install.packages('vegan')
library(vegan)

x <- c(2, 6, 158, 87, 2, 7, 1, 20, 19, 93, 2, 211, 240)    #podenky lokality HLU2
Shannon1 <- diversity(x, index = "shannon", MARGIN = 1, base = exp(1)) #shannon index diverzity s prirodzenym logaritmom; mozeme pouzit aj index = "simpson"
Shannon2 <- diversity(x, index = "shannon", MARGIN = 1, base = 2)      #shannon index diverzity s logaritmom pri zaklade 2

Shannon1
[1] 1.791299

Shannon2
[1] 2.584299


vtaky <- read.csv("c:/DANKA HLAVNY ADRESAR/Vyuka/Bi5980 Biodiverzita/Biodiverzita vyuka 2015/03_2015_data.csv",sep=";",dec=",", header=T)

vtaky
head(vtaky)
tail(vtaky)
attach(vtaky)

Shannon1 <- diversity(X2001, index = "shannon", MARGIN = 1, base = exp(1))
Shannon1
[1] 2.621192

S <- specnumber(X2001) ## rowSums(X2001 > 0) does the same...
J <- Shannon1/log(S)

-----------------------------------------------
rarefy Rarefaction Species Richness


S <- specnumber(X1996) # observed number of species
(raremax <- min(rowSums(X1996)))    # ??? preco mi toto nechce spocitat?
Srare <- rarefy(X1996, raremax)
plot(S, Srare, xlab = "Observed No. of Species", ylab = "Rarefied No. of Species")
abline(0, 1)
rarecurve(X1996, step = 20, sample = raremax, col = "blue", cex = 0.6)

???? niekde je chyba ???