update documentation.

grunwaldlab · Jul 7, 2015 · 7adfedf · 7adfedf
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: poppr
 Type: Package
 Title: Genetic Analysis of Populations with Mixed Reproduction
-Version: 1.1.5.99-684
+Version: 1.1.5.99-686
 Date: 2015-07-07
 Authors@R: c(person(c("Zhian", "N."), "Kamvar", role = c("cre", "aut"),
     email = "kamvarz@science.oregonstate.edu"),

diff --git a/R/poppr.R b/R/poppr.R
@@ -122,7 +122,7 @@
 #' \itemize{
 #' \item \code{\link{as.genclone}} - Converts genind objects to genclone objects
 #' \item \code{\link{missingno}} - Handles missing data
-#' \item \code{\link{clonecorrect}} - Clones censors at a specified population hierarchy
+#' \item \code{\link{clonecorrect}} - Clone-censors at a specified population hierarchy
 #' \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

diff --git a/man/imsn.Rd b/man/imsn.Rd
@@ -20,8 +20,7 @@ Creating and plotting MSNs requires three steps:
 \enumerate{
 \item Create a distance matrix from your data
 \item Create a minimum spanning network with your data and the matrix
-\item Visualize the minimum spanning network with your data and the minimum
-spanning network}
+\item Visualize the minimum spanning network}
 The function \code{\link{plot_poppr_msn}} is currently the most flexible way
 of visualizing your minimum spanning network, but with 20 parameters, it can
 become pretty intimidating trying to find the right display for your MSN.

diff --git a/man/poppr-package.Rd b/man/poppr-package.Rd
@@ -80,7 +80,7 @@ This package relies on the \pkg{\link[adegenet]{adegenet}} package.
 
 \itemize{
 \item \code{\link{getfile}} - Provides a quick GUI to grab files for import
-\item \code{\link{read.genalex}} - Read GenAlEx formatted csv files to a genind object
+\item \code{\link{read.genalex}} - Reads GenAlEx formatted csv files to a genind object
 \item \code{\link{genind2genalex}} - Converts genind objects to GenAlEx formatted csv files
 \item \code{\link{genclone2genind}} - Removes the @mlg slot from genclone objects
 }
@@ -91,11 +91,11 @@ This package relies on the \pkg{\link[adegenet]{adegenet}} package.
 \itemize{
 \item \code{\link{as.genclone}} - Converts genind objects to genclone objects
 \item \code{\link{missingno}} - Handles missing data
-\item \code{\link{clonecorrect}} - Clone censors at a specified population hierarchy
+\item \code{\link{clonecorrect}} - Clone-censors at a specified population hierarchy
 \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}} - Recodes polyploid data sets with missing alleles imported as "0"
 }
 }
 
@@ -135,8 +135,8 @@ This package relies on the \pkg{\link[adegenet]{adegenet}} package.
 \item \code{\link{mlg.vector}} - Returns a vector of a numeric multilocus genotype assignment for each individual
 \item \code{\link{mlg.id}} - Finds all individuals associated with a single multilocus genotype
 \item \code{\link{mlg.filter}} - Collapses MLGs by genetic distance
-\item \code{\link{filter_stats}} - Calculate mlg.filter for all algorithms and plot
-\item \code{\link{cutoff_predictor}} - predict cutoff threshold from mlg.filter.
+\item \code{\link{filter_stats}} - Calculates mlg.filter for all algorithms and plots
+\item \code{\link{cutoff_predictor}} - Predicts cutoff threshold from mlg.filter.
 \item \code{\link{mll.custom}} - Allows for the custom definition of multilocus lineages
 \item \code{\link{mll.levels}} - Allows the user to change levels of custom MLLs.
 \item \code{\link{diversity_stats}} - Creates a table of diversity indices for multilocus genotypes.
@@ -161,7 +161,7 @@ This package relies on the \pkg{\link[adegenet]{adegenet}} package.
 \section{Visualization}{
 
 \itemize{
-\item \code{\link{imsn}} - interactive construction and visualization of minimum spanning networks
+\item \code{\link{imsn}} - Interactive construction and visualization of minimum spanning networks
 \item \code{\link{plot_poppr_msn}} - Plots minimum spanning networks produced in poppr with scale bar and legend
 \item \code{\link{greycurve}} - Helper to determine the appropriate parameters for adjusting the grey level for msn functions
 \item \code{\link{bruvo.msn}} - Produces minimum spanning networks based off Bruvo's distance colored by population