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2 Cluster Peces
2 Cluster Peces
Rosana Ferrero
5 de febrero de 2014
ndice
1. Anlisis cluster con R: datos de peces (ambos mtodos).
1.1. Anlisis jerrquico . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.1.1. PASO 1. Eleccin de variables (o casos) . . . . . . . . . . .
1.1.2. PASO 2. Eleccin de la tcnica cluster . . . . . . . . . . . .
1.1.3. PASO 3: Determinar el nmero de conglomerados finales
1.1.4. PASO 4. Representacin e interpretacin de los resultados
1.2. Anlisis no jerrquico . . . . . . . . . . . . . . . . . . . . . . . . .
1.2.1. Particin por k-medias . . . . . . . . . . . . . . . . . . . . .
1.2.2. k-medoides (PAM) . . . . . . . . . . . . . . . . . . . . . . .
1.3. PLUS: Anlisis extra para mejorar la interpretacin y validacin.
1.3.1. Comparacin con datos ambientales. . . . . . . . . . . . .
1.3.2. Ensables de especies . . . . . . . . . . . . . . . . . . . . . .
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2
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5
8
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17
17
24
1.
Anlisis cluster jerrquico y no jerrquico para datos de abundancia de peces a lo largo del ro Doubs
(francs-suizo) obtenidos por Verneaux (1973) y las caractersticas ambientales del sitio. Se quiere analizar:
a) Si existen distintos ensambles de peces a lo largo del cauce del ro. b) Cmo los cambios ambientales
registrados en el ro se relacionan con los cambios en la estructura de los ensambles de peces. Tenemos
30 filas (sitios), 27 especies de peces (columnas del archivo spe), 11 variables ambientales (columnas del
archivo env) y las coordenadas espaciales de los sitios (columnas del archivo spa). Para obtener ms detalles
de los datos puedes preguntar en R sobre los datos doubs del paquete ade4.
1.1.
Anlisis jerrquico
# --------- Anlisis jerrquico --------# cargamos los paquetes que vamos a necesitar (activar vegan luego de
# ade4 para evitar conflictos)
library(ade4)
library(vegan)
library(gclus)
library(cluster)
library(RColorBrewer)
library(labdsv)
library(mvpart)
library(MVPARTwrap)
# cargamos algunas funciones que hemos de necesitar (los archivos
# deben estar en nuestro directorio de trabajo)
source("hcoplot.R")
source("test.a.R")
source("coldiss.R")
1.1.1.
1.1.2.
## null device
##
1
## [1] 0.7656
# Average
spe.ch.UPGMA.coph <- cophenetic(spe.ch.UPGMA)
cor(spe.ch, spe.ch.UPGMA.coph)
## [1] 0.8608
# Ward
spe.ch.ward.coph <- cophenetic(spe.ch.ward)
cor(spe.ch, spe.ch.ward.coph)
## [1] 0.7985
cor(spe.ch, spe.ch.ward.coph, method = "spearman")
## [1] 0.7661
# el mayor coeficiente de correlacin cofentica corresponde al
# mtodo UPGMA
# Diagrama de Shepard ---- Para ilustrar las relaciones entre la
# matriz de distancias original y la matriz de distancias cofentica
par(mfrow = c(2, 2))
plot(spe.ch, spe.ch.single.coph, xlab = "Chord distance", ylab = "Cophenetic distance",
asp = 1, xlim = c(0, sqrt(2)), ylim = c(0, sqrt(2)), main = c("Single linkage",
paste("Cophenetic correlation =", round(cor(spe.ch, spe.ch.single.coph),
3))))
abline(0, 1)
lines(lowess(spe.ch, spe.ch.single.coph), col = "red")
plot(spe.ch, spe.ch.comp.coph, xlab = "Chord distance", ylab = "Cophenetic distance",
asp = 1, xlim = c(0, sqrt(2)), ylim = c(0, sqrt(2)), main = c("Complete linkage",
paste("Cophenetic correlation =", round(cor(spe.ch, spe.ch.comp.coph),
3))))
abline(0, 1)
