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 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 R/mkinparplot.R (limited to 'R') 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) +} -- cgit v1.2.1