library(ape)
library(geiger)
library(ade4)
library(picante)
library(phytools)

# load tree produced by MrBayes
tree<-read.nexus("minnows.tre")

# get a list of outgroup taxa
outgroup<-c("Moxostoma_duquesnii","Moxostoma_erythrurum","Moxostoma_macrolepidotum")

# root the tree based on one of the outgroup species
rooted_tree<-root(tree,outgroup[1])

# drop the outgroup species
rooted_tree<-drop.tip(rooted_tree,outgroup)

# plot tree
plot.phylo(rooted_tree)

# Read the trait data, we are interested in the "eggs" column which has egg size
traits<-read.csv("minnow_data.csv",sep=",", header=T,row.names="species")

# sort traits frame to match tree
traits<-traits[match(rooted_tree$tip.label[],row.names(traits)),]

# Make a pretty picture. Map egg size onto the phylogeny 
egg_size<-as.numeric(traits$egg)
names(egg_size)<-row.names(traits)
contMap(rooted_tree,egg_size)

habitat<-factor(traits$habitat)
names(habitat)<-row.names(traits)