lines(lowess(spe.ch, spe.ch.comp.coph), col = "red")
plot(spe.ch, spe.ch.UPGMA.coph, xlab = "Chord distance", ylab = "Cophenetic distance",
asp = 1, xlim = c(0, sqrt(2)), ylim = c(0, sqrt(2)), main = c("UPGMA",
paste("Cophenetic correlation =", round(cor(spe.ch, spe.ch.UPGMA.coph),
3))))
abline(0, 1)
lines(lowess(spe.ch, spe.ch.UPGMA.coph), col = "red")
plot(spe.ch, spe.ch.ward.coph, xlab = "Chord distance", ylab = "Cophenetic distance",
asp = 1, xlim = c(0, sqrt(2)), ylim = c(0, max(spe.ch.ward$height)),
main = c("Ward clustering", paste("Cophenetic correlation =", round(cor(spe.ch,
spe.ch.ward.coph), 3))))
abline(0, 1)
lines(lowess(spe.ch, spe.ch.ward.coph), col = "red")
# Distancia de Gower (1983) -----(gow.dist.single <- sum((spe.ch - spe.ch.single.coph)^2))
## [1] 95.41
4
1.2
1.0
1
9
5
15
16
19
spe.ch
hclust (*, "complete")
spe.ch
hclust (*, "average")
Cluster Dendrogram
Cluster Dendrogram
Cluster Dendrogram
1.1.3.
#
#
#
#
1.5
spe.ch
hclust (*, "ward")
1
15
16
19
17
18
2
3
7
10
4
6
13
14
11
12
5
9
20
21
22
26
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28
29
30
25
23
24
Height
1.0
0.5
0.0
20
21
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26
27
28
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30
25
23
24
5
9
15
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18
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3
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10
4
6
1
13
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12
Height
2
3
7
11
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14
6
4
12
spe.ch
hclust (*, "centroid")
25
20
30
26
29
21
22
27
28
17
18
23
24
15
10
19
16
9
5
0.5
0.1
0.3
Height
2.0
0.7
2.5
spe.ch
hclust (*, "single")
17
18
13
14
4
6
12
2
3
7
11
26
27
28
29
21
22
20
30
23
24
25
10
0.6
Height
0.2
12
2
3
7
11
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16
10
4
6
19
17
18
29
30
20
21
22
26
27
28
25
23
24
0.2
0.4
1
0.6
Height
23
24
12
4
6
2
3
7
13
14
30
20
21
22
29
26
27
28
17
18
11
19
16
15
10
25
0.8
1.0
5
1
0.6
0.4
0.2
Height
Cluster Dendrogram
1.4
Cluster Dendrogram
0.8
Cluster Dendrogram
spe.ch
hclust (*, "ward")
## null device
##
1
plot(spe.ch.ward$height, nrow(spe):2, type = "S", main = "Fusion levels - Chord - Ward",
ylab = "k (number of clusters)", xlab = "h (node height)", col = "grey")
text(spe.ch.ward$height, nrow(spe):2, nrow(spe):2, col = "red", cex = 0.8)
# Nmero ptimo de cluster segn el ancho de silueta -------# (Rousseeuw quality index)
# graficamos el ancho medio de silueta para todas las particiones,
# excepto para la trivial (k=1) creamos un vector nulo para ir
# agregando los valores
asw <- numeric(nrow(spe))
# creamos un loop para los clculos
for (k in 2:(nrow(spe) - 1)) {
sil <- silhouette(cutree(spe.ch.ward, k = k), spe.ch)
asw[k] <- summary(sil)$avg.width
}
k.best <- which.max(asw)
# graficamos
}
kt
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
kt[i, 2] <- mt
1
2
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28
29
k
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
r
0.0000
0.6554
0.7081
0.7155
0.6429
0.6741
0.6865
0.6879
0.6926
0.6499
0.6464
0.6396
0.6304
0.5009
0.4960
0.4375
0.4027
0.3950
0.3852
0.3571
0.3424
0.3271
0.3111
0.2931
0.2512
0.1971
0.1615
0.1149
0.0000
n = 29
2
3
12
7
11
13
4
14
1
6
10
17
16
9
18
5
19
15
21
22
27
29
28
30
26
20
23
24
25
1 : 11 | 0.37
2 : 7 | 0.04
3 : 8 | 0.60
4 : 3 | 0.34
0.0
0.2
0.4
0.6
0.8
Silhouette width si
Average silhouette width : 0.35
1.1.4.
