install.packages(c('vegan', 'gclus', 'cluster', 'vegan', 'ade4'))

library(gclus)
library(cluster)
library(vegan)
library(ade4)

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getwd()
setwd("E:/cesta*********")
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spe1 <- read.table('poi.csv', sep=";", header=TRUE, dec=".")

spe  <- spe1[-8,]                                                   ## vylucime riadok 8, kde boli same 0 ##

dist.y <- dist(spe,method='euclidean')

vare.y <- as.data.frame(as.matrix(dist.y))                         ### spravi nam to z tej trojuholnikovej matice stvorcovu
write.table(vare.y, file="pokus.csv", sep=";")                   ### zapisalo nam to do suboru pokus.csv

dist.cela <- dist(spe, method = "euclidean", diag = TRUE, upper = TRUE) ## spravi celu maticu



?vegdist

   vegdist(x, method="bray", binary=FALSE, diag=FALSE, upper=FALSE,
        na.rm = FALSE, ...) 

spe.b1<-vegdist(spe, "jaccard",  binary=TRUE, diag=TRUE, upper=TRUE)
spe.b2<-vegdist(spe, "bray", binary=FALSE, diag=TRUE, upper=TRUE)


write.table(as.matrix(spe.b1), file="spe.b1.csv", sep=";")
write.table(as.matrix(spe.b2), file="spe.b2.csv", sep=";")

write.table(as.data.frame(as.matrix(spe.b1)), file="spe.b1.csv", sep=";")

write.table(as.data.frame(as.matrix(spe.b2)), file="spe.b2.csv", sep=";")

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