From 545d4bdfe1fc532f6d5d1718ee08444430d2976f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 10 Nov 2017 15:15:21 +0100 Subject: Delete trailing whitespace, update README.html --- DESCRIPTION | 4 ++-- GNUmakefile | 6 +++--- README.html | 5 ++--- README.md | 56 ++++++++++++++++++++++++++++---------------------------- 4 files changed, 35 insertions(+), 36 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4f61178e..a86eeadd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 0.9.46.2 Date: 2017-10-10 -Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), +Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", comment = c(ORCID = "0000-0003-4371-6538")), person("Katrin", "Lindenberger", role = "ctb"), @@ -26,4 +26,4 @@ LazyData: yes Encoding: UTF-8 VignetteBuilder: knitr BugReports: http://github.com/jranke/mkin/issues -URL: http://github.com/jranke/mkin +URL: https://cgit.jrwb.de/mkin/about diff --git a/GNUmakefile b/GNUmakefile index c28dc221..6aa45f8a 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -34,10 +34,10 @@ all: build $(TGZ): $(pkgfiles) vignettes "$(RBIN)/R" CMD build . 2>&1 | tee build.log -$(TGZVNR): $(pkgfiles) +$(TGZVNR): $(pkgfiles) "$(RBIN)/R" CMD build . --no-build-vignettes;\ mv $(TGZ) $(TGZVNR) - + build: $(TGZ) build-no-vignettes: $(TGZVNR) @@ -84,7 +84,7 @@ pd_articles: git add -A git commit -m 'Static documentation articles rebuilt by pkgdown::build_articles()' -e -r-forge: +r-forge: git archive master > $(HOME)/mkin.tar;\ cd $(RFDIR) && rm -r `ls` && tar -xf $(HOME)/mkin.tar;\ rm -r $(SDDIR)/*;\ diff --git a/README.html b/README.html index 3dfcbb40..a38856bd 100644 --- a/README.html +++ b/README.html @@ -121,7 +121,7 @@ $(document).ready(function () {

mkin

-

+

The R package mkin provides calculation routines for the analysis of chemical degradation data, including multicompartment kinetics as needed for modelling the formation and decline of transformation products, or if several compartments are involved.

