#Script for analyses

#Install phytools, Claddis and dispeRse
library(devtools)
devtools::install_github("liamrevell/phytools")
devtools::install_github("graemetlloyd/Claddis")
devtools::install_github("laurasoul/dispeRse")

#Required libraries
library(ape)
library(paleotree)
library(phytools)
library(Claddis)
library(dispeRse)
library(cluster)

#Clustering analyses of palaeocoordinate data
coordinates<-read.table("palaeocoords.txt", header=TRUE)

#Cluster analysis for k=5-15
porc.list<-rep(list(list()),15)
fit.list<-rep(list(list()),15)
for (j in 5:15)

{fit=kmeans(coordinates, j, nstart = 10)
porc=fit$betweenss/fit$totss
	for (k in 1:10000)
	{
		fit2=kmeans(coordinates, j, nstart = 10)
		porc2=fit2$betweenss/fit2$totss
		if (porc2>porc)
		{
			porc=porc2
			fit2=fit		}
}
porc->porc.list[[j]]
fit2->fit.list[[j]]
	}
	
#Input source tree
complete.tree<-read.nexus("SD1.nexus")

#Read in taxa and ages
taxon.ages <- as.matrix(read.table("Taxon_occs.txt", header = TRUE, row.names=1, sep = "\t"))

#Read in taxon-region matrices for each time bin
lopingian<-as.matrix(read.table("lopingian.txt", header=TRUE, row.names=1, sep="\t"))
earlyTriassic<-as.matrix(read.table("earlyTriassic.txt", header=TRUE, row.names=1, sep="\t"))
anisian<-as.matrix(read.table("anisian.txt", header=TRUE, row.names=1, sep="\t"))
ladinian<-as.matrix(read.table("ladinian.txt", header=TRUE, row.names=1, sep="\t"))
earlyLateTriassic<-as.matrix(read.table("earlyLateTriassic.txt", header=TRUE, row.names=1, sep="\t"))
lateLateTriassic<-as.matrix(read.table("lateLateTriassic.txt", header=TRUE, row.names=1, sep="\t"))
earlyEarlyJurassic<-as.matrix(read.table("earlyEarlyJurassic.txt", header=TRUE, row.names=1, sep="\t"))
lateEarlyJurassic<-as.matrix(read.table("lateEarlyJurassic.txt", header=TRUE, row.names=1, sep="\t"))

#Produce trees isolating the taxa present in each time bin
lopingian.tree <- drop.tip(dated.tree, setdiff(dated.tree$tip.label, rownames(lopingian)))
earlyTriassic.tree <- drop.tip(dated.tree, setdiff(dated.tree$tip.label, rownames(earlyTriassic)))
anisian.tree <- drop.tip(dated.tree, setdiff(dated.tree$tip.label, rownames(anisian)))
ladinian.tree <- drop.tip(dated.tree, setdiff(dated.tree$tip.label, rownames(ladinian)))
earlyLateTriassic.tree <- drop.tip(dated.tree, setdiff(dated.tree$tip.label, rownames(earlyLateTriassic)))
lateLateTriassic.tree <- drop.tip(dated.tree, setdiff(dated.tree$tip.label, rownames(lateLateTriassic)))
earlyEarlyJurassic.tree <- drop.tip(dated.tree, setdiff(dated.tree$tip.label, rownames(earlyEarlyJurassic)))
lateEarlyJurassic.tree <- drop.tip(dated.tree, setdiff(dated.tree$tip.label, rownames(lateEarlyJurassic)))

#Calculating phylogenetic biogeographical connectedness from these trees requires that each be ultrametric. Here is a function to ultrametricise trees (author: Graeme Lloyd):
ultrametricise <- function(tree) {
    # Get maximum path length:
    max.path.length <- max(diag(vcv(tree)))
    # Add extra branch length to all tips in order to reach maximum path length:
    tree$edge.length[match(1:Ntip(tree), tree$edge[, 2])] <- tree$edge.length[match(1:Ntip(tree), tree$edge[, 2])] + (max.path.length - diag(vcv(tree))[tree$tip.label])
    # Return re-scaled tree:
    return(tree)
}

