From 3151647526f299686b68420a83ae38cd7f3d08f5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 9 Nov 2015 09:05:15 +0100 Subject: Rebuild vignettes and static documentation --- inst/web/index.html | 452 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 452 insertions(+) create mode 100644 inst/web/index.html (limited to 'inst/web/index.html') diff --git a/inst/web/index.html b/inst/web/index.html new file mode 100644 index 00000000..a08af34f --- /dev/null +++ b/inst/web/index.html @@ -0,0 +1,452 @@ + + + + +Index. mkin 0.9-41 + + + + + + + + + + + + + + + +
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mkin

+ +

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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

+ +

You can install the latest released version from +CRAN from within R:

+ +
install.packages("mkin")
+
+ +

If looking for the latest features, you can install directly from +github, e.g. using the devtools package. +Using quick = TRUE skips docs, multiple-architecture builds, demos, and +vignettes, to make installation as fast and painless as possible.

+ +
require(devtools)
+install_github("jranke/mkin", quick = TRUE)
+
+ +

Background

+ +

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, +detailed guidance and helpful tools have been developed as detailed in +'Credits and historical remarks' below.

+ +

Usage

+ +

For a start, have a look a the code examples provided for +plot.mkinfit +and +plot.mmkin, and +at the package vignettes +FOCUS L and +FOCUS D.

+ +

Documentation

+ +

The HTML documentation is +maintained at the R-Forge project site.

+ +

Features

+ +
    +
  • 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.
    • +
  • Model optimisation with +mkinfit +internally using the modFit function from the FME package, +but using the Port routine nlminb per default.
    • +
  • 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.
    • +
  • 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.
    • +
  • Iteratively reweighted least squares fitting is implemented in a similar way +as in KinGUII and CAKE (see below). Simply add the argument +reweight = "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, +either IORE kinetics (often producing failures of the integration algorithm) +or SFORB kinetics (working nicely) can be used for the metabolite, adding one +respectively two parameters to the system.
    • +
+ +

GUI

+ +

There is a graphical user interface that I consider useful for real work. Please +refer to its documentation page +for installation instructions and a manual.

+ +

News

+ +

Yes, there is a ChangeLog, for the latest CRAN release +and one for the github master branch.

+ +

Credits and historical remarks

+ +

mkin would not be possible without the underlying software stack consisting +of R and the packages deSolve, +minpack.lm 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 +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 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.

+ +

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 +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.

+ +

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.

+ + +

Help topics

+ +

Main functions

+

Essential functionality

+ + +
    + +
  • + mkinmod
    Function to set up a kinetic model with one or more state variables +
    • + +
  • + mkinfit
    Fit a kinetic model to data with one or more state variables +
    • + +
  • + mmkin
    Fit one or more kinetic models with one or more state variables to one or more datasets +
    • + +
+

Show results

+

Functions working on mkinfit objects

+ + +
    + +
  • + plot.mkinfit
    Plot the observed data and the fitted model of an mkinfit object +
    • + +
  • + summary.mkinfit(print.summary.mkinfit)
    Summary method for class "mkinfit" +
    • + +
  • + mkinresplot
    Function to plot residuals stored in an mkin object +
    • + +
  • + mkinparplot
    Function to plot the confidence intervals obtained using +
    • + +
  • + endpoints
    Function to calculate endpoints for further use from kinetic models fitted with mkinfit +
    • + +
  • + mkinerrmin
    Calculate the minimum error to assume in order to pass the variance test +
    • + +
+

Work with mmkin objects

+

Functions working with aggregated results

+ + +
    + +
  • + [.mmkin
    Subsetting method for mmkin objects
    • + +
  • + plot.mmkin
    Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object +
    • + +
+

Datasets and known results

+ + + +

Helper functions

+ + +
    + +
  • + mkin_wide_to_long
    Convert a dataframe with observations over time into long format +
    • + +
  • + mkin_long_to_wide
    Convert a dataframe from long to wide format +
    • + +
  • + mkinsub
    Function to set up a kinetic submodel for one state variable +
    • + +
  • + mkinds
    A dataset class for mkin
    • + +
  • + print.mkinds
    Print mkinds objects +
    • + +
  • + print.mkinmod
    Print mkinmod objects +
    • + +
  • + mkinpredict
    Produce predictions from a kinetic model using specifc parameters +
    • + +
  • + transform_odeparms(backtransform_odeparms)
    Functions to transform and backtransform kinetic parameters for fitting +
    • + +
  • + ilr(invilr)
    Function to perform isometric log-ratio transformation +
    • + +
  • + geometric_mean
    Calculate the geometric mean
    • + +
+

Analytical solutions

+

Parent only model solutions

+ + + +

Deprecated functions

+

Functions that have been superseeded

+ + +
    + +
  • + mkinplot
    Plot the observed data and the fitted model of an mkinfit object +
    • + +
+
+ +
+

Vignettes

+ + +

Dependencies

+
    +
  • Depends: minpack.lm, rootSolve, inline, parallel
    • +
  • Imports: stats, graphics, methods, FME, deSolve, R6
    • +
  • Suggests: knitr, testthat, microbenchmark
    • + +
+

Authors

+
    +
  • Johannes Ranke [aut, cre, cph]
    • +
  • Katrin Lindenberger [ctb]
    • +
  • RenĂ© Lehmann [ctb]
    • +
  • Eurofins Regulatory AG [cph]
    • +
+ +
+
+ + +
+ + \ No newline at end of file -- cgit v1.2.1