Installation

@@ -146,8 +146,7 @@ $(document).ready(function () {
  • Highly flexible model specification using mkinmod, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.
  • 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.
    • +
  • 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 RenĂ© Lehmann for the nice cooperation on this, especially the isometric logration 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.
    • diff --git a/README.md b/README.md index e83a3494..05911f62 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ if several compartments are involved. ## Installation -You can install the latest released version from +You can install the latest released version from [CRAN](https://cran.r-project.org/package=mkin) from within R: ```r @@ -20,7 +20,7 @@ install.packages("mkin") In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an -important role. For the evaluation of pesticide degradation experiments, +important role. For the evaluation of pesticide degradation experiments, detailed guidance and helpful tools have been developed as detailed in 'Credits and historical remarks' below. @@ -28,37 +28,37 @@ detailed guidance and helpful tools have been developed as detailed in For a start, have a look a the code examples provided for [`plot.mkinfit`](http://kinfit.r-forge.r-project.org/mkin_static/reference/plot.mkinfit.html) -and -[`plot.mmkin`](http://kinfit.r-forge.r-project.org/mkin_static/reference/plot.mmkin.html), and +and +[`plot.mmkin`](http://kinfit.r-forge.r-project.org/mkin_static/reference/plot.mmkin.html), and at the package vignettes [`FOCUS L`](http://kinfit.r-forge.r-project.org/mkin_static/articles/FOCUS_L.html) and [`FOCUS D`](http://kinfit.r-forge.r-project.org/mkin_static/articles/FOCUS_D.html). ## Documentation -The HTML documentation is available at +The HTML documentation is available at [jrwb.de](https://pkgdown.jrwb.de/mkin), at -[github](http://jranke.github.io/mkin) +[github](http://jranke.github.io/mkin) and at [R-Forge](http://kinfit.r-forge.r-project.org/mkin_static/index.html). ## Features * Highly flexible model specification using [`mkinmod`](http://kinfit.r-forge.r-project.org/mkin_static/reference/mkinmod.html), - including equilibrium reactions and using the single first-order + including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable. -* As of version 0.9-39, fitting of several models to several datasets, optionally in +* As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example [`plot.mmkin`](http://kinfit.r-forge.r-project.org/mkin_static/reference/plot.mmkin.html). * Model solution (forward modelling) in the function - [`mkinpredict`](http://kinfit.r-forge.r-project.org/mkin_static/reference/mkinpredict.html) - is performed either using the analytical solution for the case of + [`mkinpredict`](http://kinfit.r-forge.r-project.org/mkin_static/reference/mkinpredict.html) + 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 + generated C code, see [vignette `compiled_models`](http://kinfit.r-forge.r-project.org/mkin_static/articles/compiled_models.html). The autogeneration of C code was inspired by the [`ccSolve`](https://github.com/karlines/ccSolve) package. Thanks @@ -74,8 +74,8 @@ and at [R-Forge](http://kinfit.r-forge.r-project.org/mkin_static/index.html). * 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 + 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. @@ -86,10 +86,10 @@ and at [R-Forge](http://kinfit.r-forge.r-project.org/mkin_static/index.html). (see below) is calculated for each observed variable. * Iteratively reweighted least squares fitting is implemented in a similar way as in KinGUII and CAKE (see below). Simply add the argument - `reweight.method = "obs"` to your call to `mkinfit` and a separate variance + `reweight.method = "obs"` to your call to `mkinfit` and a separate variance componenent for each of the observed variables will be optimised in a second stage after the primary optimisation algorithm has converged. -* When a metabolite decline phase is not described well by SFO kinetics, +* When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite. ## GUI @@ -97,7 +97,7 @@ and at [R-Forge](http://kinfit.r-forge.r-project.org/mkin_static/index.html). There is a graphical user interface that I consider useful for real work. Please refer to its [documentation page](http://kinfit.r-forge.r-project.org/gmkin_static) for installation instructions and a manual. - + ## News Yes, there is a ChangeLog, for the latest [CRAN release](https://cran.r-project.org/package=mkin/news.html) @@ -112,7 +112,7 @@ and [FME](https://cran.r-project.org/package=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 +the work done by the [FOCUS Degradation Kinetics Workgroup](http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics), as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014. @@ -120,18 +120,18 @@ 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](http://kinfit.r-forge.r-project.org/kinfit_static/index.html) (now deprecated) was -[started in 2008](https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=2) and +The companion package +[kinfit](http://kinfit.r-forge.r-project.org/kinfit_static/index.html) (now deprecated) was +[started in 2008](https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=2) and [first published](https://cran.r-project.org/src/contrib/Archive/kinfit/) on CRAN on 01 May 2010. -The first `mkin` code was -[published on 11 May 2010](https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=8) and the +The first `mkin` code was +[published on 11 May 2010](https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=8) and the [first CRAN version](https://cran.r-project.org/src/contrib/Archive/mkin) on 18 May 2010. -In 2011, Bayer Crop Science started to distribute an R based successor to KinGUI named +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, amongst other refinements, a closed source graphical user interface (GUI), iteratively reweighted least squares (IRLS) optimisation of the variance for each of the @@ -146,19 +146,19 @@ website](http://showcase.tessella.com/products/cake), where you can also find a zip archive of the R scripts derived from `mkin`, published under the GPL license. -Finally, there is -[KineticEval](http://github.com/zhenglei-gao/KineticEval), which contains +Finally, there is +[KineticEval](http://github.com/zhenglei-gao/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. ## Development -Contributions are welcome! Your +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 +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 +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). -- cgit v1.2.1