Update documentation for #112

R/bootstraping.R

@@ -122,6 +122,7 @@
 #'   \code{\link{prevosti.dist}} \code{\link{diss.dist}} 
 #'   \code{\link{bruvo.boot}} \code{\link[ape]{boot.phylo}} 
 #'   \code{\link[adegenet]{dist.genpop}} \code{\link{dist}}
+#'   \code{\link{bootgen2genind}} \code{\linkS4class{bootgen}}
 #'   
 #' @export
 #' @keywords bootstrap
@@ -137,10 +138,30 @@
 #' 
 #' set.seed(9999)
 #' # Generate a tree using custom distance
-#' bindist <- function(x) dist(x$tab, method = "binary")
+#' bindist <- function(x) dist(tab(x), method = "binary")
 #' binnan <- aboot(nan9, dist = bindist)
 #' 
 #' \dontrun{
+#' # Distances from other packages.
+#' #
+#' # Sometimes, distance functions from other packages will have the constraint
+#' # that the incoming data MUST be genind. Internally, aboot uses the 
+#' # bootgen class ( class?bootgen ) to shuffle loci, and will throw an error
+#' # The function bootgen2genind helps fix that. Here's an example of a function
+#' # that expects a genind class from above
+#' bindist <- function(x){
+#'   stopifnot(is.genind(x))
+#'   dist(tab(x), method = "binary")
+#' }
+#' #
+#' # Fails:
+#' # aboot(nan9, dist = bindist)
+#' ## Error: is.genind(x) is not TRUE
+#' #
+#' # Add bootgen2genind to get it working!
+#' # Works:
+#' aboot(nan9, dist = function(x) bootgen2genind(x) %>% bindist)
+#' 
 #' # AFLP data
 #' data(Aeut)
 #' 

R/poppr.R

@@ -112,6 +112,8 @@
 #' \item \code{\link{read.genalex}} (x) - Reads GenAlEx formatted csv files to a genind object
 #' \item \code{\link{genind2genalex}} (m) - Converts genind objects to GenAlEx formatted csv files
 #' \item \code{\link{genclone2genind}} (m) - Removes the @@mlg slot from genclone objects
+#' \item \code{\link{genclone2genind}} (m) - Removes the @@mlg slot from genclone objects
+#' \item \code{\link{bootgen2genind}} (x) - see \code{\link{aboot}} for details)
 #' }
 #' @section Data manipulation:
 #' \itemize{