- Use mkinmod$spec instead of mkinmod$map wherever possible, in order to make it possible to

  to modify mkinmod$map when the mapping of internal to observed variables should be changed.
  Note that such modifications will confuse plot.mkinfit and summary.mkinfit. Setting the class
  attribute to modFit makes summary.modFit useable in such a case

1 files changed, 4 insertions, 4 deletions

diff --git a/R/mkinfit.R b/R/mkinfit.R
index 3e47479..fd53627 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -1,6 +1,6 @@
 # $Id$

 

-# 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

@@ -42,7 +42,7 @@ mkinfit <- function(mkinmod, observed,
   mod_vars <- names(mkinmod$diffs)

 

   # Get the names of observed variables

-  obs_vars = names(mkinmod$map)

+  obs_vars = names(mkinmod$spec)

 

   # Subset observed data with names of observed data in the model

   observed <- subset(observed, name %in% obs_vars)

@@ -110,12 +110,12 @@ mkinfit <- function(mkinmod, observed,
   # or a numeric ode solver from the deSolve package

   if (!solution_type %in% c("auto", "analytical", "eigen", "deSolve"))

      stop("solution_type must be auto, analytical, eigen or de Solve")

-  if (solution_type == "analytical" && length(mkinmod$map) > 1)

+  if (solution_type == "analytical" && length(mkinmod$spec) > 1)

      stop("Analytical solution not implemented for models with metabolites.")

   if (solution_type == "eigen" && !is.matrix(mkinmod$coefmat))

      stop("Eigenvalue based solution not possible, coefficient matrix not present.")

   if (solution_type == "auto") {

-    if (length(mkinmod$map) == 1) {

+    if (length(mkinmod$spec) == 1) {

       solution_type = "analytical"

     } else {

       if (is.matrix(mkinmod$coefmat)) {