## Manon Dartois et al - PeerJ
## Molecular genetic diversity of seaweeds morphologically related to Ulva rigida at three sites along the French Atlantic coast

library(vegan)

# number of specimens per haplotypes per site

lt <- c(
118,
0,
0,
0,
0)
conc <- c(
36,
61,
9,
10,
2)
rosc <- c(
38,
34,
0,
31, 
0)

t(matrix(c(lt, conc, rosc), ncol = 3)) -> dat

# compute diversity H and evenness J

H <- diversity(dat)
J <- H/log(specnumber(dat))

apply(dat, 2, sum) -> all.sites
matrix(all.sites, ncol = 5) -> b

# rarefaction curves

S <- specnumber(b) # observed number of species
(raremax <- min(rowSums(b)))
Srare <- rarefy(b, se = T,raremax)
rarecurve(b, step = 1, sample = raremax, col = "blue", cex = 0.6)

S <- specnumber(dat) # observed number of species
(raremax <- min(rowSums(dat)))
Srare <- rarefy(dat, raremax)
plot(S, Srare, xlab = "Observed No. of Haplotypes", ylab = "Rarefied No. of Species")
abline(0, 1)
rarecurve(dat, step = 1, sample = raremax, col = "blue", cex = 0.6)

# Preston's veiled haplotypes

preston <- prestondistr(colSums(b))
plot(preston)
veiledspec(preston)