1.0
23
200
22
21
20 19
26
16
15
13
28
150
17
14
27
y coordinate (km)
18
29
12
30
11
Downstream
100
10
9
50
7
6
Upstream
100
Cluster 1
Cluster 2
Cluster 3
Cluster 4
5
4
3
100
200
x coordinate (km)
1.2.
Anlisis no jerrquico
1.2.1.
#
#
#
#
#
# con 4 grupos
set.seed(1)
spe.kmeans <- kmeans(spe.norm, centers = 4, nstart = 100)
300
spebc.ward.g
1 2 3 4
1 0 0 0 3
2 11 1 0 0
3 0 6 0 0
4 0 0 8 0
Length
partition 261
results
18
criterion
1
size
90
Class
-none-none-none-none-
Mode
numeric
numeric
character
numeric
spe.KM.cascade$results
##
##
##
##
##
##
1
2
3
4
5
6
1
2
3
4
5
6
CHA TRU VAI LOC OMB BLA HOT TOX VAN CHE BAR SPI GOU BRO PER BOU
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
2
0
0
1
0
0
0
0
0
0
0
0
0
0
0
1
1
0
0
2
1
0
0
0
3
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
5
4
3
0
0
0
0
0
0
0
0
0
0
0
0
0
5
5
5
0
0
0
0
0
0
0
0
0
1
0
0
PSO ROT CAR TAN BCO PCH GRE GAR BBO ABL ANG
23
0
0
0
0
0
0
0
1
0
2
0
24
1
0
0
0
0
0
2
2
1
5
0
25
0
1
0
0
0
0
1
1
0
3
0
1
0
0
0
0
0
0
0
0
0
0
0
2
0
0
0
0
0
0
0
0
0
0
0
3
0
0
0
0
0
0
0
0
0
0
0
23
24
25
1
2
3
TRU
CHA
OMB
VAI
LOC
BLA
CHE
VAN
ABL
GOU
TOX
BRO
GAR
PER
HOT
TAN
BAR
SPI
GRE
ROT
PSO
CAR
BOU
BBO
ANG
BCO
222
111111 111122222223
34512346701234559678901267890
...3554351355542.321.......1.
..........12233..211.........
..........12342...11.......1.
....4554444455431343311....1.
....355554142452354352111111.
............234..5211......1.
