From e959fde98f95f3595e01490b67892678bbcd1b27 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 7 May 2014 14:47:28 +0200
Subject: Fork the gmkin GUI from mkin. See ChangeLog for details

---
 R/plot.mkinfit.R | 98 --------------------------------------------------------
 1 file changed, 98 deletions(-)
 delete mode 100644 R/plot.mkinfit.R

(limited to 'R/plot.mkinfit.R')

diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R
deleted file mode 100644
index 4132d96..0000000
--- a/R/plot.mkinfit.R
+++ /dev/null
@@ -1,98 +0,0 @@
-# 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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