#Ultrametricise the trees
lopingian.tree <- ultrametricise(lopingian.tree)
earlyTriassic.tree <- ultrametricise(earlyTriassic.tree)
anisian.tree <- ultrametricise(anisian.tree)
ladinian.tree <- ultrametricise(ladinian.tree)
earlyLateTriassic.tree <- ultrametricise(earlyLateTriassic.tree)
lateLateTriassic.tree <- ultrametricise(lateLateTriassic.tree)
earlyEarlyJurassic.tree <- ultrametricise(earlyEarlyJurassic.tree)
lateEarlyJurassic.tree <- ultrametricise(lateEarlyJurassic.tree)

#Sensitivty analyses into maximum tree length cutoff

#Generate time-calibrated supertree for these sensitvity analyses
dated.tree <- timePaleoPhy(complete.tree, taxon.ages, "mbl", vartime=1)

# Empty matrix to store phylogenetic BC values for k 1-100:
phyloBC <- matrix(0, nrow = 9, ncol = 100)

# For k values of 1 to 100:
for(i in 1:100) {
    # Get Permian and Triassic phylogenetic BCs:
    phyloBC.lopingian <- BC(lopingian, lopingian.tree, jackknife = TRUE, k = i)
    phyloBC.earlyTriassic <- BC(earlyTriassic, earlyTriassic.tree, jackknife = TRUE, k = i)
    phyloBC.anisian <- BC(anisian, anisian.tree, jackknife = TRUE, k = i)
    phyloBC.ladinian <- BC(ladinian, ladinian.tree, jackknife = TRUE, k = i)
    phyloBC.earlyLateTriassic <- BC(earlyLateTriassic, earlyLateTriassic.tree, jackknife = TRUE, k = i)
    phyloBC.lateLateTriassic <- BC(lateLateTriassic, lateLateTriassic.tree, jackknife = TRUE, k = i)
    phyloBC.earlyEarlyJurassic <- BC(earlyEarlyJurassic, earlyEarlyJurassic.tree, jackknife = TRUE, k = i)
    phyloBC.lateEarlyJurassic <- BC(lateEarlyJurassic, lateEarlyJurassic.tree, jackknife = TRUE, k = i)

    # Store the BC value in the matrix:
    phyloBC[2, i] <- phyloBC.lopingian$BC_observed["Biogeographic_connectedness"]
    phyloBC[3, i] <- phyloBC.earlyTriassic$BC_observed["Biogeographic_connectedness"]
    phyloBC[4, i] <- phyloBC.anisian$BC_observed["Biogeographic_connectedness"]
    phyloBC[5, i] <- phyloBC.ladinian$BC_observed["Biogeographic_connectedness"]
    phyloBC[6, i] <- phyloBC.earlyLateTriassic$BC_observed["Biogeographic_connectedness"]
    phyloBC[7, i] <- phyloBC.lateLateTriassic$BC_observed["Biogeographic_connectedness"]
    phyloBC[8, i] <- phyloBC.earlyEarlyJurassic$BC_observed["Biogeographic_connectedness"]
    phyloBC[9, i] <- phyloBC.lateEarlyJurassic$BC_observed["Biogeographic_connectedness"]

    # Output loop position:
    cat(i, " ")   
}

#Output results
write.table(phyloBC, "k_outputs.txt")

#Perform aphylogenetic analyses

aphyloBC.lopingian<-BC(lopingian, jackknife = TRUE)
aphyloBC.earlyTriassic<-BC(earlyTriassic, jackknife = TRUE)
aphyloBC.anisian<-BC(anisian, jackknife = TRUE)
aphyloBC.ladinian<-BC(ladinian, jackknife = TRUE)
aphyloBC.earlyLateTriassic<-BC(earlyLateTriassic, jackknife = TRUE)
aphyloBC.lateLateTriassic<-BC(lateLateTriassic, jackknife = TRUE)
aphyloBC.earlyEarlyJurassic<-BC(earlyEarlyJurassic, jackknife = TRUE)
aphyloBC.lateEarlyJurassic<-BC(lateEarlyJurassic, jackknife = TRUE)

