From 161ec8fb10e1b60a97d294bdd4f21ed2230c236d Mon Sep 17 00:00:00 2001 From: Johannes Ranke 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 +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 } -- cgit v1.2.1