#Loading required packages
library(picante)
library(ggtree)
library(ggplot2)
library(flextable)

#Loading required data 
KcalcTable_Nature <- read.csv("Kcalc_Table.csv", row.names=1)
Naturenames<- read.tree("Species_Names.nwk")
KcalcTable_Nature
#Setting tip label
Naturenames$tip.label
set.seed(2032021)


#Performign the Kcalc analysis on infection prevalence for the 10^6 treatment 
InfectionPrev = KcalcTable_Nature$X.Infection
names(InfectionPrev) = KcalcTable_Nature$SpeciesNames
InfectionPrev
#The following line calculates the Blomberg's K
Kcalc(InfectionPrev[Naturenames$tip.label], Naturenames)
#This line compares our observed K value to a randomly generate K value and determines whether
# there is a phylogenetic signal
phylosignal(InfectionPrev[Naturenames$tip.label],Naturenames,reps=1000)

#Performing the Kcalc analysis on % mortality for the 10^6 treatment 
PrevMort = KcalcTable_Nature$X..Mortality
names(PrevMort) = KcalcTable_Nature$SpeciesNames
PrevMort
#The following line calculates the Blomberg's K
Kcalc(PrevMort[Naturenames$tip.label], Naturenames)
#This line compares our observed K value to a randomly generate K value and determines whether
# there is a phylogenetic signa
phylosignal(PrevMort[Naturenames$tip.label],Naturenames,reps=1000)

#####Takeaway--> Infection prevalence and percentage mortality are phylogenetically related 
AbreviatedNames<-KcalcTable_Nature$AbrevSpecies
d2<-data.frame(label=Naturenames$tip.label,Infection=InfectionPrev,Mortality=PrevMort,AbrevNames=AbreviatedNames)
d2
#Circular graph with Mortality prevalence
NatureFigureMortality<-ggtree(Naturenames,layout="circular")
NatureFigureMortality<-NatureFigureMortality%<+%d2+
  geom_hilight(node=59, fill="chartreuse2",alpha=0.2,extend=-10)+ 
  geom_hilight(node=56, fill="red",alpha=0.2,extend=-10)+ 
  geom_hilight(node=71, fill="orange",alpha=0.2,extend=-10)+ 
  geom_hilight(node=70, fill="dodgerblue",alpha=0.2,extend=-10)+
  geom_hilight(node=63, fill="gray71",alpha=0.2,extend=-10)+
  geom_hilight(node=42, fill="darkgreen",alpha=0.2,extend=-10)+
  geom_hilight(node=66, fill="aquamarine2",alpha=0.2,extend=-10)+
  geom_hilight(node=16, fill="purple",alpha=0.2,extend=-10)+
  geom_hilight(node=1, fill="deeppink4",alpha=0.2,extend=-10)+
  geom_hilight(node=28, fill="navyblue",alpha=0.2,extend=-10)+geom_tiplab(aes(label=(AbrevNames)),size=2.8,fontface="bold.italic",hjust=0.024,offset=9)+
  geom_tippoint(aes(size=Mortality),alpha=0.65)+theme(legend.position="right")+labs(size="% Mortality")
NatureFigureMortality