#Perform complete phylogenetic analyses on 100 dated trees

#Generate 100 dated trees with random resolution of polytomies
trees<-timePaleoPhy(tree=complete.tree, timeData=taxon.ages, type="mbl", ntrees=100, vartime=1, randres=TRUE) 

#Analyses across 100 trees
for (i in 1:100) {
phy<-trees[[i]]
lopingian.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lopingian))))
earlyTriassic.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(earlyTriassic))))
anisian.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(anisian))))
ladinian.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(ladinian))))
earlyLateTriassic.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(earlyLateTriassic))))
lateLateTriassic.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lateLateTriassic))))
earlyEarlyJurassic.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(earlyEarlyJurassic))))
lateEarlyJurassic.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lateEarlyJurassic))))

phyloBC.lopingian<-BC(lopingian, lopingian.tree, jackknife = TRUE, k=15)
phyloBC.earlyTriassic<-BC(earlyTriassic, earlyTriassic.tree, jackknife = TRUE, k=15)
phyloBC.anisian<-BC(anisian, anisian.tree, jackknife = TRUE, k=15)
phyloBC.ladinian<-BC(ladinian, ladinian.tree, jackknife = TRUE, k=15)
phyloBC.earlyLateTriassic<-BC(earlyLateTriassic, earlyLateTriassic.tree, jackknife = TRUE, k=15)
phyloBC.lateLateTriassic<-BC(lateLateTriassic, lateLateTriassic.tree, jackknife = TRUE, k=15)
phyloBC.earlyEarlyJurassic<-BC(earlyEarlyJurassic, earlyEarlyJurassic.tree, jackknife = TRUE, k=15)
phyloBC.lateEarlyJurassic<-BC(lateEarlyJurassic, lateEarlyJurassic.tree, jackknife = TRUE, k=15)

print(i)
}

#Analyses of Laurasian and Gondwanan BC separately

#Read in Laurasian datasets
lopingian.laurasia<-as.matrix(read.table("lopingianLaurasia.txt", header=TRUE, row.names=1, sep="\t"))
earlyTriassic.laurasia<-as.matrix(read.table("earlyTriassicLaurasia.txt", header=TRUE, row.names=1, sep="\t"))
anisian.laurasia<-as.matrix(read.table("anisianLaurasia.txt", header=TRUE, row.names=1, sep="\t"))
ladinian.laurasia<-as.matrix(read.table("ladinianLaurasia.txt", header=TRUE, row.names=1, sep="\t"))
earlyLateTriassic.laurasia<-as.matrix(read.table("earlyLateTriassicLaurasia.txt", header=TRUE, row.names=1, sep="\t"))
lateLateTriassic.laurasia<-as.matrix(read.table("lateLateTriassicLaurasia.txt", header=TRUE, row.names=1, sep="\t"))
earlyEarlyJurassic.laurasia<-as.matrix(read.table("earlyEarlyJurassicLaurasia.txt", header=TRUE, row.names=1, sep="\t"))
lateEarlyJurassic.laurasia<-as.matrix(read.table("lateEarlyJurassicLaurasia.txt", header=TRUE, row.names=1, sep="\t"))

#Read in Gondwanan datasets
lopingian.gondwana<-as.matrix(read.table("lopingianGondwana.txt", header=TRUE, row.names=1, sep="\t"))
earlyTriassic.gondwana<-as.matrix(read.table("earlyTriassicGondwana.txt", header=TRUE, row.names=1, sep="\t"))
anisian.gondwana<-as.matrix(read.table("anisianGondwana.txt", header=TRUE, row.names=1, sep="\t"))
ladinian.gondwana<-as.matrix(read.table("ladinianGondwana.txt", header=TRUE, row.names=1, sep="\t"))
earlyLateTriassic.gondwana<-as.matrix(read.table("earlyLateTriassicGondwana.txt", header=TRUE, row.names=1, sep="\t"))
lateLateTriassic.gondwana<-as.matrix(read.table("lateLateTriassicGondwana.txt", header=TRUE, row.names=1, sep="\t"))
earlyEarlyJurassic.gondwana<-as.matrix(read.table("earlyEarlyJurassicGondwana.txt", header=TRUE, row.names=1, sep="\t"))
lateEarlyJurassic.gondwana<-as.matrix(read.table("lateEarlyJurassicGondwana.txt", header=TRUE, row.names=1, sep="\t"))

