data<-read.table(file="PNG_transects.txt",header=TRUE)
head(data)
tail(data)
PA<-replace(PA<-data,PA>1,1)
species_recorded <- NULL
hold_temp<-NULL
for (i in 1:ncol(PA)){ 
	temp<- grep(1,PA[,i])
	hold_temp<-c(hold_temp,temp) 
	species_recorded<-c(species_recorded,length(unique(hold_temp))) 
	}
plot(species_recorded, xlab= "Transect number", ylab="Total number of species")


N<-100
M<-matrix(NA,nrow=N,ncol=ncol(PA))  # to hold the results of N (100) random sequences
for (i in 1:N){
to_add_seq<-sample(1:50, 50,replace=FALSE)
species_recorded<-NULL
hold_temp<-NULL
for (j in to_add_seq){ # automatically steps through all values in the list to_add_seq
temp<-grep(1,PA[,j])    
hold_temp<-c(hold_temp,temp)  
species_recorded<-c(species_recorded,length(unique(hold_temp))) }
M[i,]<- species_recorded
}
head(M)

plot(NULL,xlim=c(1,50),ylim=c(1,93),xlab="Transect number", ylab="Total number of species")
for (i in 1:100) points(c(1:50),M[i,],pch= 15,cex=0.2)
points(c(1:50),colMeans(M),col="red",pch=16)
lines(smooth.spline(c(1:50),colMeans(M), spar=0.4, all.knots=F),lwd=2, lty=1,col="blue")

#### Calculation of Shannon and Simpson indices
propPNGbutts<-PNG_butterflies/sum(PNG_butterflies)
Simpson<-1-sum(propPNGbutts^2)
Simpson
ShannonH<--sum(propPNGbutts*log(propPNGbutts,2))
ShannonH
species_observed<-NULL; Simpson_transect<-NULL; Shannon_transect<-NULL
for (i in 1:length(data)){
temp<-data[which(data[,i]>0),i]
species_observed<-c(species_observed,length(temp))
Simpson_transect<-c(Simpson_transect,1-sum((temp/sum(temp))^2))
Shannon_transect<-c(Shannon_transect,-sum(sum((temp/sum(temp)) * log(temp/sum(temp),2))))}
par(mfrow=c(2,2))
plot(species_observed,Simpson_transect,xlab="Number of butterflies spp in transect",ylab="Simpson's Index",pch=18,col="cyan3")
plot(species_observed,Shannon_transect,xlab="Number of butterflies spp in transect",ylab="Shannon's Index",pch=18,col="chocolate")
plot(Shannon_transect,Simpson_transect,xlab="Shannon",ylab="Simpson",col="red")

#install.packages("vegan")
library(vegan)
SW<-diversity(propPNGbutts,index="shannon",MARGIN=1,base=exp(1))
SW
ShannonH<--sum(propPNGbutts*log(propPNGbutts))
ShannonH