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# Copyright (C) 2010-2014 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/>
if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "variable", "observed"))
plot.mkinfit <- function(x, fit = x,
obs_vars = names(fit$mkinmod$map),
xlab = "Time", ylab = "Observed",
xlim = range(fit$data$time),
ylim = "default",
col_obs = 1:length(fit$mkinmod$map),
pch_obs = col_obs,
lty_obs = rep(1, length(fit$mkinmod$map)),
add = FALSE, legend = !add,
show_residuals = FALSE, maxabs = "auto",
lpos = "topright", inset = c(0.05, 0.05), ...)
{
if (add && show_residuals) stop("If adding to an existing plot we can not show residuals")
if (ylim[[1]] == "default") {
ylim = c(0, max(subset(fit$data, variable %in% obs_vars)$observed, na.rm = TRUE))
}
solution_type = fit$solution_type
parms.all <- c(fit$bparms.optim, fit$bparms.fixed)
ininames <- c(
rownames(subset(fit$start, type == "state")),
rownames(subset(fit$fixed, type == "state")))
odeini <- parms.all[ininames]
# Order initial state variables
names(odeini) <- sub("_0", "", names(odeini))
odeini <- odeini[names(fit$mkinmod$diffs)]
outtimes <- seq(xlim[1], xlim[2], length.out=100)
odenames <- c(
rownames(subset(fit$start, type == "deparm")),
rownames(subset(fit$fixed, type == "deparm")))
odeparms <- parms.all[odenames]
out <- mkinpredict(fit$mkinmod, odeparms, odeini, outtimes,
solution_type = solution_type, atol.deSolve = fit$atol, rtol.deSolve = fit$rtol)
# Set up the plot if not to be added to an existing plot
if (add == FALSE) {
if (show_residuals) {
oldpar <- par(no.readonly = TRUE)
layout(matrix(c(1, 2), 2, 1), heights = c(2, 1.3))
par(mar = c(3, 4, 4, 2) + 0.1)
}
plot(0, type="n",
xlim = xlim, ylim = ylim,
xlab = xlab, ylab = ylab, ...)
}
# Plot the data and model output
names(col_obs) <- names(pch_obs) <- names(lty_obs) <- names(fit$mkinmod$map)
for (obs_var in obs_vars) {
points(subset(fit$data, variable == obs_var, c(time, observed)),
pch = pch_obs[obs_var], col = col_obs[obs_var])
}
matlines(out$time, out[obs_vars], col = col_obs[obs_vars], lty = lty_obs[obs_vars])
if (legend == TRUE) {
legend(lpos, inset= inset, legend = obs_vars,
col = col_obs[obs_vars], pch = pch_obs[obs_vars], lty = lty_obs[obs_vars])
}
# Show residuals if requested
if (show_residuals) {
par(mar = c(5, 4, 0, 2) + 0.1)
residuals <- subset(fit$data, variable %in% obs_vars, residual)
if (maxabs == "auto") maxabs = max(abs(residuals), na.rm = TRUE)
plot(0, type="n",
xlim = xlim,
ylim = c(-1.2 * maxabs, 1.2 * maxabs),
xlab = xlab, ylab = "Residuals")
for(obs_var in obs_vars){
residuals_plot <- subset(fit$data, variable == obs_var, c("time", "residual"))
points(residuals_plot, pch = pch_obs[obs_var], col = col_obs[obs_var])
}
abline(h = 0, lty = 2)
par(oldpar, no.readonly = TRUE)
}
}
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