# BIOL 410 Tutorial 10

# assign the BCIveg_number.csv data set to the object dat

dat <- dat[,2:21]
datpa <- dat
datpa[datpa>0] <- 1

S = rowSums(datpa)
N = rowSums(dat)
species.richness <- S

margalef <- (S-1)/log(N)
menhinick <- S/sqrt(N)

plot(S-1,log(N))
plot(S,sqrt(N))

plot(S,margalef)
plot(S,menhinick)

n.nm1 <- dat*(dat-1)
sumn.nm1 <- rowSums(n.nm1)
N.Nm1 <- N*(N-1)

D = sumn.nm1/N.Nm1 

Id <- 1 - D

pi <- dat/rowSums(dat)

pilnpi <- pi*(log(pi))
pilnpi[is.na(pilnpi)] <- 0
H <- -1*rowSums(pilnpi)

plot(Id,H)

Es <- H/log(S)

plot(D,Es)

gama <- colSums(dat)
gama[gama>0] <- 1
gama <- sum(gama)
beta1 <- gama/mean(S)

jacard.pair <- function(b,f){
	beta.a <- sum(b==f & b > 0)
	beta.b <- sum(b!=f & b > 0)
	beta.c <- sum(b!=f & f > 0)
	
	jacard <- 1-(beta.a/(beta.a + beta.b + beta.c))
	return(jacard)
}

beta2.a <- jacard.pair(as.numeric(datpa[11,]),as.numeric(datpa[12,]))