From 30f42c84a89f90322df36e28a9a91858721a6c58 Mon Sep 17 00:00:00 2001 From: Paul Staab Date: Wed, 28 Dec 2016 13:53:43 +0100 Subject: [PATCH] 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 | 1 + DESCRIPTION | 2 +- LICENSE | 2 +- NEWS.md | 2 +- README.md | 12 ++++++------ cran-comments.md | 14 -------------- man/feat_mutation.Rd | 10 ++++++++++ 7 files changed, 20 insertions(+), 23 deletions(-) delete mode 100644 cran-comments.md diff --git a/.gitignore b/.gitignore index b9f2e74..c1e864c 100644 --- a/.gitignore +++ b/.gitignore @@ -10,3 +10,4 @@ *.so .Rproj.user vignettes/abc_cache +cran-comments.md diff --git a/DESCRIPTION b/DESCRIPTION index 67564e7..bf6f7f1 100644 --- a/DESCRIPTION +++ b/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( diff --git a/LICENSE b/LICENSE index 5a49820..ad90a6b 100644 --- a/LICENSE +++ b/LICENSE @@ -1,2 +1,2 @@ -YEAR: 2015 +YEAR: 2015-2016 COPYRIGHT HOLDER: Paul Staab diff --git a/NEWS.md b/NEWS.md index 6aba609..eef46c4 100644 --- a/NEWS.md +++ b/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, diff --git a/README.md b/README.md index dbaa6f8..524c931 100644 --- a/README.md +++ b/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. diff --git a/cran-comments.md b/cran-comments.md deleted file mode 100644 index d21cd52..0000000 --- a/cran-comments.md +++ /dev/null @@ -1,14 +0,0 @@ -This version fixes the test errors caused by the new version of dependency 'rehh'. - -## Test environments -* Fedora 24 (local), R 3.3.1 -* Ubuntu 14.04 (travis-CI), R 3.3.1 -* Windows (on AppVeyor), R-devel -* win-builder (R-devel and R-release) - -## R CMD check results -There were no ERRORs, WARNINGs or significant NOTEs. - -## Downstream dependencies -The package 'jaatha', currently the only reverse dependency of 'coala', passed -R CMD check with 'OK'. diff --git a/man/feat_mutation.Rd b/man/feat_mutation.Rd index fb3d09a..5093ad5 100644 --- a/man/feat_mutation.Rd +++ b/man/feat_mutation.Rd @@ -82,6 +82,16 @@ type of substitution. The rates are assumed to be symmetric model <- coal_model(5, 1) + feat_mutation(5) + sumstat_seg_sites() simulate(model) +# A model with a mutation of 5.0 for the first 10 loci, and 7.5 for the +# second 10 loci +model <- coal_model(4) + + locus_averaged(10, 100) + + locus_averaged(10, 100) + + feat_mutation(5.0, locus_group = 1) + + feat_mutation(7.5, locus_group = 2) + + sumstat_seg_sites() +simulate(model) + # A model with 7 mutations per locus: model <- coal_model(5, 1) + feat_mutation(7, fixed = TRUE) +