From 05070242dbb3d663613011d1aab07b24be8ae137 Mon Sep 17 00:00:00 2001 From: Eric Archer Date: Tue, 11 Apr 2017 07:22:10 -0700 Subject: [PATCH] v2.0.2 on CRAN --- DESCRIPTION | 9 +++++++-- R/structure.R | 2 +- README.md | 3 ++- man/structure.Rd | 2 +- 4 files changed, 11 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 716e8d7..1569477 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,12 @@ Package: strataG Title: Summaries and Population Structure Analyses of Genetic Data -Description: A toolkit for analyzing stratified population genetic data. -Version: 2.0.1 +Description: A toolkit for analyzing stratified population genetic data. + Functions are provided for summarizing and checking loci + (haploid, diploid, and polyploid), single stranded DNA sequences, + calculating most population subdivision metrics, and running external programs + such as structure and fastsimcoal. The package is further described in + Archer et al (2016) . +Version: 2.0.2 License: GNU General Public License Authors@R: c( EA = person("Eric", "Archer", email = "eric.archer@noaa.gov", role = c("aut", "cre")), diff --git a/R/structure.R b/R/structure.R index 51ab9d9..9b8d530 100644 --- a/R/structure.R +++ b/R/structure.R @@ -65,7 +65,7 @@ #' #' @references Pritchard, J.K., M. Stephens, P. Donnelly. 2000. Inference of #' population structure using multilocus genotype data. Genetics 155:945-959.\cr -#' \url{http://pritchardlab.stanford.edu/structure.html} +#' \url{http://web.stanford.edu/group/pritchardlab/structure.html} #' #' @seealso \code{\link{structurePlot}}, \code{\link{evanno}}, #' \code{\link{clumpp}} diff --git a/README.md b/README.md index bcf28b7..311fe8a 100755 --- a/README.md +++ b/README.md @@ -62,7 +62,7 @@ Archer, F. 2016. *strataG*: An *R* package for manipulating, summarizing and ana * send a pull request: * e-mail: -## version 2.0.0 (current on GitHub) +## version 2.0.2 (current on GitHub) * NOTE: In order to speed up indexing the data in large data sets, this version changes the underlying structure of the `gtypes` object by replacing the `@loci` data.frame slot with a `@data` data.table slot. The data.table has a `id` character column, a `strata` character column, and every column afterwards represents one locus. The `@strata` slot has been removed. * The `loci` accessor has been removed. @@ -72,6 +72,7 @@ Archer, F. 2016. *strataG*: An *R* package for manipulating, summarizing and ana * Fixed computational errors in population structure metrics due to incorrect sorting of stratification. * Added `maf` to return minimum allele frequency for each locus. * Added `ldNe` to calculate Ne. +* Added `expandHaplotypes` to expand the haplotypes in a `gtypes` object to one sequence per individual. ## version 1.0.6 diff --git a/man/structure.Rd b/man/structure.Rd index ebb55f4..20934b8 100644 --- a/man/structure.Rd +++ b/man/structure.Rd @@ -127,7 +127,7 @@ structurePlot(q.mat) \references{ Pritchard, J.K., M. Stephens, P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.\cr - \url{http://pritchardlab.stanford.edu/structure.html} + \url{http://web.stanford.edu/group/pritchardlab/structure.html} } \seealso{ \code{\link{structurePlot}}, \code{\link{evanno}},