diff options
| -rw-r--r-- | DESCRIPTION | 21 | ||||
| -rw-r--r-- | NEWS.md | 4 | ||||
| -rw-r--r-- | R/mkinfit.R | 2 |
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 @@ -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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