121...121211.1325223132423443
..1....112....35.532222312233
253...............22355555555
.12...11.1...122.212445534455
.................4433222.1122
..1..121.....1.4.111123324354
121....1.......54122555545555
......21.......4.123123411245
.1................11222311121
......12......131111244435435
.............12..233244524353
.................143232111135
.21................1123445555
..1............2....122211225
.1...............111122323453
.................111112312435
..................12233323455
.1..................123424545
..................11122223445
....................113423345
11
##
##
##
PCH ......................1212345
sites species
29
27
head(spe[ord.KM$sites, ord.KM$species])
##
##
##
##
##
##
##
##
##
##
##
##
##
##
TRU CHA OMB VAI LOC BLA CHE VAN ABL GOU TOX BRO GAR PER HOT TAN
0
0
0
0
0
0
1
0
2
0
0
0
1
0
0
0
0
0
0
0
0
0
2
0
5
1
0
0
2
0
1
0
0
0
0
0
0
0
1
1
3
2
0
1
1
0
0
0
3
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
5
0
0
4
3
0
0
0
0
0
0
0
0
0
0
0
5
0
0
5
5
0
0
0
0
0
0
1
0
0
0
0
BAR SPI GRE ROT PSO CAR BOU BBO ANG BCO PCH
23
0
0
0
0
0
0
0
0
0
0
0
24
0
0
2
0
1
0
0
1
0
0
0
25
0
0
1
1
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
2
0
0
0
0
0
0
0
0
0
0
0
3
0
0
0
0
0
0
0
0
0
0
0
23
24
25
1
2
3
1
2
3
4
CHA
0.00000
0.10380
0.06168
0.00000
TRU
0.000000
0.542301
0.122088
0.006691
VAI
0.00000
0.50087
0.26994
0.02506
LOC
0.00000
0.43326
0.35943
0.06987
OMB
0.000000
0.114024
0.032665
0.006691
12
ssi
criterion
10
2
10
8
6
4
2
10
15
20
25
0.08
Objects
1.2.2.
#
#
#
#
#
#
0.12
0.16
Values
k-medoides (PAM)
# graficamos
plot(1:nrow(spe), asw, type = "h", main = "Choice of the number of clusters",
xlab = "k (number of clusters)", ylab = "Average silhouette width")
axis(1, k.best, paste("optimum", k.best, sep = "\n"), col = "red", font = 2,
col.axis = "red")
points(k.best, max(asw), pch = 16, col = "red", cex = 1.5)
# la opcin ptima para PAM es k=2 con asw=0.3841
# Si an as elegimos k=4 clusters para comparar con los anteriores
# mtodos
13
Medoids:
ID
[1,] "11" "12"
[2,] "6" "6"
[3,] "16" "17"
[4,] "25" "26"
Clustering vector:
1 2 3 4 5 6 7
1 1 1 2 2 2 1
25 26 27 28 29 30
4 4 4 4 4 4
Objective function:
build
swap
0.4426 0.4391
9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
2 2 1 1 1 1 1 3 3 3 3 4 4 4 4 4
##
##
##
##
##
##
##
##
##
##
##
##
##
##
29
4
3
0.36427
30
4
3
0.36421
24
4
3
0.31070
25
4
3
0.26599
20
4
3
0.23650
23
4
3
0.21030
Average silhouette width per cluster:
[1] 0.302892 0.003827 0.306963 0.360150
Average silhouette width of total data set:
[1] 0.2736
Available components:
[1] "medoids"
"id.med"
[6] "clusinfo"
"silinfo"
"clustering" "objective"
"diss"
"call"
13
12
2
14
11
3
1
7
15
6
10
9
5
4
17
18
16
19
26
27
28
22
21
29
30
24
25
20
23
"isolation"
##
##
##
##
1
2
3
4
8
3
0
0
1
2
4
0
0
0
0
8
0
0
0
3
table(spe.ch.pam.g, spe.kmeans$cluster)
##
## spe.ch.pam.g 1 2 3 4
##
1 0 9 0 0
##
2 0 3 2 0
##
3 0 0 4 0
##
4 3 0 0 8
# los resultados de PAM difieren mucho de los mtodos anteriores
# Qu solucin (PAM o k-means) tiene mejor silhouette? ----par(mfrow = c(1, 2))
k <- 4
sil <- silhouette(spe.kmeans$cluster, spe.ch)
rownames(sil) <- row.names(spe)
plot(sil, main = "Silhouette plot - k-means", cex.names = 0.8, col = 2:(k +
1))
plot(silhouette(spe.ch.pam), main = "Silhouette plot - PAM", cex.names = 0.8,
col = 2:(k + 1))
#
#
#
#
#
16
0.3
0.2
0.1
0.0
optimum
2
10
15
20
25
30
k (number of clusters)
4 clusters Cj
j : n1j | :ave
si
3 iCj
| 0.34
n = 29
23
24
25
2
12
3
7
11
13
14
4
1
6
10
15
17
18
16
9
5
19
22
21
27
28
29
30
26
20
13
12
2
14
11
3
1
7
15
6
10
9
5
4
17
18
16
19
26
27
28
22
21
29
30
24
25
20
23
2 : 12 | 0.37
3 : 6 | 0.08
4 : 8 | 0.59
0.0
0.2
0.4
0.6
0.8
4 clusters Cj
j : nj | aveiCj si
n = 29
1.0
1 : 9 | 0.30
2 : 5 | 0.004
3 : 4 | 0.31
4 : 11 | 0.36
0.0
Silhouette width si
0.2
0.4
0.6
0.8
Silhouette width si
1.3.
