From 328d1173db2395c1a5705b5f0980e2956db8be1f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 13 Feb 2025 12:43:29 +0100 Subject: Update wordlist, bump date and simplify DESCRIPTION Also, the R-Universe URL that the badge points to is updated --- DESCRIPTION | 15 +- R/mkinpredict.R | 4 +- R/nlme.R | 2 +- README.md | 2 +- docs/404.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 6 +- docs/index.html | 6 +- docs/news/index.html | 2 +- docs/reference/index.html | 2 +- docs/reference/mkinpredict.html | 158 ++++++++++---------- docs/reference/nlme-1.png | Bin 78105 -> 76554 bytes docs/reference/nlme-2.png | Bin 90402 -> 88313 bytes docs/reference/nlme.html | 137 ++++++++---------- docs/search.json | 2 +- inst/WORDLIST | 310 ++++++++++++++++++++++++++-------------- log/check.log | 15 +- man/mkinpredict.Rd | 4 +- man/nlme.Rd | 2 +- 19 files changed, 374 insertions(+), 297 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3c1c4f7d..71fa3d99 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 1.2.9 -Date: 2024-04-27 +Date: 2025-02-13 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "johannes.ranke@jrwb.de", @@ -15,14 +15,13 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006, models, model solution based on eigenvalues if possible or using numerical solvers. If a C compiler (on windows: 'Rtools') is installed, differential equation models are solved using automatically generated C functions. - Heteroscedasticity can be taken into account using variance by variable or - two-component error models as described by Ranke and Meinecke (2018) - . Hierarchical degradation models can - be fitted using nonlinear mixed-effects model packages as a back end as - described by Ranke et al. (2021) . Please + Inhomogeneous errors can be taken into account using variance by variable or + two-component error models . Hierarchical + degradation models can be fitted using nonlinear mixed-effects model packages + as a back end . Please note that no warranty is implied for correctness of results or fitness for a particular purpose. -Depends: R (>= 2.15.1), +Depends: R (>= 4.1.0) Imports: stats, graphics, methods, parallel, deSolve (>= 1.35), R6, inline (>= 0.3.19), numDeriv, lmtest, pkgbuild, nlme (>= 3.1-151), saemix (>= 3.2), rlang, vctrs Suggests: knitr, rbenchmark, tikzDevice, testthat, rmarkdown, covr, vdiffr, @@ -36,4 +35,4 @@ VignetteBuilder: knitr BugReports: https://github.com/jranke/mkin/issues/ URL: https://pkgdown.jrwb.de/mkin/ Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.2.9000 diff --git a/R/mkinpredict.R b/R/mkinpredict.R index 60456fb2..4c6d7862 100644 --- a/R/mkinpredict.R +++ b/R/mkinpredict.R @@ -22,7 +22,7 @@ #' variables. The third possibility "eigen" is fast in comparison to uncompiled #' ODE models, but not applicable to some models, e.g. using FOMC for the #' parent compound. -#' @param method.ode The solution method passed via [mkinpredict] to [ode]] in +#' @param method.ode The solution method passed via [mkinpredict] to `deSolve::ode()` in #' case the solution type is "deSolve" and we are not using compiled code. #' When using compiled code, only lsoda is supported. #' @param use_compiled If set to \code{FALSE}, no compiled version of the @@ -36,7 +36,7 @@ #' the observed variables (default) or for all state variables (if set to #' FALSE). Setting this to FALSE has no effect for analytical solutions, #' as these always return mapped output. -#' @param na_stop Should it be an error if [ode] returns NaN values +#' @param na_stop Should it be an error if `deSolve::ode()` returns NaN values #' @param \dots Further arguments passed to the ode solver in case such a #' solver is used. #' @return A matrix with the numeric solution in wide format diff --git a/R/nlme.R b/R/nlme.R index 6b2d06d0..de82d99c 100644 --- a/R/nlme.R +++ b/R/nlme.R @@ -126,7 +126,7 @@ nlme_function <- function(object) { #' @rdname nlme #' @importFrom rlang !!! -#' @return A \code{\link{groupedData}} object +#' @return A `nlme::groupedData` object #' @export nlme_data <- function(object) { if (nrow(object) > 1) stop("Only row objects allowed") diff --git a/README.md b/README.md index 8d7952ee..2d3720ca 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![](https://www.r-pkg.org/badges/version/mkin)](https://cran.r-project.org/package=mkin) -[![mkin status badge](https://jranke.r-universe.dev/badges/mkin)](https://jranke.r-universe.dev/ui/#package:mkin) +[![mkin status badge](https://jranke.r-universe.dev/badges/mkin)](https://jranke.r-universe.dev/#package:mkin) [![Build Status](https://app.travis-ci.com/jranke/mkin.svg?token=Sq9VuYWyRz2FbBLxu6DK&branch=main)](https://app.travis-ci.com/jranke/mkin) diff --git a/docs/404.html b/docs/404.html index 22e29157..f05b97f3 100644 --- a/docs/404.html +++ b/docs/404.html @@ -88,7 +88,7 @@ Content not found. Please use links in the navbar.
-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/docs/articles/index.html b/docs/articles/index.html index 0d62e494..0c3e7449 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -101,7 +101,7 @@
-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/docs/authors.html b/docs/authors.html index 56bae28c..26399e08 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -83,14 +83,14 @@

Citation

Source: DESCRIPTION

-

Ranke J (2024). +

Ranke J (2025). mkin: Kinetic Evaluation of Chemical Degradation Data. R package version 1.2.9, https://pkgdown.jrwb.de/mkin/. 

@Manual{,
   title = {mkin: Kinetic Evaluation of Chemical Degradation Data},
   author = {Johannes Ranke},
-  year = {2024},
+  year = {2025},
   note = {R package version 1.2.9},
   url = {https://pkgdown.jrwb.de/mkin/},
 }
@@ -105,7 +105,7 @@ R package version 1.2.9, https://pkgdown
-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/docs/index.html b/docs/index.html index 915a3243..8c1a7c59 100644 --- a/docs/index.html +++ b/docs/index.html @@ -9,8 +9,8 @@ - - + + Skip to contents @@ -256,7 +256,7 @@ Von Götz N, Nörtersheuser P, Richter O (1999) Population based analysis of pes
-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/docs/news/index.html b/docs/news/index.html index eeb84a76..44de0536 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -656,7 +656,7 @@
-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/docs/reference/index.html b/docs/reference/index.html index 63e1e634..1448bbe6 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -722,7 +722,7 @@
-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 860c7cfc..13f42da0 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -1,78 +1,65 @@ -Produce predictions from a kinetic model using specific parameters — mkinpredict • mkinProduce predictions from a kinetic model using specific parameters — mkinpredict • mkin +kinetic parameters and initial values for the state variables."> Skip to contents - -