From 4a91212601c379498202f8a5cecdee085f2cbe0a Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 26 Apr 2014 08:42:29 +0200
Subject: Fix the default case for obs_vars in plot.mkinfit()

---
 R/plot.mkinfit.R    | 16 +++++-----------
 man/plot.mkinfit.Rd |  5 +++--
 2 files changed, 8 insertions(+), 13 deletions(-)

diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R
index 2b85977..80cf45f 100644
--- a/R/plot.mkinfit.R
+++ b/R/plot.mkinfit.R
@@ -18,7 +18,7 @@
 if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "variable", "observed"))
 
 plot.mkinfit <- function(x, fit = x,
-  obs_vars = vector(),
+  obs_vars = names(fit$mkinmod$map),
   xlab = "Time", ylab = "Observed",
   xlim = range(fit$data$time), 
   ylim = c(0, max(subset(fit$data, variable %in% obs_vars)$observed, na.rm = TRUE)),
@@ -31,12 +31,6 @@ 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")))
@@ -64,13 +58,13 @@ 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 vars) {
+  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[vars], col = col_obs[vars], lty = lty_obs[vars])
+  matlines(out$time, out[obs_vars], col = col_obs[obs_vars], lty = lty_obs[obs_vars])
   if (legend == TRUE) {
-    legend(lpos, inset= inset, legend = vars,
-      col = col_obs[vars], pch = pch_obs[vars], lty = lty_obs[vars])
+    legend(lpos, inset= inset, legend = obs_vars,
+      col = col_obs[obs_vars], pch = pch_obs[obs_vars], lty = lty_obs[obs_vars])
   }
 }
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index 41682ad..4ae82a5 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -10,7 +10,7 @@
 }
 \usage{
 \method{plot}{mkinfit}(x, fit = x,
-  obs_vars = vector(),
+  obs_vars = names(fit$mkinmod$map),
   xlab = "Time", ylab = "Observed", 
   xlim = range(fit$data$time), ylim = c(0, max(fit$data$observed, na.rm = TRUE)),
   col_obs = 1:length(fit$mkinmod$map), pch_obs = col_obs, 
@@ -26,7 +26,8 @@
   }
   \item{obs_vars}{
     A character vector of names of the observed variables for which the 
-    data and the model should be plotted.
+    data and the model should be plotted. Defauls to all observed variables
+    in the model.
   }
   \item{xlab}{
     label for the x axis.
-- 
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