#Laurasia analyses
for (i in 1:100) {
phy<-trees[[i]]
lopingian.tree_laurasia <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lopingian.laurasia))))
earlyTriassic.tree_laurasia <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(earlyTriassic.laurasia))))
anisian.tree_laurasia <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(anisian.laurasia))))
ladinian.tree_laurasia <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(ladinian.laurasia))))
earlyLateTriassic.tree_laurasia <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(earlyLateTriassic.laurasia))))
lateLateTriassic.tree_laurasia <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lateLateTriassic.laurasia))))
earlyEarlyJurassic.tree_laurasia <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(earlyEarlyJurassic.laurasia))))
lateEarlyJurassic.tree_laurasia <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lateEarlyJurassic.laurasia))))

phyloBC.lopingian_laurasia<-BC(lopingian.laurasia, lopingian.tree_laurasia, jackknife = TRUE, k=15)
phyloBC.earlyTriassic_laurasia<-BC(earlyTriassic.laurasia, earlyTriassic.tree_laurasia, jackknife = TRUE, k=15)
phyloBC.anisian_laurasia<-BC(anisian.laurasia, anisian.tree_laurasia, jackknife = TRUE, k=15)
phyloBC.ladinian_laurasia<-BC(ladinian.laurasia, ladinian.tree_laurasia, jackknife = TRUE, k=15)
phyloBC.earlyLateTriassic_laurasia<-BC(earlyLateTriassic.laurasia, earlyLateTriassic.tree_laurasia, jackknife = TRUE, k=15)
phyloBC.lateLateTriassic_laurasia<-BC(lateLateTriassic.laurasia, lateLateTriassic.tree_laurasia, jackknife = TRUE, k=15)
phyloBC.earlyEarlyJurassic_laurasia<-BC(earlyEarlyJurassic.laurasia, earlyEarlyJurassic.tree_laurasia, jackknife = TRUE, k=15)
phyloBC.lateEarlyJurassic_laurasia<-BC(lateEarlyJurassic.laurasia, lateEarlyJurassic.tree_laurasia, jackknife = TRUE, k=15)

print(i)
}

#Gondwana analyses
for (i in 1:100) {
phy<-trees[[i]]
lopingian.tree_gondwana <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lopingian.gondwana))))
earlyTriassic.tree_gondwana <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(earlyTriassic.gondwana))))
anisian.tree_gondwana <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(anisian.gondwana))))
ladinian.tree_gondwana <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(ladinian.gondwana))))
earlyLateTriassic.tree_gondwana <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(earlyLateTriassic.gondwana))))
lateLateTriassic.tree_gondwana <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lateLateTriassic.gondwana))))
earlyEarlyJurassic.tree_gondwana <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(earlyEarlyJurassic.gondwana))))
lateEarlyJurassic.tree_gondwana <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lateEarlyJurassic.gondwana))))

