Prepare release v0.5.0 (#182)

* bump version

* update license year

* use cannonical links in README

* use cannonical link

* replace url with cannonical form

.gitignore

@@ -10,3 +10,4 @@
 *.so
 .Rproj.user
 vignettes/abc_cache
+cran-comments.md

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: coala
-Version: 0.4.1.9006
+Version: 0.5.0
 License: MIT + file LICENSE
 Title: A Framework for Coalescent Simulation
 Authors@R: c(

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2015
+YEAR: 2015-2016
 COPYRIGHT HOLDER: Paul Staab

NEWS.md

@@ -1,7 +1,7 @@
 coala 0.5.0
 ===========
 
-* Major interal refactoring on how simulators interface with coala (#174).
+* Major internal refactoring on how simulators interface with coala (#174).
 * Support for calculating an expanded version of MCMF (#173, #179). This
   feature was contributed by Jorge E. Amaya Romero (@jorgeamaya).
 * Introduces the optional `locus_group` argument for features. Using it, 

README.md

@@ -28,21 +28,21 @@ 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](https://cran.r-project.org/web/packages/coala/vignettes/coala-install.html) and
+["Using External Simulators" vignette](https://cran.r-project.org/package=coala/vignettes/coala-install.html) and
 in [the wiki](https://github.com/statgenlmu/coala/wiki/Installation).
 
 
 Usage & Help
 ------------
 Coala comes with a
-[vignette](https://cran.r-project.org/web/packages/coala/vignettes/coala-intro.html)
+[vignette](https://cran.r-project.org/package=coala/vignettes/coala-intro.html)
 that explains the packages concepts and is a good place to start. It also has a 
-[vignette containing a few example applications](https://cran.r-project.org/web/packages/coala/vignettes/coala-examples.html).
+[vignette containing a few example applications](https://cran.r-project.org/package=coala/vignettes/coala-examples.html).
 
 Detailed information about coala's functions is provided via R's help system. 
 Call `help(_function_)` in R to view them. They usually also contain examples and further links.
 
-The [ABC vignette](https://cran.r-project.org/web/packages/coala/vignettes/coala-abc.html) 
+The [ABC vignette](https://cran.r-project.org/package=coala/vignettes/coala-abc.html) 
 gives an example on how coala can be used to conduct the simulations for [Approximate Bayesian
 Computation](https://en.wikipedia.org/wiki/Approximate_Bayesian_computation).
 
@@ -65,7 +65,7 @@ result$sfs
 ```
 
 More examples can be found in the 
-[examples vignette](https://cran.r-project.org/web/packages/coala/vignettes/coala-examples.html).
+[examples vignette](https://cran.r-project.org/package=coala/vignettes/coala-examples.html).
 
 
 Problems
@@ -96,7 +96,7 @@ devtools::install_github('statgenlmu/coala')
 
 on Linux and OS X. This requires that you have `devtools` and a compiler or 
 Xcode installed. Bug reports and pull request on GitHub are highly appreciated.
-The [extending coala vignette](https://cran.r-project.org/web/packages/coala/vignettes/coala-extend.html)
+The [extending coala vignette](https://cran.r-project.org/package=coala/vignettes/coala-extend.html)
 contains information on how to create new summary statistics and add simulators
 to coala. The [wiki](https://github.com/statgenlmu/coala/wiki) also contains a few
 resources for developers.