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authorJohannes Ranke <jranke@uni-bremen.de>2014-05-07 14:47:28 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2014-05-07 14:47:28 +0200
commite959fde98f95f3595e01490b67892678bbcd1b27 (patch)
tree992c56223a31c6937091dd5f9eeef63c2dd9e579 /R/plot.mkinfit.R
parentd846ac7691ab648afbb5a98bbca91911396a95bf (diff)
Fork the gmkin GUI from mkin. See ChangeLog for details
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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 == "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 = fit$atol, rtol = fit$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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