minor documentation changes.

grunwaldlab · Feb 3, 2015 · f9e28d7 · f9e28d7
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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"
 }
 }