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link vignettes on CRAN instead of rpub.com
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paulstaab committed Oct 16, 2015
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Expand Up @@ -9,7 +9,7 @@ coala
Coala is an R package that allows to simulate biological sequences according
to a given model of evolution. It can call a number of efficient
simulators based on
[Coalescent Theory](https://en.wikipedia.org/wiki/Coalescent_theory).
[coalescent theory](https://en.wikipedia.org/wiki/Coalescent_theory).
All simulators can be combined with the program _seq-gen_ to simulate finite
site mutation models.
Coala also directly imports the simulation results into `R`, and allows to
Expand All @@ -31,14 +31,15 @@ install.packages("coala")

If you want to use the simulation programs `ms`, `msms` or `seqgen`,
they need to be installed separately. This is described in the
["Using External Simulators" vignette](http://rpubs.com/paulstaab/coala-installation).
["Using External Simulators" vignette](https://cran.r-project.org/web/packages/coala/vignettes/installation.html).


Usage
-----
Coala comes with a [vignette](http://rpubs.com/paulstaab/coala-introduction)
Coala comes with a
[vignette](https://cran.r-project.org/web/packages/coala/vignettes/introduction.html)
that explains the packages concepts and is a good place to start.
The [ABC vignette](http://rpubs.com/paulstaab/coala-abc) gives an example
The [ABC vignette](https://cran.r-project.org/web/packages/coala/vignettes/abc.html) gives an example
on how coala can be used to conduct the simulations for an Approximate Bayesian
Computation analysis.

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