Exemple de CAH (classification ascendante hiérarchique) avec R 1. Code R Fichier xmp2.r : # # (gH) -_- xmp2.r ; TimeStamp (unix) : 09 Novembre 2017 vers 14:10 library(vegan) # pour vegdist() library(ape) # pour as.phylo() et plot.phylo() # lecture des données xmp2 <- as.matrix(read.table("xmp2.data",header=FALSE,row.names=1)) print(xmp2) # calcul de la matrice des distances mdc <- vegdist(x=xmp2,method="jaccard") print(mdc) # classification hiérarchique cah <- hclust(mdc,method="average") print(cah) desc <- data.frame(cbind(round(cah$height,3),cah$merge)) names(desc) <- c("Niveau","Aine","Benjamin") print(desc) # tracé via plot.hclust et plot.phylo plot(cah, hang=-1,main="Dendrogramme 1") plot.phylo(as.phylo(cah), direction="leftwards",main="Dendrogramme 2",label.offset=0.01) 2. Résultats V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 V14 V15 V16 V17 V18 V19 V20 V21 V22 V23 V24 V25 V26 V27 V28 V29 V30 V31 V32 V33 V34 V35 V36 V37 V38 V39 V40 V41 V42 V43 V44 V45 V46 V47 V48 V49 V50 V51 SA4380 1 1 1 0 0 1 1 0 1 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SA4276 1 1 1 0 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SA4280 1 1 1 0 0 1 1 0 1 0 0 0 1 0 0 1 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 1 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 SA4282 1 1 1 0 0 1 1 0 1 1 0 0 0 1 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 SB4274 0 1 1 0 0 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 SC4277 1 1 0 0 1 1 1 1 0 1 0 0 0 0 1 1 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 SC4381 1 1 0 0 1 1 1 1 0 1 0 0 0 0 0 0 1 1 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 SC4378 1 1 0 0 1 1 1 1 0 1 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SD4281 1 1 0 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 1 1 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 SD4283 1 1 0 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 1 0 1 1 1 1 1 1 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 1 ZZ4283 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SA4380 SA4276 SA4280 SA4282 SB4274 SC4277 SC4381 SC4378 SD4281 SD4283 SA4276 0.4800000 SA4280 0.5384615 0.4800000 SA4282 0.5384615 0.4800000 0.4800000 SB4274 0.5600000 0.5000000 0.5600000 0.4347826 SC4277 0.5925926 0.5925926 0.5925926 0.5925926 0.5000000 SC4381 0.6428571 0.5925926 0.6428571 0.5925926 0.3636364 0.3478261 SC4378 0.5652174 0.5000000 0.5652174 0.5000000 0.5238095 0.3500000 0.3500000 SD4281 0.5600000 0.5000000 0.5000000 0.5000000 0.5217391 0.4347826 0.5000000 0.2777778 SD4283 0.5200000 0.5200000 0.5200000 0.5200000 0.4782609 0.3913043 0.4583333 0.4000000 0.3333333 ZZ4283 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 Call: hclust(d = mdc, method = "average") Cluster method : average Distance : jaccard Number of objects: 11 Niveau Aine Benjamin 1 0.278 -8 -9 2 0.348 -6 -7 3 0.367 -10 1 4 0.414 2 3 5 0.435 -4 -5 6 0.480 -1 -2 7 0.509 -3 6 8 0.509 4 5 9 0.549 7 8 10 1.000 -11 9                 3. Données Fichier xmp2.data : SA4380 1 1 1 0 0 1 1 0 1 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SA4276 1 1 1 0 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SA4280 1 1 1 0 0 1 1 0 1 0 0 0 1 0 0 1 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 1 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 SA4282 1 1 1 0 0 1 1 0 1 1 0 0 0 1 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 SB4274 0 1 1 0 0 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 SC4277 1 1 0 0 1 1 1 1 0 1 0 0 0 0 1 1 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 SC4381 1 1 0 0 1 1 1 1 0 1 0 0 0 0 0 0 1 1 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 SC4378 1 1 0 0 1 1 1 1 0 1 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SD4281 1 1 0 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 1 1 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 SD4283 1 1 0 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 1 0 1 1 1 1 1 1 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 1 ZZ4283 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

 

 

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