library(paleotree)
library(ape)

# Requires a file of time bin ranges called "Ranges.txt"
# Requires a file of taxon first and last appearance bins based on the Ranges file called "Taxa.txt"

##### DATING USING CAL3 #####

# Load in geological stages

Ranges<-read.table("Ranges.txt", header=TRUE, row.names=1)

# Load in First and Last Appearance dates

taxa<-read.table("Taxa.txt", header=TRUE, row.names=1)

# Get into the right format

data<-list(Ranges, taxa)

# ML optimisation for sampling probability and extinction rates

SPres<-getSampProbDisc(data)

# Establish means for interval length

intLength<--apply(data[[1]],1,diff)

meanInt<-mean(intLength)

# Calculate sampling rate

sRate<-sProb2sRate(SPres[[2]][2], int.length=meanInt)

# Calculate diversification and extinction rate

divRate<-SPres[[2]][1]/meanInt

# Load trees for cal3

trees<-read.nexus("trees.nex")

# Get consensus of trees

contree<-consensus(trees)

# Date trees with cal3

datedtrees<-bin_cal3TimePaleoPhy(CFO, data, brRate=divRate, extRate=divRate, sampRate=sRate, ntrees=1000, plot=FALSE)


#### NB This will randomise polytomies 1000 times ####


##########    RATES     ANALYSIS    ###########


# Read Matrix
matrix<-ReadMorphNexus("Discrete Matrix.nex")

# Ensure no falsely uncoded characters
if (any(matrix$max.vals == NA)=TRUE) {
matrix$max.vals[is.na(x)] <- 1
matrix$min.vals[is.na(x)] <- 0
}


# Ensure no zero-length branches by adding smallest possible duration (0.01 years, or 3.65 days). This allows the function to work without really affecting the dating.

for (i in 1:1000) {
datedtrees[[i]]$edge.length<-(datedtrees[[i]]$edge.length+0.00000001)
}

# Generate lists in which the rates and significances are going to go

tree.per.bin.rates<-list
tree.per.bin.sig<-list

# Calculate rates for each tree at alpha level of 0.01

for (i in 1:1000) {

treerates<-DiscreteCharacterRate(datedtrees[[i]], matrix, Ranges[,1], alpha=0.01)

tree.per.bin.rates<-cbind(tree.per.bin.rates, treerates$per.bin.rates[,4])

tree.per.bin.sig<-cbind(tree.per.bin.sig, treerates$per.bin.rates[,8])

}