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){   
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")