geneva

library(dplyr)
library(ggmap)
library(ggsn)


#Download map data for South Bimini
pngMAP_df <-  get_map(location = c(lon = -79.275, lat = 25.71),
                      source = "google",
                      zoom = 13,
                      color="bw",

geneva

# aRe We There Yet (RWTY) Tutorial

# Bayesian Phylogenetic Inference using Markov Chain Monte Carlo (mcmc)
### Introduced in late 90s, now wildly popular
### Implemented in many software packages: MrBayes, BEAST, PhlyoBayes

# Phylogenetic inference computationally expensive, number of possible
# rooted trees for 60 taxa > number of protons in known universe
# Exhausitive tree search via optimality criteria such as maximum parsimony
# or maximum liklihood is NP-Hard

geneva

###########################################
# Functions for the analysis of AFLP data #
#           Anthony J Geneva              #
#             9 April 2013                #
###########################################

###########################################
# This function converts the binary table 
# output from RawGeno to a format that can 
# be read by AFLPScore

geneva

# This function converts the binary table output from 
# RawGeno to a format that can be read by AFLPScore


##################################
#  RawGeno_2_AFLPscore function  #
##################################

RawGeno_2_AFLPscore <- function(outfilename)
{

geneva

library(vegan)
class <- "Anthony"

dat <- read.table(paste(class,".dat", sep=""), sep = "\t", header=TRUE)

#######PieChart############

piedata <- matrix(ncol=1, nrow=length(unique(dat[,1])))
names <- levels(unique(dat[,1]))
rownames(piedata) <- names