fix invalid url note

Author: paulstaab

.Rbuildignore

@@ -12,3 +12,4 @@
 ^src\/scrm\/random\/mersenne_twister\.cc$
 ^src\/scrm\/random\/mersenne_twister\.h$
 ^src\/scrm\/random\/speedtest\.cc$
+^cran-comments\.md$

README.md

@@ -1,8 +1,8 @@
 [![Linux Build Status](https://travis-ci.org/scrm/scrm-r.svg?branch=master)](https://travis-ci.org/scrm/scrm-r)
 [![Windows Build Status](https://ci.appveyor.com/api/projects/status/octt2w69byiq198s/branch/master?svg=true)](https://ci.appveyor.com/project/paulstaab/scrm-r/branch/master)
 [![Coverage Status](https://coveralls.io/repos/github/scrm/scrm-r/badge.svg?branch=master)](https://coveralls.io/github/scrm/scrm-r?branch=master)
-[![CRAN Status](http://www.r-pkg.org/badges/version/scrm)](http://cran.r-project.org/web/packages/scrm)
-[![CRAN RStudio Mirror Downloads](http://cranlogs.r-pkg.org/badges/scrm)](https://cran.r-project.org/package=scrm)
+[![CRAN Status](http://www.r-pkg.org/badges/version/scrm)](https://cran.r-project.org/package=scrm)
+
 
 scrm R Package
 =======================

inst/CITATION

@@ -10,6 +10,5 @@ bibentry(
   volume = 31,
   number = 10,
   pages = '1680-1682',
-  doi = '10.1093/bioinformatics/btu861',
   url = 'http://bioinformatics.oxfordjournals.org/content/31/10/1680'
 )

vignettes/scrm-Arguments.Rmd

@@ -22,7 +22,7 @@ scrm is uses a syntax compatible with the popular program [ms][1]. There are, ho
     * `-eI` (sampling haplotypes at multiple time points) and
     * `-oSFS` (generates frequency spectra). 
 
-For all other options, you can also refer to [ms' manual][2] to get a detailed description of what the commands are doing. scrm should happily execute any ms command that does not contain `-c` and `-s`. Also scrm has somewhat stricter requirements regarding the order of arguments if population admixture (`-es`) is involved.
+For all other options, you can also refer to [ms' manual][1] to get a detailed description of what the commands are doing. scrm should happily execute any ms command that does not contain `-c` and `-s`. Also scrm has somewhat stricter requirements regarding the order of arguments if population admixture (`-es`) is involved.
 
 ## General Syntax
 The arguments for calling _scrm_ are
@@ -61,7 +61,7 @@ decline in population sizes.
 * `-t < $\theta$ >`: Set the mutation rate to $\theta = 4N_0u$, where _u_ is the neutral mutation rate per locus. If this options is given, scrm generates the segregating sites output.
 * `-transpose-segsites` or `--transpose-segsites`: If given, the segregating sites are printed with each row representing a mutation and each column representing a haplotype, rather than the other way round. Additionally, the time at which a mutation occurred is reported (in units of _4 * N0_ generations) [since v1.7.0].
 * `-T`: Print the local genealogies in newick format.
-* `-O`: Print the local genealogies in the `oriented forest` format as described in [Kelleher _et al._ (2014)](http://dx.doi.org/10.1016/j.tpb.2014.05.001) [since v1.2].
+* `-O`: Print the local genealogies in the `oriented forest` format as described in [Kelleher _et al._ (2014)][2] [since v1.2].
 * `-L`: Print the TMRCA and the local tree length for each segment (behaves different to ms). Both values are scaled in coalescent time units, e.g. in _4 * N0_ generations.
 * `-oSFS`: Print the site frequency spectrum. Requires that the mutation rate $\theta$ is given with the '-t' option.
 * `-SC [ms|rel|abs]`: Scaling of sequence positions. Either relative to the locus length between 0 and 1 (`rel`), absolute in base pairs (`abs`) or `ms`'s scaling (default) where the positions in the _segregating sites_ output are relative, and the positions in the trees output are absolute (`ms`) [since v1.3.0]. 
@@ -117,4 +117,4 @@ length of the sequence as second argument, while `-sr` just has the rate as argu
 
 
 [1]: http://home.uchicago.edu/~rhudson1/source/mksamples.html
-[2]: https://webshare.uchicago.edu/users/rhudson1/Public/ms.folder/msdoc.pdf?ticket=t_DunQ7c99
+[2]: http://www.sciencedirect.com/science/article/pii/S0040580914000355