diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2014-01-17 16:27:46 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2014-01-17 16:27:46 +0100 |
| commit | af4a101d2cca91598ec5d1dc297c31a75517b139 (patch) | |
| tree | c1a15831bd668f96b5b4a3b0308af7977ac335ea /R/mkinfit.R | |
| parent | 66620036c4943c03072b113a63fcd983390102b8 (diff) | |
- 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
Diffstat (limited to 'R/mkinfit.R')
| -rw-r--r-- | R/mkinfit.R | 8 |
1 files changed, 4 insertions, 4 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R index 3e47479f..fd536277 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)) {
|