1.3.1.
17
1.0
# -----------------# Comparacin con datos ambientales--------# Relacin entre los clusters de peces y 4 variables ambientales
# basados en los resultados del cluster k-means -----------------#
# Validacin externa:
#
#
#
#
#
#
#
#
#
attach(env)
# Boxplots para variables cualitativas ambientales: altitud,
# pendiente, oxgeno y amonio
par(mfrow = c(2, 2))
boxplot(sqrt(alt) ~ spe.kmeans$cluster, main = "Altitude", las = 1, ylab = "sqrt(alt)",
col = 2:5, varwidth = TRUE)
boxplot(log(pen) ~ spe.kmeans$cluster, main = "Slope", las = 1, ylab = "log(pen)",
col = 2:5, varwidth = TRUE)
boxplot(oxy ~ spe.kmeans$cluster, main = "Oxygen", las = 1, ylab = "oxy",
col = 2:5, varwidth = TRUE)
boxplot(sqrt(amm) ~ spe.kmeans$cluster, main = "Ammonium", las = 1, ylab = "sqrt(amm)",
col = 2:5, varwidth = TRUE)
# Ponemos a prueba los supuestos del ANOVA Residuos normales . Ho:
# la variable tiene distribucin normal
shapiro.test(resid(lm(sqrt(alt) ~ as.factor(spe.kmeans$cluster))))
## Shapiro-Wilk normality test with resid(lm(sqrt(alt) ~ as.factor(spe.kmeans$cluster)))
## W = 0.9624, p-value = 0.3756
shapiro.test(resid(lm(log(pen) ~ as.factor(spe.kmeans$cluster))))
## Shapiro-Wilk normality test with resid(lm(log(pen) ~ as.factor(spe.kmeans$cluster)))
## W = 0.9518, p-value = 0.204
shapiro.test(resid(lm(oxy ~ as.factor(spe.kmeans$cluster))))
## Shapiro-Wilk normality test with resid(lm(oxy ~ as.factor(spe.kmeans$cluster)))
## W = 0.9394, p-value = 0.09674
shapiro.test(resid(lm(sqrt(amm) ~ as.factor(spe.kmeans$cluster))))
## Shapiro-Wilk normality test with resid(lm(sqrt(amm) ~ as.factor(spe.kmeans$cluster)))
## W = 0.954, p-value = 0.2319
# no rechazamos normalidad
# Homogeneidad de varianza. Ho: las varianzas son iguales entre
# grupos
bartlett.test(sqrt(alt), as.factor(spe.kmeans$cluster))
18
plot(TukeyHSD(fm1))
TukeyHSD(fm2, ordered = TRUE)
##
##
##
##
##
##
##
##
##
##
##
##
##
##
plot(TukeyHSD(fm2))
TukeyHSD(fm3, ordered = TRUE)
##
##
##
##
##
##
##
##
##
##
##
##
##
##
1-2
4-3
1-3
1-4
plot(TukeyHSD(fm3))
kruskalmc(alt ~ as.factor(spe.kmeans$cluster))
##
##
##
##
##
##
##
##
##
##
detach(env)
#
#
#
#
#
#
#
#
#
#
#
#
1
2
3
4
1
0
7
2
0
2
0
4
4
3
3
1
0
0
5
4
2
1
0
0
# agregamos nombres
21
chisqPostHoc(M2)
##
##
##
##
##
##
##
##
#
#
#
#
fdr method.
