From e04fcfcfe06377ec180125e54fe4f458b0747a76 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 13 Nov 2019 21:48:52 +0100 Subject: Improve README --- docs/index.html | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'docs/index.html') diff --git a/docs/index.html b/docs/index.html index 231ef39f..c89fc122 100644 --- a/docs/index.html +++ b/docs/index.html @@ -127,14 +127,14 @@
  • As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example plot.mmkin.
  • Model solution (forward modelling) in the function mkinpredict is performed either using the analytical solution for the case of parent only degradation, an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the deSolve package (default is lsoda).
  • If a C compiler is installed, the kinetic models are compiled from automatically generated C code, see vignette compiled_models. The autogeneration of C code was inspired by the ccSolve package. Thanks to Karline Soetaert for her work on that.
    • -
  • By default, kinetic rate constants and kinetic formation fractions are transformed internally using transform_odeparms 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 that is now used for the formation fractions.
    • +
  • By default, kinetic rate constants and kinetic formation fractions are transformed internally using transform_odeparms 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 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 standard errors are also backtransformed to the correct scale, and will not include meaningless values like negative rate constants or formation fractions adding up to more than 1, which can not occur in a single experiment with a single defined radiolabel position.
  • The usual one-sided t-test for significant difference from zero is nevertheless shown based on estimators for the untransformed parameters.
  • Summary and plotting functions. The summary of an mkinfit object is in fact a full report that should give enough information to be able to approximately reproduce the fit with other tools.
  • The chi-squared error level as defined in the FOCUS kinetics guidance (see below) is calculated for each observed variable.
  • When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite.
  • Three different error models can be selected using the argument error_model to the mkinfit 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 can be selected using the argument error_model = "tc".
    • @@ -163,7 +163,7 @@

    Development

    -

    Contributions are welcome! Your mkin fork 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 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.

    +

    Contributions are welcome!

    -- cgit v1.2.1 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 --- docs/index.html | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) (limited to 'docs/index.html') 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 v1.2.1 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 --- docs/index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'docs/index.html') 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 v1.2.1 From 70fe6d14e27fa8fb0634856ecc45a27f4f689d88 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 9 Jan 2020 17:50:23 +0100 Subject: Remove unused FME package from DESCRIPTION text --- docs/index.html | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) (limited to 'docs/index.html') diff --git a/docs/index.html b/docs/index.html index fcb9c90b..fe334eb8 100644 --- a/docs/index.html +++ b/docs/index.html @@ -14,11 +14,10 @@ + solvers. If a C compiler (on windows: Rtools) is installed, differential + equation models are solved using automatically generated C functions. Please + note that no warranty is implied for correctness of results or fitness for a + particular purpose.">