phyloBC.lopingian_gondwana<-BC(lopingian.gondwana, lopingian.tree_gondwana, jackknife = TRUE, k=15)
phyloBC.earlyTriassic_gondwana<-BC(earlyTriassic.gondwana, earlyTriassic.tree_gondwana, jackknife = TRUE, k=15)
phyloBC.anisian_gondwana<-BC(anisian.gondwana, anisian.tree_gondwana, jackknife = TRUE, k=15)
phyloBC.ladinian_gondwana<-BC(ladinian.gondwana, ladinian.tree_gondwana, jackknife = TRUE, k=15)
phyloBC.earlyLateTriassic_gondwana<-BC(earlyLateTriassic.gondwana, earlyLateTriassic.tree_gondwana, jackknife = TRUE, k=15)
phyloBC.lateLateTriassic_gondwana<-BC(lateLateTriassic.gondwana, lateLateTriassic.tree_gondwana, jackknife = TRUE, k=15)
phyloBC.earlyEarlyJurassic_gondwana<-BC(earlyEarlyJurassic.gondwana, earlyEarlyJurassic.tree_gondwana, jackknife = TRUE, k=15)
phyloBC.lateEarlyJurassic_gondwana<-BC(lateEarlyJurassic.gondwana, lateEarlyJurassic.tree_gondwana, jackknife = TRUE, k=15)

print(i)
}

#Read in cross-extinction subset analyses
#Minimum-size lower-level (~family) surviving clades
lopingian.survivors_min<-as.matrix(read.table("lopingianSurvsMin.txt", header=TRUE, row.names=1, sep="\t"))
earlyTriassic.survivors_min<-as.matrix(read.table("earlyTriassicSurvsMin.txt", header=TRUE, row.names=1, sep="\t"))
lateLateTriassic.survivors_min<-as.matrix(read.table("lateLateTriassicSurvsMin.txt", header=TRUE, row.names=1, sep="\t"))
earlyEarlyJurassic.survivors_min<-as.matrix(read.table("earlyJurassicSurvsMin.txt", header=TRUE, row.names=1, sep="\t"))

#Maximum-size lower-level (~family) surviving clades - only difference is in pre-extinction plots, as taxon content for post-extinction time bins will equal the minimum estimate
lopingian.survivors_max<-as.matrix(read.table("lopingianSurvsMax.txt", header=TRUE, row.names=1, sep="\t"))
lateLateTriassic.survivors_max<-as.matrix(read.table("lateLateTriassicSurvsMax.txt", header=TRUE, row.names=1, sep="\t"))

#Analysis of these subsets
for (i in 1:100) {
phy<-trees[[i]]
lopingian.tree_min <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lopingian.survivors_min))))
earlyTriassic.tree_min <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(earlyTriassic.survivors_min))))
lateLateTriassic.tree_min <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lateLateTriassic.survivors_min))))
earlyEarlyJurassic.tree_min <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(earlyEarlyJurassic.survivors_min))))

lopingian.tree_max <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lopingian.survivors_max))))
lateLateTriassic.tree_max <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lateLateTriassic.survivors_max))))

phyloBC.lopingian_min<-BC(lopingian.survivors_min, lopingian.tree_min, jackknife = TRUE, k=15)
phyloBC.earlyTriassic_min<-BC(earlyTriassic.survivors_min, earlyTriassic.tree_min, jackknife = TRUE, k=15)
phyloBC.lateLateTriassic_min<-BC(lateLateTriassic.survivors_min, lateLateTriassic.tree_min, jackknife = TRUE, k=15)
phyloBC.earlyEarlyJurassic_min<-BC(earlyEarlyJurassic.survivors_min, earlyEarlyJurassic.tree_min, jackknife = TRUE, k=15)
phyloBC.lopingian_max<-BC(lopingian.survivors_max, lopingian.tree_max, jackknife = TRUE, k=15)
phyloBC.lateLateTriassic_miax<-BC(lateLateTriassic.survivors_max, lateLateTriassic.tree_max, jackknife = TRUE, k=15)
 