adj.p
NaN
0.0054
NaN
0.0322
0.0322
NaN
Adjusted p-values
comparison
1 sp_c1 vs. sp_c2
2 sp_c1 vs. sp_c3
3 sp_c1 vs. sp_c4
4 sp_c2 vs. sp_c3
5 sp_c2 vs. sp_c4
6 sp_c3 vs. sp_c4
produce NaN cuando hay ceros en los datos Para columnas, vemos que
existen diferencias significativas entre 1-3, 1-4, 2-3. Para
filas, vemos que existen diferencias significativas entre 1-2, 1-3,
2-4.
Altitude
Slope
4
30
3
2
log(pen)
sqrt(alt)
25
20
1
0
1
15
Oxygen
Ammonium
12
1.2
1.0
sqrt(amm)
0.8
0.6
0.4
6
0.2
0.0
4
1
31
41
32
42
43
42
32
41
31
21
21
43
oxy
10
23
1.3.2.
Ensables de especies
1) Abundancias medias en los clusters de sitios (k-means) ------Calcularemos estadsticos simples (abundancias medias) a partir de
las tipologas obtenidas con el anlisis cluster, y miraremos qu
especies estn presentes en mayor abundancia o qu especies son
especficas de cada cluster de sitios
## LOC GAR VAI VAN CHE TOX GOU PER BAR SPI BLA TAN TRU BRO
## 3.67 3.17 2.83 2.83 2.50 2.33 1.83 1.83 1.67 1.67 1.50 1.50 1.33 1.33
## ABL BOU CHA HOT PSO CAR ROT ANG OMB GRE BCO BBO PCH
## 1.17 0.83 0.67 0.67 0.67 0.67 0.50 0.50 0.33 0.33 0.17 0.17 0.00
group3.domin
## LOC GAR VAI VAN CHE TOX GOU PER BAR SPI BLA TAN
##
1
2
3
4
5
6
7
8
9 10 11 12
group4.domin <- which(group4 > mean(group4))
group4 #para el grupo 4
## ABL GAR GOU GRE TAN BAR BBO BOU BRO CHE BCO PSO ANG PER
## 5.00 4.88 4.38 4.12 4.00 3.75 3.62 3.50 3.25 3.12 3.12 3.00 3.00 2.75
## CAR VAN PCH SPI ROT HOT TOX LOC VAI TRU OMB BLA CHA
## 2.62 2.25 2.25 2.12 2.12 1.62 1.50 1.00 0.38 0.12 0.12 0.12 0.00
group4.domin
## ABL GAR GOU GRE TAN BAR BBO BOU BRO CHE BCO PSO ANG PER CAR
##
1
2
3
4
5
6
7
8
9 10 11 12 13 14 15
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
$Concordance_analysis
W
F
Prob.F
Corrected prob.F
Chi2
Prob.perm
Corrected prob.perm
Group.1
4.545e-01
1.333e+01
5.222e-43
1.044e-42
2.164e+02
1.000e-03
2.000e-03
Group.2
8.364e-01
1.022e+01
3.487e-13
3.487e-13
7.026e+01
1.000e-03
2.000e-03
$Correction.type
[1] "holm"
attr(,"class")
[1] "kendall.global"
Miramos los p-valores corregidos para el test de permutacin como
ambos grupos tienen p<0.05, decimos que todos los grupos son
significativos a nivel global i.e. de manera global, contienen
especies que son concordantes (al menos algunas especies son
concordantes) Si no fuera significativo para algunos grupos,
indicara que esos grupos deberan ser subdivididos en menores
grupos.
