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-rw-r--r--DESCRIPTION2
-rw-r--r--NEWS.md4
-rw-r--r--R/mkinerrmin.R7
-rw-r--r--TODO1
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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