print(i)
}

#Perform analyss of youngest clades in all time bines

#Analyses of only clades diverging <2Ma prior to and after the boundary

#Read in matrices
lopingian<-as.matrix(read.table("lopingianSurvs2.txt", header=TRUE, row.names=1, sep="\t"))
earlyTriassic<-as.matrix(read.table("earlyTriassicSurvs2.txt", header=TRUE, row.names=1, sep="\t"))
anisian<-as.matrix(read.table("anisianSurvs2.txt", header=TRUE, row.names=1, sep="\t"))
ladinian<-as.matrix(read.table("ladinianSurvs2.txt", header=TRUE, row.names=1, sep="\t"))
midTriassic<-as.matrix(read.table("middleTriassicSurvs2.txt", header=TRUE, row.names=1, sep="\t"))
earlyLateTriassic<-as.matrix(read.table("earlyLateTriassicSurvs2.txt", header=TRUE, row.names=1, sep="\t"))
lateLateTriassic<-as.matrix(read.table("lateLateTriassicSurvs2.txt", header=TRUE, row.names=1, sep="\t"))
lateTriassic<-as.matrix(read.table("lateTriassicSurvs2.txt", header=TRUE, row.names=1, sep="\t"))
earlyEarlyJurassic<-as.matrix(read.table("earlyEarlyJurassicSurvs2.txt", header=TRUE, row.names=1, sep="\t"))
lateEarlyJurassic<-as.matrix(read.table("lateEarlyJurassicSurvs2.txt", header=TRUE, row.names=1, sep="\t"))
earlyJurassic<-as.matrix(read.table("earlyJurassicSurvs2.txt", header=TRUE, row.names=1, sep="\t"))

#Perform analyses
for (i in 1:100) {
  phy<-trees[[i]]
  lopingian.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lopingian))))
  earlyTriassic.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(earlyTriassic))))
  anisian.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(anisian))))
  ladinian.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(ladinian))))
  midTriassic.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(midTriassic))))
  earlyLateTriassic.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(earlyLateTriassic))))
  lateLateTriassic.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lateLateTriassic))))
  lateTriassic.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lateTriassic))))
  earlyEarlyJurassic.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(earlyEarlyJurassic))))
  lateEarlyJurassic.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(lateEarlyJurassic))))
  earlyJurassic.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(earlyJurassic))))
  
  phyloBC.lopingian<-BC(lopingian, lopingian.tree, jackknife = TRUE, k=15)
  phyloBC.earlyTriassic<-BC(earlyTriassic, earlyTriassic.tree, jackknife = TRUE, k=15)
  phyloBC.anisian<-BC(anisian, anisian.tree, jackknife = TRUE, k=15)
  phyloBC.ladinian<-BC(ladinian, ladinian.tree, jackknife = TRUE, k=15)
  phyloBC.midTriassic<-BC(midTriassic, midTriassic.tree, jackknife = TRUE, k=15)
  phyloBC.earlyLateTriassic<-BC(earlyLateTriassic, earlyLateTriassic.tree, jackknife = TRUE, k=15)
  phyloBC.lateLateTriassic<-BC(lateLateTriassic, lateLateTriassic.tree, jackknife = TRUE, k=15)
  phyloBC.lateTriassic<-BC(lateTriassic, lateTriassic.tree, jackknife = TRUE, k=15)
  phyloBC.earlyEarlyJurassic<-BC(earlyEarlyJurassic, earlyEarlyJurassic.tree, jackknife = TRUE, k=15)
  phyloBC.lateEarlyJurassic<-BC(lateEarlyJurassic, lateEarlyJurassic.tree, jackknife = TRUE, k=15)
  phyloBC.earlyJurassic<-BC(earlyJurassic, earlyJurassic.tree, jackknife = TRUE, k=15)
  
  print(i)
}

#Perform pBC reanalysis of Sidor et al. (2013) datasets for comparison
permianSidor<-as.matrix(read.table("permianSidor.txt", row.names=1, sep="\t"))
triassicSidor<-as.matrix(read.table("triassicSidor.txt", row.names=1, sep="\t"))

for (i in 1:100) {
  phy<-trees[[i]]
  permianSidor.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(permianSidor))))
  triassicSidor.tree <- ultrametricise(drop.tip(phy, setdiff(complete.tree$tip.label, rownames(triassicSidor))))
    
  phyloBC.lopingian<-BC(permianSidor, permianSidor.tree, jackknife = TRUE, k=15)
  phyloBC.earlyTriassic<-BC(triassicSidor, triassicSidor.tree, jackknife = TRUE, k=15)

  print(i)
}