Regression tree
multivariate (MRT), 61, 122, 126–138
univariate, 126, 129, 130
Replacement, 36, 178, 369, 388–404
Resampling, 79, 80
Response variable, see Variable, response
R functions
adonis2 {vegan}, 239, 244
aem {adespatial}, 350, 351
agnes {cluster}, 69
anova.cca {vegan}, 221
bestnmds {labdsv}, 195
beta.div {adespatial}, 386, 387
beta.div.comp {adespatial}, 395–402
betadisper {vegan}, 239, 264
biplot.pcoa {ape}, 190, 191
biplot.rda {vegan}, 159
CA.newr, 181, 182, 201
calibrate {vegan}, 232
cancor {stats}, 277
capscale {vegan}, 250, 251
cascadeKM {vegan}, 98, 99
cc {CCA}, 277
cca {vegan}, 157, 158, 176–181, 226,
257, 283, 356
CCorA {vegan}, 275
cell2nb {spdep}, 352
chclust {rioja}, 138
classification {taxize}, 408
cleanplot.pca.R, 159, 160
clustIndex {cclust}, 98
cmdscale {stats}, 188–190, 195
cmeans {e1701}, 142
coca {cocorresp}, 274, 278
coef.cca {vegan}, 212
coinertia {ade4}, 278–281
coldiss.R, 43, 46
cophenetic {stats}, 71
coverscale {vegan}, 94
create.dbMEM.model {adespatial}, 348
cutree {stats}, 77
daisy {cluster}, 49, 50, 56, 57
dbFD {FD}, 405, 406
dbmem {adespatial}, 317, 320
dbrda {vegan}, 250, 251, 402
decorana {vegan}, 183
decostand {vegan}, 21, 22, 39, 55–57, 166
dist {stats}, 57
dist.binary {ade4}, 56, 57
dist.ldc {adespatial}, 38–40, 56, 57, 188
diversity {vegan}, 372, 375
dnearneigh {spdep}, 304
drawmap.R, 92
dudi.pca {ade4}, 154, 278
dudi.pco {ade4}, 278
envfit {vegan}, 168, 169, 179, 188, 189, 194
fanny {cluster}, 141–145
forward.sel {adespatial}, 227, 229, 261
fourthcorner {ade4}, 294
functcomp {FD}, 406
geoXY {SoDA}, 5, 48, 305
goodness {vegan}, 195, 217
gowdis {FD}, 50, 409
grpdist.R, 83
hclust {stats}, 63, 66, 68–70
hcoplot.R, 89
HMFA {FactoMineR}, 283
imputePCA {missMDA}, 172
indval {labdsv}, 121
isoMDS {MASS}, 195
kendall.global {vegan}, 112, 114
kendall.post {vegan}, 113
kmeans {stats}, 97, 98, 104
ktab.data.frame {ade4}, 282
LCBD.comp {adespatial}, 396
lda {MASS}, 264–268
listw2mat {spdep}, 345
mantel.correlog {vegan}, 306
MCA {FactoMineR}, 184
mca {MASS}, 184
metaMDS {vegan}, 193
mfa {ade4}, 282
MFA {FactoMineR}, 282, 283
MRT {MVPARTwrap}, 133
mso {vegan}, 356
multipatt{indicspecies}, 123
mvpart {mvpart}, 130, 132
nb2listw {spdep}, 345
nbdists {spdep}, 345
order.single {gclus}, 43
ordiR2step {vegan}, 227, 229, 230, 261, 329
ordistep {vegan}, 227–230, 261
ordisurf {vegan}, 179
p.adjust {stats}, 309
p.adjust.4thcorner {ade4}, 294
pairs {graphics}, 31
pam {cluster}, 103
PCA.newr, 154, 170, 171, 200
pcnm {vegan}, 320
pcoa {ape}, 190–192, 201
plot.links.R, 304
plt.cc {CCA}, 277
poly {stats}, 248, 310
polyvars.R, 248
prc {vegan}, 269
prcomp {stats}, 154, 163, 164
