# 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[, c("Estimate", "Lower", "Upper")])) 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")))) 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 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)), parname_index, parnames, pos = ifelse(position == "left", 4, 2)) values.upper.nonInf <- ifelse(values["Upper", ] == Inf, 1.5 * xlim[[2]], values["Upper", ]) # Suppress warnings for non-existing arrow lengths suppressWarnings(arrows(as.numeric(values["Lower", ]), parname_index, as.numeric(values.upper.nonInf), parname_index, code = 3, angle = 90, length = 0.05)) } par(oldpars) }