diff --git a/DESCRIPTION b/DESCRIPTION index f217fc5d..a82fd555 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: poppr Type: Package Title: Genetic Analysis of Populations With Mixed Reproduction -Version: 1.1.2.99-56 -Date: 2015-02-02 +Version: 1.1.3 +Date: 2015-02-03 Authors@R: c(person(c("Zhian", "N."), "Kamvar", role = c("cre", "aut"), email = "kamvarz@science.oregonstate.edu"), person(c("Javier", "F."), "Tabima", role = "aut", diff --git a/NEWS b/NEWS index 9ef12775..6d1ce013 100644 --- a/NEWS +++ b/NEWS @@ -1,4 +1,4 @@ -poppr 1.1.2.99 +poppr 1.1.3 =========== NEW FEATURES * new arguments to `plot_poppr_msn` to allow for easier manipulation of node sizes and of labeling diff --git a/R/sandbox.r b/R/sandbox.r index ee297855..15d4e1c5 100755 --- a/R/sandbox.r +++ b/R/sandbox.r @@ -94,18 +94,18 @@ genind_hierarchy <- function(x, df = NULL, dfname = "population_hierarchy"){ return(x) } -gen2polysat <- function(gen, newploidy = gen@ploidy){ - if (!require(polysat)){ - stop("User needs polysat installed") - } - gen <- recode_polyploids(gen, newploidy) - gendf <- genind2df(gen, sep = "/", usepop = FALSE) - gendf <- lapply(gendf, strsplit, "/") - gendf <- lapply(gendf, lapply, as.numeric) - ambig <- new("genambig", samples = indNames(gen), loci = locNames(gen)) - lapply(names(gendf), function(x) Genotypes(ambig, loci = x) <<- gendf[[x]]) - return(ambig) -} +# gen2polysat <- function(gen, newploidy = gen@ploidy){ +# if (!require(polysat)){ +# stop("User needs polysat installed") +# } +# gen <- recode_polyploids(gen, newploidy) +# gendf <- genind2df(gen, sep = "/", usepop = FALSE) +# gendf <- lapply(gendf, strsplit, "/") +# gendf <- lapply(gendf, lapply, as.numeric) +# ambig <- new("genambig", samples = indNames(gen), loci = locNames(gen)) +# lapply(names(gendf), function(x) Genotypes(ambig, loci = x) <<- gendf[[x]]) +# return(ambig) +# } new_graph_pops <- function(graph, dat, color){ diff --git a/vignettes/algo.Rnw b/vignettes/algo.Rnw index 34f22e24..8abe1301 100644 --- a/vignettes/algo.Rnw +++ b/vignettes/algo.Rnw @@ -51,7 +51,7 @@ \scalebox{-1}[1]{\jala{}} } -\title{Algorithms and equations utilized in poppr version 1.1.2.99-56} +\title{Algorithms and equations utilized in poppr version 1.1.3} \author{Zhian N. Kamvar$^{1}$\ and Niklaus J. Gr\"unwald$^{1,2}$\\\scriptsize{1) Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR}\\\scriptsize{2) Horticultural Crops Research Laboratory, USDA-ARS, diff --git a/vignettes/poppr_manual.Rnw b/vignettes/poppr_manual.Rnw index 3913a248..3f143cdc 100644 --- a/vignettes/poppr_manual.Rnw +++ b/vignettes/poppr_manual.Rnw @@ -51,7 +51,7 @@ \scalebox{-1}[1]{\jala{}} } -\title{Data import and manipulation in poppr version 1.1.2.99-56} +\title{Data import and manipulation in poppr version 1.1.3} \author{Zhian N. Kamvar$^{1}$\ and Niklaus J. Gr\"unwald$^{1,2}$\\\scriptsize{1) Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR}\\\scriptsize{2) Horticultural Crops Research Laboratory, USDA-ARS,