From e04fcfcfe06377ec180125e54fe4f458b0747a76 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 13 Nov 2019 21:48:52 +0100 Subject: Improve README --- README.md | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index e89bdc72..602324fa 100644 --- a/README.md +++ b/README.md @@ -71,7 +71,7 @@ and at [R-Forge](http://kinfit.r-forge.r-project.org/mkin_static/index.html). so their estimators can more reasonably be expected to follow a normal distribution. This has the side effect that no constraints are needed in the optimisation. Thanks to René Lehmann for the nice - cooperation on this, especially the isometric logration transformation + cooperation on this, especially the isometric log-ratio transformation that is now used for the formation fractions. * A side effect of this is that when parameter estimates are backtransformed to match the model definition, confidence intervals calculated from @@ -91,9 +91,9 @@ and at [R-Forge](http://kinfit.r-forge.r-project.org/mkin_static/index.html). * Three different error models can be selected using the argument `error_model` to the [`mkinfit`](https://pkgdown.jrwb.de/mkin/reference/mkinfit.html) function. -* Iteratively reweighted least squares fitting is now obsolete, and the - variance by variable error model should now be specified as `error_model - = "obs"`. +* The 'variance by variable' error model which is often fitted using + Iteratively Reweighted Least Squares (IRLS) should now be specified as + `error_model = "obs"`. * A two-component error model similar to the one proposed by [Rocke and Lorenzato](https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html) can be selected using the argument `error_model = "tc"`. @@ -160,11 +160,4 @@ will hopefully be able to learn from each other in the future as well. ## Development -Contributions are welcome! Your -[mkin fork](https://help.github.com/articles/fork-a-repo) is just a mouse click -away... The master branch on github should always be in good shape, I implement -new features in separate branches now. If you prefer subversion, project -members for the -[r-forge project](http://r-forge.r-project.org/R/?group_id=615) are welcome as well. -Generally, the source code of the latest CRAN version should be available there. -You can also browse the source code at [cgit.jrwb.de/mkin](http://cgit.jrwb.de/mkin). +Contributions are welcome! -- cgit v1.2.3 From 49d80b149ec36eb967cb6da3a8b6726e48bf0ecc Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 10 Dec 2019 20:46:05 +0100 Subject: Update and amend the README --- README.html | 19 +++++++++++++++++-- README.md | 24 +++++++++++++++++++++--- docs/index.html | 22 ++++++++++++++++++++-- 3 files changed, 58 insertions(+), 7 deletions(-) (limited to 'README.md') diff --git a/README.html b/README.html index 1e9d7932..dd4ea2c4 100644 --- a/README.html +++ b/README.html @@ -414,8 +414,8 @@ summary {

Credits and historical remarks

-

mkin would not be possible without the underlying software stack consisting of R and the packages deSolve and FME, to say the least.

-

It could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). mkin greatly profits from and largely follows the work done by the FOCUS Degradation Kinetics Workgroup, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.

+

mkin would not be possible without the underlying software stack consisting of R and the package deSolve. In previous version, mkin was also using the functionality of the FME package.

+

mkin could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). mkin greatly profits from and largely follows the work done by the FOCUS Degradation Kinetics Workgroup, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.

Also, it was inspired by the first version of KinGUI developed by BayerCropScience, which is based on the MatLab runtime environment.

The companion package kinfit (now deprecated) was started in 2008 and first published on CRAN on 01 May 2010.

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

@@ -423,6 +423,21 @@ summary {

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.

+
+

References

+ + + + + + + +
+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 +
+

Development

Contributions are welcome!

diff --git a/README.md b/README.md index 602324fa..acbad934 100644 --- a/README.md +++ b/README.md @@ -112,10 +112,11 @@ and one for the [github master branch](https://github.com/jranke/mkin/blob/maste ## Credits and historical remarks `mkin` would not be possible without the underlying software stack consisting -of R and the packages [deSolve](https://cran.r-project.org/package=deSolve) -and [FME](https://cran.r-project.org/package=FME), to say the least. +of R and the package [deSolve](https://cran.r-project.org/package=deSolve). +In previous version, `mkin` was also using the functionality of the +[FME](https://cran.r-project.org/package=FME) package. -It could not have been written without me being introduced to regulatory fate +`mkin` could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). `mkin` greatly profits from and largely follows the work done by the @@ -157,6 +158,23 @@ Finally, there is 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. +## References + + + + + +
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 +
## Development diff --git a/docs/index.html b/docs/index.html index c89fc122..2e960df1 100644 --- a/docs/index.html +++ b/docs/index.html @@ -151,8 +151,8 @@

Credits and historical remarks

-

mkin would not be possible without the underlying software stack consisting of R and the packages deSolve and FME, to say the least.

