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diff --git a/R/mkinparplot.R b/R/mkinparplot.R
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-# 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.unsorted = setdiff(deparms.optim, fractions.optim)
- rates.optim <- rownames(object$start[rates.optim.unsorted, ])
- n.plot <- c(state.optim = length(state.optim),
- rates.optim = length(rates.optim),
- fractions.optim = length(fractions.optim))
- n.plot <- n.plot[n.plot > 0]
-
- oldpars <- par(no.readonly = TRUE)
- layout(matrix(1:length(n.plot), ncol = 1), heights = n.plot + 1)
-
- s <- summary(object)
- bpar <- data.frame(t(s$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]
- 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),
- fractions.optim = range(c(0, 1, unlist(values)),
- na.rm = TRUE, finite = TRUE))
- stripchart(values["Estimate", ][length(parnames):1],
- 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("fractions.optim")) abline(v = 1, lty = 2)
- position <- ifelse(values["Estimate", ] < mean(xlim)/2, "right", "left")
- text(ifelse(position == "left", min(xlim), max(xlim)),
- length(parnames):1, parnames,
- pos = ifelse(position == "left", 4, 2))
- arrows(as.numeric(values["Lower", ]), length(parnames):1,
- as.numeric(values["Upper", ]), length(parnames):1,
- code = 3, angle = 90, length = 0.05)
- }
- par(oldpars)
-}

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