432
Index
multivariate (MRT), 61, 122, 126–138
univariate, 126, 129, 130
Replacement, 36, 178, 369, 388–404
Resampling, 79, 80
Response variable, see Variable, response
R functions
adonis2 {vegan}, 239, 244
aem {adespatial}, 350, 351
agnes {cluster}, 69
anova.cca {vegan}, 221
bestnmds {labdsv}, 195
beta.div {adespatial}, 386, 387
beta.div.comp {adespatial}, 395–402
betadisper {vegan}, 239, 264
biplot.pcoa {ape}, 190, 191
biplot.rda {vegan}, 159
CA.newr, 181, 182, 201
calibrate {vegan}, 232
cancor {stats}, 277
capscale {vegan}, 250, 251
cascadeKM {vegan}, 98, 99
cc {CCA}, 277
cca {vegan}, 157, 158, 176–181, 226,
257, 283, 356
CCorA {vegan}, 275
cell2nb {spdep}, 352
chclust {rioja}, 138
classification {taxize}, 408
cleanplot.pca.R, 159, 160
clustIndex {cclust}, 98
cmdscale {stats}, 188–190, 195
cmeans {e1701}, 142
coca {cocorresp}, 274, 278
coef.cca {vegan}, 212
coinertia {ade4}, 278–281
coldiss.R, 43, 46
cophenetic {stats}, 71
coverscale {vegan}, 94
create.dbMEM.model {adespatial}, 348
cutree {stats}, 77
daisy {cluster}, 49, 50, 56, 57
dbFD {FD}, 405, 406
dbmem {adespatial}, 317, 320
dbrda {vegan}, 250, 251, 402
decorana {vegan}, 183
decostand {vegan}, 21, 22, 39, 55–57, 166
dist {stats}, 57
dist.binary {ade4}, 56, 57
dist.ldc {adespatial}, 38–40, 56, 57, 188
diversity {vegan}, 372, 375
dnearneigh {spdep}, 304
drawmap.R, 92
dudi.pca {ade4}, 154, 278
dudi.pco {ade4}, 278
envfit {vegan}, 168, 169, 179, 188, 189, 194
fanny {cluster}, 141–145
forward.sel {adespatial}, 227, 229, 261
fourthcorner {ade4}, 294
functcomp {FD}, 406
geoXY {SoDA}, 5, 48, 305
goodness {vegan}, 195, 217
gowdis {FD}, 50, 409
grpdist.R, 83
hclust {stats}, 63, 66, 68–70
hcoplot.R, 89
HMFA {FactoMineR}, 283
imputePCA {missMDA}, 172
indval {labdsv}, 121
isoMDS {MASS}, 195
kendall.global {vegan}, 112, 114
kendall.post {vegan}, 113
kmeans {stats}, 97, 98, 104
ktab.data.frame {ade4}, 282
LCBD.comp {adespatial}, 396
lda {MASS}, 264–268
listw2mat {spdep}, 345
mantel.correlog {vegan}, 306
MCA {FactoMineR}, 184
mca {MASS}, 184
metaMDS {vegan}, 193
mfa {ade4}, 282
MFA {FactoMineR}, 282, 283
MRT {MVPARTwrap}, 133
mso {vegan}, 356
multipatt{indicspecies}, 123
mvpart {mvpart}, 130, 132
nb2listw {spdep}, 345
nbdists {spdep}, 345
order.single {gclus}, 43
ordiR2step {vegan}, 227, 229, 230, 261, 329
ordistep {vegan}, 227–230, 261
ordisurf {vegan}, 179
p.adjust {stats}, 309
p.adjust.4thcorner {ade4}, 294
pairs {graphics}, 31
pam {cluster}, 103
PCA.newr, 154, 170, 171, 200
pcnm {vegan}, 320
pcoa {ape}, 190–192, 201
plot.links.R, 304
plt.cc {CCA}, 277
poly {stats}, 248, 310
polyvars.R, 248
prc {vegan}, 269
prcomp {stats}, 154, 163, 164
432
Index