-

It could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). mkin greatly profits from and largely follows the work done by the FOCUS Degradation Kinetics Workgroup, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.

+

mkin would not be possible without the underlying software stack consisting of R and the package deSolve. In previous version, mkin was also using the functionality of the FME package.

+

mkin could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). mkin greatly profits from and largely follows the work done by the FOCUS Degradation Kinetics Workgroup, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.

Also, it was inspired by the first version of KinGUI developed by BayerCropScience, which is based on the MatLab runtime environment.

The companion package kinfit (now deprecated) was started in 2008 and first published on CRAN on 01 May 2010.

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

@@ -160,6 +160,24 @@

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.

+
+

+References

+ + + +
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 +
+

Development

-- cgit v1.2.3 From 7c8e06d4bae9ec80574147005b7e933937447220 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 10 Dec 2019 20:56:10 +0100 Subject: More additions to the README --- README.html | 2 +- README.md | 10 +++++++--- docs/index.html | 2 +- 3 files changed, 9 insertions(+), 5 deletions(-) (limited to 'README.md') diff --git a/README.html b/README.html index dd4ea2c4..d7ebe451 100644 --- a/README.html +++ b/README.html @@ -414,7 +414,7 @@ summary {

Credits and historical remarks

-

mkin would not be possible without the underlying software stack consisting of R and the package deSolve. In previous version, mkin was also using the functionality of the FME package.

+

mkin would not be possible without the underlying software stack consisting of, among others, R and the package deSolve. In previous version, mkin was also using the functionality of the FME package. Please refer to the package page on CRAN for the full list of imported and suggested R packages. Also, Debian Linux, the vim editor and the Nvim-R plugin have been invaluable in its development.

mkin could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). mkin greatly profits from and largely follows the work done by the FOCUS Degradation Kinetics Workgroup, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.

Also, it was inspired by the first version of KinGUI developed by BayerCropScience, which is based on the MatLab runtime environment.

The companion package kinfit (now deprecated) was started in 2008 and first published on CRAN on 01 May 2010.

diff --git a/README.md b/README.md index acbad934..8a0ecc50 100644 --- a/README.md +++ b/README.md @@ -111,10 +111,14 @@ and one for the [github master branch](https://github.com/jranke/mkin/blob/maste ## Credits and historical remarks -`mkin` would not be possible without the underlying software stack consisting -of R and the package [deSolve](https://cran.r-project.org/package=deSolve). +`mkin` would not be possible without the underlying software stack consisting of, +among others, R and the package [deSolve](https://cran.r-project.org/package=deSolve). In previous version, `mkin` was also using the functionality of the -[FME](https://cran.r-project.org/package=FME) package. +[FME](https://cran.r-project.org/package=FME) package. Please refer to the +[package page on CRAN](https://cran.r-project.org/package=mkin) for the full list +of imported and suggested R packages. Also, [Debian Linux](https://debian.org), +the vim editor and the [Nvim-R](https://github.com/jalvesaq/Nvim-R) plugin have +been invaluable in its development. `mkin` could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories diff --git a/docs/index.html b/docs/index.html index 2e960df1..fcb9c90b 100644 --- a/docs/index.html +++ b/docs/index.html @@ -151,7 +151,7 @@

Credits and historical remarks

-

mkin would not be possible without the underlying software stack consisting of R and the package deSolve. In previous version, mkin was also using the functionality of the FME package.

+

mkin would not be possible without the underlying software stack consisting of, among others, R and the package deSolve. In previous version, mkin was also using the functionality of the FME package. Please refer to the package page on CRAN for the full list of imported and suggested R packages. Also, Debian Linux, the vim editor and the Nvim-R plugin have been invaluable in its development.

mkin could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). mkin greatly profits from and largely follows the work done by the FOCUS Degradation Kinetics Workgroup, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.

Also, it was inspired by the first version of KinGUI developed by BayerCropScience, which is based on the MatLab runtime environment.

The companion package kinfit (now deprecated) was started in 2008 and first published on CRAN on 01 May 2010.

-- cgit v1.2.3