From c6079a807e2b400fe0c772603392aeacd887da2f Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 8 May 2019 20:57:48 +0200
Subject: Add functionality to plot the error model

by plotting squared residuals against predicted values, and
showing the variance function used in the fitted error model.

Rebuild docs
---
 R/mkinerrplot.R | 84 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 84 insertions(+)
 create mode 100644 R/mkinerrplot.R

(limited to 'R/mkinerrplot.R')

diff --git a/R/mkinerrplot.R b/R/mkinerrplot.R
new file mode 100644
index 00000000..a2adcefa
--- /dev/null
+++ b/R/mkinerrplot.R
@@ -0,0 +1,84 @@
+# Copyright (C) 2008-2014,2019 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("variable", "residual"))
+
+mkinerrplot <- function (object,
+  obs_vars = names(object$mkinmod$map),
+  xlim = c(0, 1.1 * max(object$data$predicted)),
+  xlab = "Predicted", ylab = "Squared residual",
+  maxy = "auto", legend= TRUE, lpos = "topright", 
+  col_obs = "auto", pch_obs = "auto",
+  ...)
+{
+  obs_vars_all <- as.character(unique(object$data$variable))
+
+  if (length(obs_vars) > 0){
+      obs_vars <- intersect(obs_vars_all, obs_vars)
+  } else obs_vars <- obs_vars_all
+
+  residuals <- subset(object$data, variable %in% obs_vars, residual)
+
+  if (maxy == "auto") maxy = max(residuals^2, na.rm = TRUE)
+
+  # Set colors and symbols
+  if (col_obs[1] == "auto") {
+    col_obs <- 1:length(obs_vars)
+  }
+
+  if (pch_obs[1] == "auto") {
+    pch_obs <- 1:length(obs_vars)
+  }
+  names(col_obs) <- names(pch_obs) <- obs_vars
+
+  plot(0, type = "n",
+       xlab = xlab, ylab = ylab,
+       xlim = xlim,
+       ylim = c(0, 1.2 * maxy), ...)
+
+  for(obs_var in obs_vars){
+    residuals_plot <- subset(object$data, variable == obs_var, c("predicted", "residual"))
+    points(residuals_plot[["predicted"]],
+           residuals_plot[["residual"]]^2,
+           pch = pch_obs[obs_var], col = col_obs[obs_var])
+  }
+
+  if (object$err_mod == "const") {
+    abline(h = object$errparms^2, lty = 2, col = col_obs[obs_var])
+  }
+  if (object$err_mod == "obs") {
+    for (obs_var in obs_vars) {
+      sigma_name = paste0("sigma_", obs_var)
+      abline(h = object$errparms[sigma_name]^2, lty = 2,
+             col = col_obs[obs_var])
+    }
+  }
+  if (object$err_mod == "tc") {
+    sigma_plot <- function(predicted) {
+      sigma_twocomp(predicted,
+                    sigma_low = object$errparms[1],
+                    rsd_high = object$errparms[2])^2
+    }
+    plot(sigma_plot, from = 0, to = max(object$data$predicted),
+         add = TRUE, lty = 2, col = col_obs[obs_var])
+  }
+
+  if (legend == TRUE) {
+    legend(lpos, inset = c(0.05, 0.05), legend = obs_vars,
+      col = col_obs[obs_vars], pch = pch_obs[obs_vars])
+  }
+}
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