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Diffstat (limited to 'R/mkinparplot.R')
-rw-r--r-- | R/mkinparplot.R | 62 |
1 files changed, 0 insertions, 62 deletions
diff --git a/R/mkinparplot.R b/R/mkinparplot.R deleted file mode 100644 index 28c1d2a..0000000 --- a/R/mkinparplot.R +++ /dev/null @@ -1,62 +0,0 @@ -# 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) -} |