From af7c6de4db9981ac814362c441fbac22c8faa2d7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 24 Nov 2022 09:02:26 +0100 Subject: Start online docs of the development version --- docs/dev/index.html | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) (limited to 'docs/dev/index.html') diff --git a/docs/dev/index.html b/docs/dev/index.html index 4709fe29..2615d389 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -45,7 +45,7 @@ mkin - 1.2.0 + 1.2.2 @@ -153,9 +153,9 @@

General

@@ -186,7 +186,7 @@

GUI

-

There is a graphical user interface that may be useful. Please refer to its documentation page for installation instructions and a manual.

+

There is a graphical user interface that may be useful. Please refer to its documentation page for installation instructions and a manual. It only supports evaluations using (generalised) nonlinear regression, but not simultaneous fits using nonlinear mixed-effects models.

News @@ -203,8 +203,8 @@

The first mkin code was published on 11 May 2010 and the first CRAN version on 18 May 2010.

In 2011, Bayer Crop Science started to distribute an R based successor to KinGUI named KinGUII whose R code is based on mkin, but which added, among other refinements, a closed source graphical user interface (GUI), iteratively reweighted least squares (IRLS) optimisation of the variance for each of the observed variables, and Markov Chain Monte Carlo (MCMC) simulation functionality, similar to what is available e.g. in the FME package.

Somewhat in parallel, Syngenta has sponsored the development of an mkin and KinGUII based GUI application called CAKE, which also adds IRLS and MCMC, is more limited in the model formulation, but puts more weight on usability. CAKE is available for download from the CAKE website, where you can also find a zip archive of the R scripts derived from mkin, published under the GPL license.

-

Finally, there is KineticEval, which contains a further development of the scripts used for KinGUII, so the different tools will hopefully be able to learn from each other in the future as well.

-

Thanks to René Lehmann, formerly working at the Umweltbundesamt, for the nice cooperation cooperation on parameter transformations, especially the isometric log-ratio transformation that is now used for formation fractions in case there are more than two transformation targets.

+

Finally, there is KineticEval, which contains some further development of the scripts used for KinGUII.

+

Thanks to René Lehmann, formerly working at the Umweltbundesamt, for the nice cooperation on parameter transformations, especially the isometric log-ratio transformation that is now used for formation fractions in case there are more than two transformation targets.

Many inspirations for improvements of mkin resulted from doing kinetic evaluations of degradation data for my clients while working at Harlan Laboratories and at Eurofins Regulatory AG, and now as an independent consultant.

Funding was received from the Umweltbundesamt in the course of the projects

    @@ -215,7 +215,8 @@
  • Project Number 120667 (Development of objective criteria for the evaluation of the visual fit in the kinetic evaluation of degradation data, 2019-2020)
  • Project Number 146839 (Checking the feasibility of using mixed-effects models for the derivation of kinetic modelling parameters from degradation studies, 2020-2021)
-

Thanks are due also to Emmanuelle Comets, maintainer of the saemix package, for the nice collaboration on using the SAEM algorithm and its implementation in saemix for the evaluation of chemical degradation data.

+

Thanks to everyone involved for collaboration and support!

+

Thanks are due also to Emmanuelle Comets, maintainer of the saemix package, for her interest and support for using the SAEM algorithm and its implementation in saemix for the evaluation of chemical degradation data.

References -- cgit v1.2.1 From a54bd290bc3884d0000c52c1b29bc557825d9eae Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 15 Dec 2022 14:50:28 +0100 Subject: List random effects correlations in output if any Update docs --- docs/dev/index.html | 21 +++++++++++++++------ 1 file changed, 15 insertions(+), 6 deletions(-) (limited to 'docs/dev/index.html') diff --git a/docs/dev/index.html b/docs/dev/index.html index 2615d389..4723879e 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -222,12 +222,21 @@

References

- - - + + + + + + + + +
Ranke J, Wöltjen J, Schmidt J, and Comets E (2021) Taking kinetic evaluations of degradation data to the next level with nonlinear mixed-effects models. Environments 8 (8) 71 doi:10.3390/environments8080071 -
Ranke J, Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data Environments 6 (12) 124 doi:10.3390/environments6120124 -
Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic evaluation of chemical degradation data Environmental Sciences Europe 30 17 doi:10.1186/s12302-018-0145-1 -
+Ranke J, Wöltjen J, Schmidt J, and Comets E (2021) Taking kinetic evaluations of degradation data to the next level with nonlinear mixed-effects models. Environments 8 (8) 71 doi:10.3390/environments8080071 +
+Ranke J, Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data Environments 6 (12) 124 doi:10.3390/environments6120124 +
+Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic evaluation of chemical degradation data Environmental Sciences Europe 30 17 doi:10.1186/s12302-018-0145-1 +

-- cgit v1.2.1 From 24eb77216700cf8b2f2bde3abad84c1f83f9e32a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 9 Jan 2023 06:22:04 +0100 Subject: Prebuilt PDF vignettes, summary_listing --- docs/dev/index.html | 24 ++++++++---------------- 1 file changed, 8 insertions(+), 16 deletions(-) (limited to 'docs/dev/index.html') diff --git a/docs/dev/index.html b/docs/dev/index.html index 4723879e..993b8eea 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -19,11 +19,11 @@ 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) - <doi:10.3390/environments6120124>. Interfaces to several nonlinear - mixed-effects model packages are available, some of which are described by - Ranke et al. (2021) <doi:10.3390/environments8080071>. Please note that no - warranty is implied for correctness of results or fitness for a particular - purpose."> + <doi:10.3390/environments6120124>. Hierarchical degradation models can + be fitted using nonlinear mixed-effects model packages as a backend as + described by Ranke et al. (2021) <doi:10.3390/environments8080071>. Please + note that no warranty is implied for correctness of results or fitness for a + particular purpose.">