aboutsummaryrefslogtreecommitdiff
path: root/README.md
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2018-03-03 10:39:34 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2018-03-03 10:39:34 +0100
commit5aec8e34680e05671347f7577ae36c9ad8e37063 (patch)
tree2cfc0f696cc202e9c9a7b7951930bfe88c355d23 /README.md
parent7ceb1dc732ac8674dd8dd70b798fe12378ec10af (diff)
parent8650f26f63a64ac8b72326e2679719744ac99f07 (diff)
Merge branch 'master' of kolab:mkin
Diffstat (limited to 'README.md')
-rw-r--r--README.md22
1 files changed, 11 insertions, 11 deletions
diff --git a/README.md b/README.md
index 4ff631f6..26cdcafb 100644
--- a/README.md
+++ b/README.md
@@ -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.

Contact - Imprint