From 4c6f29fe2a3ece5a85160b891c89ce0f55299c11 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 23 Jul 2014 08:34:59 +0200
Subject: Parallel metabolite formation with formation fractions in mkinerrmin

---
 DESCRIPTION    | 2 +-
 NEWS.md        | 4 ++++
 R/mkinerrmin.R | 7 ++++---
 TODO           | 1 +
 4 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index bad72501..de9ff203 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
 Title: Routines for fitting kinetic models with one or more state
   variables to chemical degradation data
 Version: 0.9-32
-Date: 2014-07-21
+Date: 2014-07-23
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), 
                     email = "jranke@uni-bremen.de"),
              person("Katrin", "Lindenberger", role = "ctb"),
diff --git a/NEWS.md b/NEWS.md
index c10a25b0..9d5129c9 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,6 +2,8 @@
 
 ## NEW FEATURES
 
+- The number of degrees of freedom is difficult to define in the case of ilr transformation of formation fractions. Now for each source compartment the number of ilr parameters (=number of optimised parameters) is divided by the number of pathways to metabolites (=number of affected data series) which leads to fractional degrees of freedom in some cases.
+
 - The default for the initial value for the first state value is now taken from the mean of the observations at time zero, if available.
 
 - The kinetic model can alternatively be specified with a shorthand name for parent only degradation models, e.g. `SFO`, or `DFOP`.
@@ -14,6 +16,8 @@
 
 ## BUG FIXES
 
+- In the determination of the degrees of freedom in `mkinerrmin`, formation fractions were accounted for multiple times in the case of parallel formation of metabolites. See the new feature described above for the solution.
+
 - `transform_rates=FALSE` in `mkinfit` now also works for FOMC and HS models.
 
 - Initial values for formation fractions were not set in all cases.
diff --git a/R/mkinerrmin.R b/R/mkinerrmin.R
index 9ebac6a4..09724730 100644
--- a/R/mkinerrmin.R
+++ b/R/mkinerrmin.R
@@ -65,11 +65,12 @@ mkinerrmin <- function(fit, alpha = 0.05)
     # Formation fractions are attributed to the target variable, so look
     # for source compartments with formation fractions
     for (source_var in fit$obs_vars) {
+      n.ff.source = length(grep(paste("^f", source_var, sep = "_"),
+                                 names(parms.optim)))
+      n.paths.source = length(fit$mkinmod$spec[[source_var]]$to)
       for (target_var in fit$mkinmod$spec[[source_var]]$to) {
         if (obs_var == target_var) {
-          n.ff.optim <- n.ff.optim +  
-                        length(grep(paste("^f", source_var, sep = "_"),
-                                    names(parms.optim))) 
+          n.ff.optim <- n.ff.optim + n.ff.source/n.paths.source
         }
       }
     }
diff --git a/TODO b/TODO
index 83524220..a9eb8b70 100644
--- a/TODO
+++ b/TODO
@@ -3,6 +3,7 @@ TODO for version 1.0
 - Complete the main package vignette named mkin to include a method description
 - Improve formatting of differential equations in the summary
 - Improve order of parameters in output
+- Write unit tests for mkinerrmin
 
 Nice to have:
 - Calculate confidence intervals for DT50 and DT90 values when only one
-- 
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