# 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 = 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) } }