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### Source Code:                                                                                                                 ###
### Tyrannosauroid integument reveals conflicting patterns of gigantism and feather evolution.                                   ###
### Phil R. Bell, Nicolás E. Campione, W. Scott Persons IV, Philip J. Currie, Peter L. Larson, Darren H. Tanke, Robert T. Bakker ###
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## Required Packages ##
library(xlsx) #reads Excel file
library(RColorBrewer) #provides different sets of colours
# Analytical Packages
library(ape)
library(phytools)
library(strap)
library(paleotree)

## New Functions ##

full.analysis <- function(tree, scale.meth) {
  data <- new.data[tree$tip.label,] #matches data and tree tip names
  #tree.scaled <- DatePhylo(tree,ages = as.matrix(data[,c("FAD","LAD")]),method = scale.meth,rlen = 1) #time-scales tree
  tree.scaled <- timePaleoPhy(tree,timeData = as.matrix(data[,c("FAD","LAD")]),type = scale.meth,vartime = 1) #time-scales tree
  
  #size analysis (continuous data)
  size.trait <- data[,"FL"]; names(size.trait) <- data[,"Genus"] #size proxy
  anc.size <- fastAnc(tree.scaled,log10(size.trait)) #ancestral state estimation (Brownian Motion)
  par(mfrow = c(1,2),mar = c(5,4,1,0)+0.1)
  phenogram(tree.scaled,c(log10(size.trait),anc.size),ylab = "log10 Femur Length",fsize = 0.55)
  
  #skin analysis (discrete data)
  missing <- which(is.na(data$Integ.1)) #missing data
  skin.trait <- data[,"Integ.2"]; names(skin.trait) <- data[,"Genus"] #skin coding
  anc.skin <- ace(skin.trait[-missing],drop.tip(tree.scaled,missing),type = "discrete") #ancestral state estimation
  plotTree(drop.tip(tree.scaled,missing),node.numbers = FALSE,setEnv = TRUE,offset = 0.5)
  nodelabels(node = 8:13,pie = anc.skin$lik.anc,piecol = brewer.pal(3,name = "Blues")[2:3],cex = 1.5)
  tiplabels(pch = 21,bg = brewer.pal(3,name = "Blues")[c(2,2,2,2,2,3,3)],cex = 1.5)
  legend("topright",legend = c("Scales","Filaments"),pch = 19,col = brewer.pal(3,name = "Blues")[2:3],bty = "n")
  #par(mfrow = c(3,2),mar = c(1,1,1,1))
  #for(i in 1:6) pie(anc.skin$lik.anc[i,],col = brewer.pal(3,name = "Blues")[2:3],main = paste("Node",i+7,sep = " "))
  
  #results
  return(list(Tree = tree.scaled,Size = size.trait,Size.Results = anc.size, Skin.Results = anc.skin))
}

## Data & Tree ##

new.data <- read.xlsx("Data.xlsx",sheetIndex = 1)
rownames(new.data) <- new.data$Genus
BCtree.par <- read.nexus("BCtree-Parsimony")
BCtree.bay <- read.nexus("BMtree-Bayesian")
plotTree(BCtree.par)
plotTree(BCtree.bay)

## Analysis ##
pdf(file = "results.pdf",width = 8.27,height = 2.92) #save output to pdf file

pars.equal <- full.analysis(BCtree.par,scale.meth = "equal")
pars.mbl <- full.analysis(BCtree.par,scale.meth = "mbl")
bays.equal <- full.analysis(BCtree.bay,scale.meth = "equal")
bays.mbl <- full.analysis(BCtree.bay,scale.meth = "mbl")

dev.off()