 1:length(parnames), parnames, pos = 3, offset = 1)
+    arrows(as.numeric(values["Lower", ]), 1:length(parnames), 
+           as.numeric(values["Upper", ]), 1:length(parnames), 
+           code = 3, angle = 90, length = 0.1)
+  }
+  par(oldpars)
+}
diff --git a/man/mkinparplot.Rd b/man/mkinparplot.Rd
new file mode 100644
index 0000000..60103b8
--- /dev/null
+++ b/man/mkinparplot.Rd
@@ -0,0 +1,35 @@
+\name{mkinparplot}
+\alias{mkinparplot}
+\title{
+  Function to plot the confidence intervals obtained using
+  \code{\link{mkinfit}}
+}
+\description{
+  This function plots the confidence intervals for the parameters
+  fitted using \code{\link{mkinfit}}.
+}
+\usage{
+  mkinparplot(object)
+}
+\arguments{
+  \item{object}{
+    A fit represented in an \code{\link{mkinfit}} object.
+  }
+}
+\value{
+  Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.
+}
+\author{
+  Johannes Ranke
+}
+
+\examples{
+model <- mkinmod(
+  T245 = list(type = "SFO", to = c("phenol")),
+  phenol = list(type = "SFO", to = c("anisole")),
+  anisole = list(type = "SFO"), use_of_ff = "max")
+fit <- mkinfit(model, subset(mccall81_245T, soil == "Commerce"), 
+  parms.ini = c(f_phenol_to_anisole = 1), fixed_parms = "f_phenol_to_anisole")
+\dontrun{mkinparplot(fit)}
+}
+\keyword{ hplot }
-- 
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