# 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)
N.optim = grep("^N_", deparms.optim, value = TRUE)
if ("g" %in% deparms.optim) fractions.optim <- c("g", fractions.optim)
rates.optim.unsorted = setdiff(deparms.optim, union(fractions.optim, N.optim))
rates.optim <- rownames(object$start[rates.optim.unsorted, ])
n.plot <- c(state.optim = length(state.optim),
rates.optim = length(rates.optim),
N.optim = length(N.optim),
fractions.optim = length(fractions.optim))
n.plot <- n.plot[n.plot > 0]
oldpars <- par(no.readonly = TRUE)
layout(matrix(1:length(n.plot), ncol = 1), heights = n.plot + 1)
s <- summary(object)
bpar <- data.frame(t(s$bpar))
par(mar = c(2.1, 2.1, 0.1, 2.1))
par(cex = 1)
for (type in names(n.plot)) {
parnames <- get(type)
values <- bpar[parnames]
values_with_confints <- data.frame(t(subset(data.frame(t(values)), !is.na(Lower))))
parnames_with_confints <- names(values_with_confints)
xlim = switch(type,
state.optim = range(c(0, unlist(values)),
na.rm = TRUE, finite = TRUE),
rates.optim = range(c(0, unlist(values)),
na.rm = TRUE, finite = TRUE),
N.optim = range(c(0, 1, unlist(values)),
na.rm = TRUE, finite = TRUE),
fractions.optim = range(c(0, 1, unlist(values)),
na.rm = TRUE, finite = TRUE))
parname_index <- length(parnames):1 # Reverse order for strip chart
names(parname_index) <- parnames
parnames_with_confints_index <- parname_index[parnames_with_confints]
stripchart(values["Estimate", ][parname_index],
xlim = xlim,
ylim = c(0.5, length(get(type)) + 0.5),
yaxt = "n")
if (type %in% c("rates.optim", "fractions.optim")) abline(v = 0, lty = 2)
if (type %in% c("N.optim", "fractions.optim")) abline(v = 1, lty = 2)
position <- ifelse(values["Estimate", ] < mean(xlim), "right", "left")
text(ifelse(position == "left", min(xlim), max(xlim)),
length(parnames):1, parnames,
pos = ifelse(position == "left", 4, 2))
values_with_confints.upper.nonInf <- ifelse(values_with_confints["Upper", ] == Inf, 1.5 * xlim[[2]], values_with_confints["Upper", ])
arrows(as.numeric(values_with_confints["Lower", ]), parnames_with_confints_index,
as.numeric(values_with_confints.upper.nonInf), parnames_with_confints_index,
code = 3, angle = 90, length = 0.05)
}
par(oldpars)
}
