#R CODE FOR CREATING TRILOBITE CLADOGRAM

#STEP 1: Loading required packages
install.packages("phangorn") #only run this the first time you start this code
library(phangorn) #run this every time you start RStudio
#END OF STEP 1

#STEP 2: Reading data files
trilo<-read.nexus.data("http://people.ucsc.edu/~mclapham/earth101/data/trilo.nex")
trilo_matrix<-read.csv("http://people.ucsc.edu/~mclapham/earth101/data/trilo_matrix.csv",row.names=1)
#END OF STEP 2

#STEP 3: Creates phylogeny and optimizes tree based on parsimony
trilo_phylo<-phyDat(trilo,type="USER",levels=c("0","1","2"))
start_tree<-as.phylo(hclust(dist(trilo_matrix),method="single"))
ptree<-optim.parsimony(start_tree,trilo_phylo)
ptree_res<-multi2di(ptree,random=F)
#END OF STEP 3

#STEP 4: plots cladogram
plot(ptree_res)
#END OF STEP 4