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

x <- c(2, 6, 158, 87, 2, 7, 1, 20, 19, 93, 2, 211, 240)    #podenky - jepice 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


# soubor "ptaci" jsou hnizdici ptaci z lokality Samorin - spolecenstva 1996 az 2001

ptaci <- read.csv("c:/DANKA HLAVNY ADRESAR/Vyuka/Bi5980 Biodiverzita/Biodiverzita vyuka 2016/03_2016_DataPtaci.csv",sep=";",dec=",", header=T)

ptaci
head(ptaci)
tail(ptaci)
attach(ptaci)

X2001

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

S <- specnumber(X2001) 
J <- Shannon1/log(S)
J


# Nosaciky -  7 lokalit, 84 druhov, tj. vsetky druhy; 
# Všetky druhy, 7 lokalit sledovanych v 2012-2014, od aprila do oktobra

Nosaciky <- read.csv("c:/DANKA HLAVNY ADRESAR/Vyuka/Bi5980 Biodiverzita/Biodiverzita vyuka 2016/03_2016_Nosaciky.csv",sep=";",dec=",", header=F)
Nosaciky

Shannon <- diversity(Nosaciky, index = "shannon", MARGIN = 1, base = exp(1))
Shannon
Simpson <- diversity(Nosaciky, index = "simpson")
Simpson

S <- specnumber(Nosaciky)
S

J <- Shannon/log(S)
J

N <- rowSums(Nosaciky)
N

# rarefaction - znovu bude tabulka otocena, tj. v radcich lokality, v sloupcich druhy
# Function rarecurve draws a rarefaction curve for each row of the input data

S <- specnumber(Nosaciky)
(raremax <- min(rowSums(Nosaciky)))
Srare <- rarefy(Nosaciky, raremax)

plot(S, Srare, xlim = c(25, 45), pch=16, ylim = c(24,30), xlab = "Observed No. of Species", ylab = "Rarefied No. of Species")
text(S, Srare, labels=rownames(Nosaciky), pos=3)

abline(0, 1)
rarecurve(Nosaciky)

# nebo - kdyz nechceme mit nazvy spolecenstev v ramecku
# rarecurve(Nosaciky, label = FALSE)
# text(N, S, labels=rownames(Nosaciky), pos=4)