diff --git a/NEWS b/NEWS index 4241fcaa..9ef12775 100644 --- a/NEWS +++ b/NEWS @@ -1,20 +1,21 @@ poppr 1.1.2.99 =========== +NEW FEATURES +* new arguments to `plot_poppr_msn` to allow for easier manipulation of node sizes and of labeling +* read.genalex can now take read text connections as input. Addresses issue #8 +* users can now specify cutoff for missing values in `aboot` + BUG FIX * Fixed issue where monomorphic loci would cause an error in `recode_polyploids` * Fixed logical error that would cause The infinite alleles model of Bruvo's distance to inflate the distance. (Found by Michael Metzger. Addresses issue #5). * AMOVA can now take subset genclone objects (Addresses issue #7). -* in mlg.table, the mlgsub argument will not subset by name instead of index (fixed in #7). +* in mlg.table, the mlgsub argument will now subset by name instead of index (fixed in #7). * Fixed issue for neighbor-joining trees where the internal function to fix negative branch lengths was accidentally shuffling the corrected branches. Addresses issue #11. * diss.dist can now be used with aboot -NEW FEATURES -* Added new arguments to `plot_poppr_msn` to allow for easier manipulation of node sizes and of labeling. -* read.genalex can now take read text connections as input. Addresses issue #8 -* users can now specify the missing cutoff in aboot - MISC * info_table will print a discrete scale as opposed to colorbar when type = "ploidy" +* attempted to make model choices for Bruvo's distance more clear in the documentation poppr 1.1.2 =========== diff --git a/R/bruvo.r b/R/bruvo.r index d634c555..e192a60b 100755 --- a/R/bruvo.r +++ b/R/bruvo.r @@ -57,7 +57,8 @@ #' @param pop a \code{\link{genind}} object #' #' @param replen a \code{vector} of \code{integers} indicating the length of the -#' nucleotide repeats for each microsatellite locus. +#' nucleotide repeats for each microsatellite locus. E.g. a locus with a (CAT) +#' repeat would have a repelen value of 3. #' #' @param add if \code{TRUE}, genotypes with zero values will be treated under #' the genome addition model presented in Bruvo et al. 2004. See the diff --git a/R/poppr.R b/R/poppr.R index 4ac5ac87..168c9fa8 100644 --- a/R/poppr.R +++ b/R/poppr.R @@ -58,7 +58,7 @@ #' \item \code{\link{informloci}} - Detects and removes phylogenetically uninformative loci #' \item \code{\link{popsub}} - Subsets genind objects by population #' \item \code{\link{shufflepop}} - Shuffles genotypes at each locus using four different shuffling algorithms -#' \item \code{\link{recode_polyploids}} - recode polyploid data sets with missing alleles imported as "0" +#' \item \code{\link{recode_polyploids}} - Recode polyploid data sets with missing alleles imported as "0" #' } #' @section Genetic distances: #' \itemize{ diff --git a/README.md b/README.md index f9d4df9a..f62fcb8f 100644 --- a/README.md +++ b/README.md @@ -47,7 +47,7 @@ If you want the absolute latest version of *poppr*, see about installing from gi ### Stable and Development versions -[![Build Status](https://travis-ci.org/grunwaldlab/poppr.png?branch=devel)](https://travis-ci.org/grunwaldlab/poppr?branch=devel) +[![Build Status](https://travis-ci.org/grunwaldlab/poppr.png?branch=devel)](https://travis-ci.org/grunwaldlab/poppr?branch=master) If the image above says "Passing", then that means it should be safe to install with the latest version of R. If it does not say "Passing", I am probably trying to fix whatever problem is causing it as fast as I can. @@ -64,16 +64,14 @@ Now you can use the `install_github()` function: #### For the latest stable release: ```s -library("devtools") -install_github(repo = "grunwaldlab/poppr") +devtools::install_github(repo = "grunwaldlab/poppr") library("poppr") ``` #### For the bleeding edge (development) version: ```s -library("devtools") -install_github(repo = "grunwaldlab/poppr", ref = "devel") +devtools::install_github(repo = "grunwaldlab/poppr@devel") library("poppr") ``` diff --git a/man/bruvo.dist.Rd b/man/bruvo.dist.Rd index cc211d9e..776d3154 100755 --- a/man/bruvo.dist.Rd +++ b/man/bruvo.dist.Rd @@ -10,7 +10,8 @@ bruvo.dist(pop, replen = 1, add = TRUE, loss = TRUE) \item{pop}{a \code{\link{genind}} object} \item{replen}{a \code{vector} of \code{integers} indicating the length of the - nucleotide repeats for each microsatellite locus.} + nucleotide repeats for each microsatellite locus. E.g. a locus with a (CAT) + repeat would have a repelen value of 3.} \item{add}{if \code{TRUE}, genotypes with zero values will be treated under the genome addition model presented in Bruvo et al. 2004. See the diff --git a/man/poppr-package.Rd b/man/poppr-package.Rd index aa6edd88..eebc3877 100644 --- a/man/poppr-package.Rd +++ b/man/poppr-package.Rd @@ -67,7 +67,7 @@ This package relies on the \pkg{\link[adegenet]{adegenet}} package. \item \code{\link{informloci}} - Detects and removes phylogenetically uninformative loci \item \code{\link{popsub}} - Subsets genind objects by population \item \code{\link{shufflepop}} - Shuffles genotypes at each locus using four different shuffling algorithms -\item \code{\link{recode_polyploids}} - recode polyploid data sets with missing alleles imported as "0" +\item \code{\link{recode_polyploids}} - Recode polyploid data sets with missing alleles imported as "0" } }