$A_posteriori_tests_Group
$A_posteriori_tests_Group[[1]]
GAR
ABL
CHE
GOU
TAN
VAN
BAR
Spearman.mean 0.3777 0.4563 -0.09825 0.4707 0.4288 0.2341 0.4528
W.per.species 0.4143 0.4883 -0.03365 0.5019 0.4624 0.2792 0.4850
Prob
0.0018 0.0002 0.75900 0.0001 0.0001 0.0413 0.0004
26
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
0.0020
GRE
0.5156
0.5441
0.0001
0.0020
TOX
0.4729
0.5040
0.0001
0.0020
$A_posteriori_tests_Group[[2]]
LOC
VAI
TRU
Spearman.mean 0.7414 0.8232 0.6976
W.per.species 0.8276 0.8822 0.7984
Prob
0.0001 0.0001 0.0001
Corrected prob 0.0020 0.0020 0.0020
$Correction.type
[1] "holm"
attr(,"class")
[1] "kendall.post"
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
7
1
9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
1 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3
$relfrq
CHA
TRU
VAI
LOC
OMB
BLA
HOT
TOX
VAN
CHE
BAR
SPI
GOU
BRO
PER
BOU
PSO
ROT
CAR
TAN
BCO
PCH
GRE
GAR
BBO
ABL
ANG
1
0.000
0.875
0.875
0.875
0.000
0.000
0.000
0.000
0.375
0.625
0.000
0.000
0.375
0.500
0.375
0.000
0.000
0.125
0.000
0.500
0.000
0.000
0.000
0.375
0.000
0.000
0.000
2
0.8
0.9
1.0
1.0
0.7
0.7
0.3
0.4
0.6
0.9
0.6
0.4
0.7
0.5
0.4
0.3
0.4
0.1
0.4
0.5
0.1
0.0
0.2
0.4
0.1
0.3
0.3
3
0.0000
0.0000
0.3333
0.5000
0.0000
0.0000
0.6667
0.5000
0.6667
1.0000
0.5000
0.5000
0.8333
0.6667
0.5000
0.5000
0.6667
0.6667
0.5000
0.5000
0.5000
0.3333
0.8333
1.0000
0.6667
1.0000
0.5000
4
0.0
0.2
0.2
0.8
0.2
0.2
1.0
0.8
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
$relabu
1
2
3
4
CHA 0.00000 1.00000 0.00000 0.00000
TRU 0.52124 0.44788 0.00000 0.03089
VAI 0.42299 0.50759 0.04338 0.02603
28
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
LOC
OMB
BLA
HOT
TOX
VAN
CHE
BAR
SPI
GOU
BRO
PER
BOU
PSO
ROT
CAR
TAN
BCO
PCH
GRE
GAR
BBO
ABL
ANG
0.40385
0.00000
0.00000
0.00000
0.00000
0.14325
0.16484
0.00000
0.00000
0.05660
0.15152
0.15419
0.00000
0.00000
0.06726
0.00000
0.11706
0.00000
0.00000
0.00000
0.12235
0.00000
0.00000
0.00000
$indval
CHA
TRU
VAI
LOC
OMB
BLA
HOT
TOX
VAN
CHE
BAR
SPI
GOU
BRO
PER
BOU
PSO
ROT
CAR
TAN
BCO
PCH
GRE
GAR
BBO
ABL
ANG
1
0.000000
0.456081
0.370119
0.353365
0.000000
0.000000
0.000000
0.000000
0.053718
0.103022
0.000000
0.000000
0.021226
0.075758
0.057819
0.000000
0.000000
0.008408
0.000000
0.058528
0.000000
0.000000
0.000000
0.045881
0.000000
0.000000
0.000000
0.42692
0.87500
0.90000
0.13636
0.38889
0.27831
0.19181
0.18932
0.23810
0.14717
0.07576
0.12335
0.08621
0.07792
0.02691
