#####A comparative study on karyotypic diversification rate in mammals


###Libraries
library("missForest")
library("geiger")
library("ape")
library("caper")
library("phytools")

###Imputation Data of Traits
imputedMamm<- missForest(trait_table)

### Model of Evolution of rKDMacro and rKDMicro
Model_BM<-fitContinuous(Phylogeny_Meredith, rKDMacro, model = "BM")
Model_OU<-fitContinuous(Phylogeny_Meredith, rKDMacro, model = "OU")
Model_White<-fitContinuous(Phylogeny_Meredith, rKDMacro, model = "white")
Model_Delta<-fitContinuous(Phylogeny_Meredith, rKDMacro, model = "delta")
Model_Speciacional<-fitContinuous(Phylogeny_Meredith, rKDMacro, model = "kappa")

### PGLS with BM model and OU model for rKDMacro and rKDMicro

##BM Model
#In Caper
conjdat0<-comparative.data(data=Table_database, phy=Phylogeny_Meredith, names.col='Species.Filo', vcv=T, vcv.dim=3)
Model_BM_1 <- pgls(rKDMacro~logBodyMass, conjdat0, lambda='ML')

#In geiger
matrix<-corBrownian(1,phy=Phylogeny_Meredith) 
Model_BM_1 <- gls(rKDMacro~logBodyMass, correlation=matrix,data=Table_database)


##OU Model 
#In geiger
matrix<-corMartins(1,phy=Phylogeny_Meredith) 
Model_OU_1 <- gls(rKDMacro~logBodyMass, correlation=matrix,data=Table_database)

### Reconstruction of the ancestral state
maps<-contMap(Phylogeny_Meredith, rKDMacro, res=100, fsize=0.6, ftype=NULL, lwd=2.5, legend=NULL,
lims=NULL, outline=F, sig=3, type="phylogram", direction="lefttwards",
plot=TRUE)
maps$cols[]<-maps$cols[length(maps$cols):1]
plot(maps, res=100, fsize=0.3, ftype=NULL, lwd=2.5, legend=NULL,
lims=NULL, outline=F, sig=3, type="phylogram", direction="lefttwards")