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Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 22 |
1 files changed, 11 insertions, 11 deletions
@@ -27,12 +27,12 @@ detailed guidance and helpful tools have been developed as detailed in ## Usage 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) +[`plot.mkinfit`](https://pkgdown.jrwb.de/mkin/reference/plot.mkinfit.html) and -[`plot.mmkin`](http://kinfit.r-forge.r-project.org/mkin_static/reference/plot.mmkin.html), and +[`plot.mmkin`](https://pkgdown.jrwb.de/mkin/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). +[`FOCUS L`](https://pkgdown.jrwb.de/mkin/articles/FOCUS_L.html) and +[`FOCUS D`](https://pkgdown.jrwb.de/mkin/articles/FOCUS_D.html). ## Documentation @@ -44,28 +44,28 @@ 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), + [`mkinmod`](https://pkgdown.jrwb.de/mkin/reference/mkinmod.html), 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`](http://kinfit.r-forge.r-project.org/mkin_static/reference/plot.mmkin.html). + [`plot.mmkin`](https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html). * Model solution (forward modelling) in the function - [`mkinpredict`](http://kinfit.r-forge.r-project.org/mkin_static/reference/mkinpredict.html) + [`mkinpredict`](https://pkgdown.jrwb.de/mkin/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 - [vignette `compiled_models`](http://kinfit.r-forge.r-project.org/mkin_static/articles/compiled_models.html). + [vignette `compiled_models`](https://pkgdown.jrwb.de/mkin/articles/compiled_models.html). The autogeneration of C code was inspired by the [`ccSolve`](https://github.com/karlines/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`](http://kinfit.r-forge.r-project.org/mkin_static/reference/transform_odeparms.html) + [`transform_odeparms`](https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.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 @@ -90,8 +90,8 @@ and at [R-Forge](http://kinfit.r-forge.r-project.org/mkin_static/index.html). componenent for each of the observed variables will be optimised in a second stage after the primary optimisation algorithm has converged. * Iterative reweighting is also possible using the two-component error model - for analytical data of - [Rocke and Lorenzato](http://kinfit.r-forge.r-project.org/mkin_static/reference/sigma_rl.html) + for analytical data of + [Rocke and Lorenzato](https://pkgdown.jrwb.de/mkin/reference/sigma_rl.html) 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. |