0.09091
0.08027
0.02069
0.00000
0.02857
0.09788
0.01734
0.07095
0.06122
0.07692
0.00000
0.00000
0.45455
0.27778
0.21828
0.25974
0.31553
0.23810
0.32075
0.22727
0.26432
0.25862
0.25974
0.31390
0.22727
0.26756
0.27586
0.14286
0.28571
0.30995
0.28902
0.42230
0.20408
2
0.800000
0.403089
0.507592
0.426923
0.612500
0.630000
0.040909
0.155556
0.166985
0.172627
0.113592
0.095238
0.103019
0.037879
0.049339
0.025862
0.031169
0.002691
0.036364
0.040134
0.002069
0.000000
0.005714
0.039152
0.001734
0.021284
0.018367
0.09231
0.12500
0.10000
0.40909
0.33333
0.36016
0.38362
0.49515
0.52381
0.47547
0.54545
0.45815
0.65517
0.66234
0.59193
0.68182
0.53512
0.70345
0.85714
0.68571
0.46982
0.69364
0.50676
0.73469
3
0.00000
0.00000
0.01446
0.03846
0.00000
0.00000
0.30303
0.13889
0.14552
0.25974
0.15777
0.11905
0.26730
0.15152
0.13216
0.12931
0.17316
0.20927
0.11364
0.13378
0.13793
0.04762
0.23810
0.30995
0.19268
0.42230
0.10204
4
0.000000
0.006178
0.005206
0.073846
0.025000
0.020000
0.409091
0.266667
0.360164
0.383616
0.495146
0.523810
0.475472
0.545455
0.458150
0.655172
0.662338
0.591928
0.681818
0.535117
0.703448
0.857143
0.685714
0.469821
0.693642
0.506757
0.734694
29
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
##
$maxcls
CHA TRU VAI LOC OMB BLA HOT TOX VAN CHE BAR SPI GOU BRO PER BOU PSO
2
1
2
2
2
2
4
4
4
4
4
4
4
4
4
4
4
ROT CAR TAN BCO PCH GRE GAR BBO ABL ANG
4
4
4
4
4
4
4
4
4
4
$indcls
CHA
TRU
VAI
LOC
OMB
BLA
HOT
TOX
VAN
CHE
0.8000 0.4561 0.5076 0.4269 0.6125 0.6300 0.4091 0.2667 0.3602 0.3836
BAR
SPI
GOU
BRO
PER
BOU
PSO
ROT
CAR
TAN
0.4951 0.5238 0.4755 0.5455 0.4581 0.6552 0.6623 0.5919 0.6818 0.5351
BCO
PCH
GRE
GAR
BBO
ABL
ANG
0.7034 0.8571 0.6857 0.4698 0.6936 0.5068 0.7347
$pval
CHA
TRU
VAI
LOC
OMB
BLA
HOT
TOX
VAN
CHE
BAR
0.001 0.021 0.001 0.011 0.007 0.005 0.052 0.283 0.128 0.029 0.009
SPI
GOU
BRO
PER
BOU
PSO
ROT
CAR
TAN
BCO
PCH
0.013 0.009 0.006 0.031 0.001 0.001 0.007 0.001 0.001 0.003 0.001
GRE
GAR
BBO
ABL
ANG
0.002 0.015 0.001 0.009 0.001
attr(,"class")
[1] "indval"
TRU
CHA
BLA
OMB
VAI
LOC
PCH
ANG
BCO
BBO
GRE
CAR
PSO
BOU
group
1
2
2
2
2
2
4
4
4
4
4
4
4
4
##
##
##
##
##
##
##
##
##
##
#
#
#
#
ROT
BRO
TAN
SPI
ABL
BAR
GOU
GAR
PER
CHE
4
4
4
4
4
4
4
4
4
4
0.5919
0.5455
0.5351
0.5238
0.5068
0.4951
0.4755
0.4698
0.4581
0.3836
0.007
0.006
0.001
0.013
0.009
0.009
0.009
0.015
0.031
0.029
11
18
17
12
14
14
20
18
15
25
31
calinski
criterion
8
7
6
2
6
5
4
3
2
10
15
Objects
20
8.0
9.0 10.0
Values
32