zkamvar

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#' INSTALLATION
#' 
#' devtools::source_gist("3c3f12926de648431937")
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#
#
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#' Adds tip colors to tiplabels of an object of class "phylo"
#' 

zkamvar

#' Subset loci in a genind object by name
#' 
#' @param dat a genind object
#' @param ... names of the loci in character format OR numeric indices of the loci.
#'
#' @return the appropriate names to use for subsetting in a genind object
#' @examples
#' library(adegenet)
#' data(nancycats)
#' # Old way:

zkamvar

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# UPDATED: 2015-07-17
#
# USAGE/INSTALLATION:
#   with devtools - devtools::source_gist("b64078a0d04d2452c905")
#   downloaded    - source("poppr_patches.R")
#
# UPDATES:
#   Fix read.genalex ( see: https://github.com/grunwaldlab/poppr/issues/58 )
#

zkamvar

#==============================================================================#
# Visualize the population hierarchy of a genclone object.
#
# Packages needed (install beforehand):
library(poppr)
library(treemap)
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# Main function
# 
# Inputs:

zkamvar

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# Quickly find the parameter that maximizes a likelihood function.
#
# This recursive function will take a range of n parameters within an interval
# and re-adjust the interval to border the maximum value and recursively call
# the function. Once the difference between the maximum value found and the 
# previous maximum value is less than the error term, the parameter value is
# returned. This is faster than the brute force method as the range is reduced
# every time the function is recursed.
#

zkamvar

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))
  for (i in names(gendf)){

zkamvar

# Two functions to plot phylo objects from ape.
#
# Both of these functions plot their respective trees. The ... gives the user
# the ability to adjust things like color or font size. 
#
nj_plot_phylo <- function(tree, ...){
  barlen <- min(median(tree$edge.length), 0.1)
  if (barlen < 0.1) barlen <- 0.01
  tree <- ladderize(tree)
  plot.phylo(tree, font = 2, adj = 0, xpd = TRUE, 

zkamvar

datasets <- vapply(strsplit(dir("data"), "\\."), "[", character(1), 1)

data_replacer <- function(x){
  # manipulate your data here
  y <- old2new_genind(x, new(class(x)))
  if ("genclone" %in% class(x)){
    y@mlg <- x@mlg
  }
  return(y)
}

zkamvar

library("stringr")
library("adegenet")

stopifnot(packageVersion("adegenet") >= 2)

generate_polyploid_data <- function(nind = 10, nloc = 2, maxploid = 4, sep = "/", genind = TRUE){
  locnames   <- paste("locus", seq(nloc), sep = "_")
  indnames   <- paste("sample", seq(nind), sep = "_")
  res        <- lapply(seq(nloc), generate_locus, nind, maxploid, sep)
  names(res) <- locnames

zkamvar

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# THIS IS NOW LOCATED AT https://raw.githubusercontent.com/zkamvar/config-files/master/.bash_prompt
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