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authorjranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>2013-11-12 01:34:29 +0000
committerjranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>2013-11-12 01:34:29 +0000
commit1e1025009d488e942fd2ab49eb70997537664f1f (patch)
tree7681f3b1ac16a4faae8ea432d05d0af1ad23b409
parentc3dbf4f7644355ec0a7fd080ad54f35156cb7791 (diff)
Merged README work from master branch
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@159 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
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--- a/README.md
+++ b/README.md
@@ -30,10 +30,54 @@ install_github("mkin", "jranke")
## Usage
For a start, have a look at the examples provided in the
-[mkinfit Documentation](http://kinfit.r-forge.r-project.org/mkin_static/mkinfit.html)
+[`mkinfit`](http://kinfit.r-forge.r-project.org/mkin_static/mkinfit.html)
+Documentation
or the package vignettes referenced from the
[mkin package documentation page](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/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.
+* Model solution (forward modelling) in the function
+ [`mkinpredict`](http://kinfit.r-forge.r-project.org/mkin_static/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`).
+ These have decreasing efficiency, and are automatically chosen
+ by default.
+* Model optimisation with
+ [`mkinfit`](http://kinfit.r-forge.r-project.org/mkin_static/mkinfit.html)
+ internally using the `modFit` function from the `FME` package,
+ which uses the least-squares Levenberg-Marquardt algorithm from
+ `minpack.lm` per default.
+* Kinetic rate constants and kinetic formation fractions are transformed
+ internally using
+ [`transform_odeparms`](http://kinfit.r-forge.r-project.org/mkin_static/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
+ cooperation on this, especially the isotropic 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).
+* 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.
+* I recently added iteratively reweighted least squares in a similar way
+ it is done 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.
+
## Credits
`mkin` would not be possible without the underlying software stack consisting
@@ -61,4 +105,9 @@ license.
Finally, I just (2013-11-11) noticed the github repositories
[StudyKin](http://github.com/zhenglei-gao/StudyKin) and
[KineticEval](http://github.com/zhenglei-gao/KineticEval), the latter of which appears to be
+<<<<<<< HEAD
actively developed.
+=======
+actively developed, so the different tools will hopefully be able to learn
+from each other in the future as well.
+>>>>>>> master

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