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-rw-r--r--DESCRIPTION21
-rw-r--r--NEWS.md4
-rw-r--r--R/mkinfit.R2
3 files changed, 15 insertions, 12 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 2cdf3d1a..bc35262d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,22 +1,21 @@
Package: mkin
Type: Package
-Title: Routines for Fitting Kinetic Models with One or More State
- Variables to Chemical Degradation Data
+Title: Kinetic evaluation of chemical degradation data
Version: 0.9.42.9000
-Date: 2016-06-06
+Date: 2016-06-17
Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
email = "jranke@uni-bremen.de"),
person("Katrin", "Lindenberger", role = "ctb"),
person("René", "Lehmann", role = "ctb"),
person("Eurofins Regulatory AG", role = "cph"))
-Description: Calculation routines based on the FOCUS Kinetics Report (2006).
- Includes a function for conveniently defining differential equation models,
- model solution based on eigenvalues if possible or using numerical solvers
- and a choice of the optimisation methods made available by the 'FME' package.
- If a C compiler (on windows: 'Rtools') is installed, differential
- equation models are solved using compiled C functions.
- Please note that no warranty is implied for correctness of results or fitness
- for a particular purpose.
+Description: Calculation routines based on the FOCUS Kinetics Report (2006,
+ 2014). Includes a function for conveniently defining differential equation
+ models, model solution based on eigenvalues if possible or using numerical
+ solvers and a choice of the optimisation methods made available by the 'FME'
+ package. If a C compiler (on windows: 'Rtools') is installed, differential
+ equation models are solved using compiled C functions. Please note that no
+ warranty is implied for correctness of results or fitness for a particular
+ purpose.
Depends: minpack.lm, rootSolve, inline, parallel
Imports: stats, graphics, methods, FME, deSolve, R6
Suggests: knitr, testthat, microbenchmark, ggplot2
diff --git a/NEWS.md b/NEWS.md
index 9b0181ed..bc593f98 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,8 @@
### Major changes
+- The title was changed to `Kinetic evaluations of chemical degradation data`
+
- `mkinfit`: Do not error out in cases where the fit converges, but the Jacobian for the untransformed model cost can not be estimated. Give a warning instead and return NA for the t-test results.
- `summary.mkinfit`: Give a warning message when the covariance matrix can not be obtained.
@@ -18,6 +20,8 @@
- `endpoints`: When the name of a substance degrading to a metabolite (e.g. a parent compound) used in the model formulation ended in the letter `f`, some rate parameters could be listed as formation fractions with mixed up names. These would also appear in the summary.
+- `mkinfit`: Check for all observed variables when checking if the user tried to fix formation fractions when fitting them using ilr transformation.
+
## mkin 0.9.42 (2016-03-25)
### Major changes
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 2302544b..c6b6915c 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -121,7 +121,7 @@ mkinfit <- function(mkinmod, observed,
# Do not allow fixing formation fractions if we are using the ilr transformation,
# this is not supported
if (transform_fractions == TRUE && length(fixed_parms) > 0) {
- if (grepl("^f_", fixed_parms)) {
+ if (any(grepl("^f_", fixed_parms))) {
stop("Fixing formation fractions is not supported when using the ilr ",
"transformation.")
}

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