From 8650f26f63a64ac8b72326e2679719744ac99f07 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 2 Mar 2018 17:23:40 +0100 Subject: Use pkgdown.jrwb.de as canonical doc URL The mkin pkgdown docs have made it to the pkgdown README :) https://github.com/r-lib/pkgdown/commit/f0ef0b58a526add2077e5899f45335a5118091f0 --- README.html | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) (limited to 'README.html') diff --git a/README.html b/README.html index 57c4d550..c9f86c6b 100644 --- a/README.html +++ b/README.html @@ -136,7 +136,7 @@ $(document).ready(function () {

Usage

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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.

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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

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Features

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  • 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.
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  • As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example plot.mmkin.
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  • 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).
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  • 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.
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  • 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.
    • +
  • 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.
    • +
  • 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.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.
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  • Iterative reweighting is also possible using the two-component error model for analytical data of Rocke and Lorenzato using the argument reweight.method = "tc".
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  • Iterative reweighting is also possible using the two-component error model for analytical data of Rocke and Lorenzato using the argument reweight.method = "tc".
  • When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite.
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