# script to import CC phylo nexus, alter focal Order tree, re-export CC phylo nexus with new tree

# remove objects from workspace
rm(list=ls())
install.packages(c('ouch','ape'))
library(ouch)
library(ape)

## run script 'tc2ape' to create function
is(tc2ape,'function') # should be true

## read in csv of example 'Hemiptera-taxon-container.csv'
hemip <- read.csv('hemiptera-taxon-container.csv',colClasses='character')
## examine structure, 2 columns
str(hemip)

# check: how many clades have blank ancestors
hemip$Container[!as.character(hemip$Container) %in% as.character(hemip$Taxon)] # should be 1 empty
# check: how many taxa?
length(hemip$Taxon[!as.character(hemip$Taxon) %in% as.character(hemip$Container)]) #  should == number of tips/taxa

## use custom function to make tree object
hemip.tr <- tc2ape(hemip)
summary(hemip.tr)
write.tree(hemip.tr)
plot(hemip.tr,cex=0.5,type='p')

## now this tree can be grafted onto other trees, analyzed using picante etc.