From d619711839afb6776f003c990e1a77c8fedf1a6a Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 26 Apr 2014 03:04:12 +0200
Subject: Enable selection of observed variables to plot

---
 R/plot.mkinfit.R    | 25 ++++++++++++++-----------
 man/plot.mkinfit.Rd | 28 +++++++++++++++++-----------
 2 files changed, 31 insertions(+), 22 deletions(-)

diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R
index d4ad6c4..2b85977 100644
--- a/R/plot.mkinfit.R
+++ b/R/plot.mkinfit.R
@@ -1,10 +1,5 @@
-# $Id: $
-
-# Copyright (C) 2010-2013 Johannes Ranke
+# Copyright (C) 2010-2014 Johannes Ranke
 # Contact: jranke@uni-bremen.de
-# The summary function is an adapted and extended version of summary.modFit
-# from the FME package, v 1.1 by Soetart and Petzoldt, which was in turn
-# inspired by summary.nls.lm
 
 # This file is part of the R package mkin
 
@@ -23,8 +18,10 @@
 if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "variable", "observed"))
 
 plot.mkinfit <- function(x, fit = x,
+  obs_vars = vector(),
   xlab = "Time", ylab = "Observed",
-  xlim = range(fit$data$time), ylim = c(0, max(fit$data$observed, na.rm = TRUE)),
+  xlim = range(fit$data$time), 
+  ylim = c(0, max(subset(fit$data, variable %in% obs_vars)$observed, na.rm = TRUE)),
   col_obs = 1:length(fit$mkinmod$map),
   pch_obs = col_obs, 
   lty_obs = rep(1, length(fit$mkinmod$map)),
@@ -34,6 +31,12 @@ plot.mkinfit <- function(x, fit = x,
   solution_type = fit$solution_type
   parms.all <- c(fit$bparms.optim, fit$bparms.fixed)
 
+	obs_vars_all <- names(fit$mkinmod$map)
+
+  if (length(obs_vars) > 0){
+      vars <- intersect(obs_vars_all, obs_vars)	
+  } else vars <- obs_vars_all
+
   ininames <- c(
     rownames(subset(fit$start, type == "state")),
     rownames(subset(fit$fixed, type == "state")))
@@ -61,13 +64,13 @@ plot.mkinfit <- function(x, fit = x,
   }
   # 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)) {
+  for (obs_var in 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[-1], col = col_obs, lty = lty_obs)
+  matlines(out$time, out[vars], col = col_obs[vars], lty = lty_obs[vars])
   if (legend == TRUE) {
-    legend(lpos, inset= inset, legend=names(fit$mkinmod$map),
-      col=col_obs, pch=pch_obs, lty=lty_obs)
+    legend(lpos, inset= inset, legend = vars,
+      col = col_obs[vars], pch = pch_obs[vars], lty = lty_obs[vars])
   }
 }
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index ccf2960..41682ad 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -9,7 +9,9 @@
   the observed data together with the solution of the fitted model.
 }
 \usage{
-\method{plot}{mkinfit}(x, fit = x, xlab = "Time", ylab = "Observed", 
+\method{plot}{mkinfit}(x, fit = x,
+  obs_vars = vector(),
+  xlab = "Time", ylab = "Observed", 
   xlim = range(fit$data$time), ylim = c(0, max(fit$data$observed, na.rm = TRUE)),
   col_obs = 1:length(fit$mkinmod$map), pch_obs = col_obs, 
   lty_obs = rep(1, length(fit$mkinmod$map)),
@@ -18,10 +20,14 @@
 \arguments{
   \item{x}{
     Alias for fit introduced for compatibility with the generic S3 method.  
-}
+  }
   \item{fit}{
     an object of class \code{\link{mkinfit}}.
-}
+  }
+  \item{obs_vars}{
+    A character vector of names of the observed variables for which the 
+    data and the model should be plotted.
+  }
   \item{xlab}{
     label for the x axis.
   }
@@ -36,28 +42,28 @@
   }
   \item{col_obs}{
     colors used for plotting the observed data and the corresponding model prediction lines.
-}
+  }
   \item{pch_obs}{
     symbols to be used for plotting the data.
-}
+  }
   \item{lty_obs}{
     line types to be used for the model predictions.
-}
+  }
   \item{add}{
     should the plot be added to an existing plot?
-}
+  }
   \item{legend}{
     should a legend be added to the plot?
-}
+  }
   \item{lpos}{
     position of the legend. Passed to \code{\link{legend}} as the first argument.
-}
+  }
   \item{inset}{
     Passed to \code{\link{legend}} if applicable.
-}
+  }
   \item{\dots}{
    further arguments passed to \code{\link{plot}}.
-}
+  }
 }
 \value{
   The function is called for its side effect.
-- 
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