From df916b91c90f80e2c68f3e136a7b6e07b8c6bae1 Mon Sep 17 00:00:00 2001
From: jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date: Mon, 26 Nov 2012 23:03:19 +0000
Subject: - Added an S3 plot method for mkinfit models - Fixed a bug in the
 mkinfit summary method which crashed on missing covariance matrices

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@58 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
---
 R/mkinfit.R      |  2 +-
 R/mkinplot.R     | 38 ++------------------------------------
 R/plot.mkinfit.R | 45 +++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 48 insertions(+), 37 deletions(-)
 create mode 100644 R/plot.mkinfit.R

(limited to 'R')

diff --git a/R/mkinfit.R b/R/mkinfit.R
index 0215596..3649b20 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -317,7 +317,7 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), .
     print(x$SFORB, digits=digits,...)
   }    
 
-  printcor <- !is.null(x$cov.unscaled)
+  printcor <- is.numeric(x$cov.unscaled)
   if (printcor){
     Corr <- cov2cor(x$cov.unscaled)
     rownames(Corr) <- colnames(Corr) <- rownames(x$par)
diff --git a/R/mkinplot.R b/R/mkinplot.R
index 546c506..b9becfd 100644
--- a/R/mkinplot.R
+++ b/R/mkinplot.R
@@ -1,38 +1,4 @@
-mkinplot <- function(fit, xlab = "Time", ylab = "Observed", xlim = range(fit$data$time), ylim = range(fit$data$observed, na.rm = TRUE), legend = TRUE, ...)
+mkinplot <- function(fit, ...)
 {
-  solution_type = fit$solution_type
-  fixed <- fit$fixed$value
-  names(fixed) <- rownames(fit$fixed)
-  parms.all <- c(fit$parms.all, fixed)
-  ininames <- c(
-    rownames(subset(fit$start, type == "state")),
-    rownames(subset(fit$fixed, type == "state")))
-  odeini <- parms.all[ininames]
-  names(odeini) <- names(fit$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, ...)
-
-  # Plot the data and model output
-  plot(0, type="n", 
-    xlim = xlim, ylim = ylim,
-    xlab = xlab, ylab = ylab, ...)
-  col_obs <- pch_obs <- lty_obs <- 1:length(fit$mkinmod$map)
-  names(col_obs) <- names(pch_obs) <- names(lty_obs) <- names(fit$mkinmod$map)
-  for (obs_var in names(fit$mkinmod$map)) {
-    points(subset(fit$data, variable == obs_var, c(time, observed)), 
-      pch = pch_obs[obs_var], col = col_obs[obs_var])
-  }
-  matlines(out$time, out[-1])
-  if (legend == TRUE) {
-    legend("topright", inset=c(0.05, 0.05), legend=names(fit$mkinmod$map),
-      col=col_obs, pch=pch_obs, lty=lty_obs)
-  }
+  plot(fit, ...)
 }
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R
new file mode 100644
index 0000000..1858aa8
--- /dev/null
+++ b/R/plot.mkinfit.R
@@ -0,0 +1,45 @@
+plot.mkinfit <- function(x, fit = x,
+  xlab = "Time", ylab = "Observed",
+  xlim = range(fit$data$time), ylim = range(fit$data$observed, na.rm = TRUE), 
+  col_obs = 1:length(fit$mkinmod$map),
+  pch_obs = col_obs, lty_obs = rep(1, length(fit$mkinmod$map)),
+  add = FALSE, legend = !add, ...)
+{
+  solution_type = fit$solution_type
+  fixed <- fit$fixed$value
+  names(fixed) <- rownames(fit$fixed)
+  parms.all <- c(fit$parms.all, fixed)
+  ininames <- c(
+    rownames(subset(fit$start, type == "state")),
+    rownames(subset(fit$fixed, type == "state")))
+  odeini <- parms.all[ininames]
+  names(odeini) <- names(fit$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) {
+    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 names(fit$mkinmod$map)) {
+    points(subset(fit$data, variable == obs_var, c(time, observed)), 
+      pch = pch_obs[obs_var], col = col_obs[obs_var])
+  }
+  matlines(out$time, out[-1], col = col_obs, lty = lty_obs)
+  if (legend == TRUE) {
+    legend("topright", inset=c(0.05, 0.05), legend=names(fit$mkinmod$map),
+      col=col_obs, pch=pch_obs, lty=lty_obs)
+  }
+}
-- 
cgit v1.2.1