predict {vegan, stats}, 161–163, 178
procrustes {vegan}, 173
pvclust {pvclust}, 79
quickMEM.R, 327, 328
quicksti {adespatial}, 364–366
Rao.R, 381, 409
rarecurve {vegan}, 378
rarefy {vegan}, 376
rcc {CCA}, 277
rda {vegan}, 154–166, 178, 205, 206,
208, 209, 212, 217, 323, 356
rlq {ade4}, 291
rpart {rpart}, 129
RsquareAdj {vegan}, 213, 217
scores {vegan}, 164
scores.listw {adespatial}, 345, 346
screestick.R, 283
shapiro.test {stats}, 275, 322
silhouette {cluster}, 81
sp.correlogram {spdep}, 304
specpool {vegan}, 380
stimodels {adespatial}, 364–366
strassoc {indicspecies}, 123–126
stressplot {vegan}, 195
tabasco {vegan}, 181
test.a.R, 116
test.W {adespatial}, 335
triangle.plot {ade4}, 400
triplot.rda.R, 217, 218
varpart {vegan}, 235, 329
vegclust {vegclust}, 146–150
vegdist {vegan}, 49, 56, 57
vegemite {vegan}, 94, 181
vif.cca {vegan}, 226
wascores {vegan}, 188, 189, 194
wcmdscale {vegan}, 188
Richness difference, 369, 388–404
RLQ analysis, 204, 281, 288, 290, 291, 293,
295–297
R mode, 35, 36, 38, 51–55, 59, 113, 115, 187
R-square (R
2
), 128, 131, 134, 169, 182, 185,
186, 195, 211–213, 222, 227, 235,
256, 276, 310, 323, 324, 330, 332,
333, 349
adjusted, 213, 217, 222, 223, 227–230,
233–235, 237, 247, 248, 262,
276, 322, 324, 332, 335, 340,
341, 348, 403
negative, 235, 330, 332
Ružička, see Dissimilarity, Ružička
RV coefficient, see Coefficient, RV
S
Sampling interval, see Interval, sampling
Scale
broad, 303, 325, 330, 332, 356, 359
dependence, 358
fine, 300, 302, 303, 323, 325, 327, 329, 330,
332, 333
large, 303
medium, 325, 332
regional, 300
small, 303
spatial, 299, 302–303, 316, 347–348, 370,
383, 412
Scale-dependence, see Scale, dependence
Scaling, 153, 155–157, 159–161, 165, 168,
170, 173, 175, 178, 180, 185–188,
190, 191, 210–212, 214, 216–218,
224, 225, 231, 242, 243, 245, 246,
249, 251, 258–260, 350, 403
type 1, 153, 156, 157, 159, 160, 165, 168,
173, 175, 178, 185, 187, 190, 191,
211, 212, 214, 216–218, 224, 225,
231, 242, 243, 251, 258–260, 403
type 2, 153, 155, 157, 159–161, 168, 175,
178, 180, 186, 188, 210–212, 214,
216–218, 224, 245, 246, 249,
258–260
type 3, 157
Scalogram, 323, 324
Scores
site, 94, 157, 163, 164, 205, 210–214,
216–218, 224, 231, 257, 260, 269,
272, 281, 285, 286, 322
species, 157, 210, 211, 216, 250, 251,
256, 257, 260, 272, 291
Scree plot, 158, 176, 283
Selection
backward, 228
forward, 226–230, 235–237, 244, 247,
249, 260–262, 310, 320, 322, 324,
327, 329, 335, 340, 348
stepwise, 226
Semi-quantitative, 12, 21, 37, 170
Semivariance, 335
Shannon, 371, 373, 375, 380
Shapiro-Wilk test, see Test, Shapiro-Wilk
Shepard, 195
Silhouette
plot, 87–89, 102, 104, 142–144
width, 80–82
Sill, 358
Index
433
procrustes {vegan}, 173
pvclust {pvclust}, 79
quickMEM.R, 327, 328
quicksti {adespatial}, 364–366
Rao.R, 381, 409
rarecurve {vegan}, 378
rarefy {vegan}, 376
rcc {CCA}, 277
rda {vegan}, 154–166, 178, 205, 206,
208, 209, 212, 217, 323, 356
rlq {ade4}, 291
rpart {rpart}, 129
RsquareAdj {vegan}, 213, 217
scores {vegan}, 164
scores.listw {adespatial}, 345, 346
screestick.R, 283
shapiro.test {stats}, 275, 322
silhouette {cluster}, 81
sp.correlogram {spdep}, 304
specpool {vegan}, 380
stimodels {adespatial}, 364–366
strassoc {indicspecies}, 123–126
stressplot {vegan}, 195
tabasco {vegan}, 181
test.a.R, 116
test.W {adespatial}, 335
triangle.plot {ade4}, 400
triplot.rda.R, 217, 218
varpart {vegan}, 235, 329
vegclust {vegclust}, 146–150
vegdist {vegan}, 49, 56, 57
vegemite {vegan}, 94, 181
vif.cca {vegan}, 226
wascores {vegan}, 188, 189, 194
wcmdscale {vegan}, 188
Richness difference, 369, 388–404
RLQ analysis, 204, 281, 288, 290, 291, 293,
295–297
R mode, 35, 36, 38, 51–55, 59, 113, 115, 187
R-square (R
2
), 128, 131, 134, 169, 182, 185,
186, 195, 211–213, 222, 227, 235,
256, 276, 310, 323, 324, 330, 332,
333, 349
adjusted, 213, 217, 222, 223, 227–230,
233–235, 237, 247, 248, 262,
276, 322, 324, 332, 335, 340,
341, 348, 403
negative, 235, 330, 332
Ružička, see Dissimilarity, Ružička
RV coefficient, see Coefficient, RV
S
Sampling interval, see Interval, sampling
Scale
broad, 303, 325, 330, 332, 356, 359
dependence, 358
fine, 300, 302, 303, 323, 325, 327, 329, 330,
332, 333
large, 303
medium, 325, 332
regional, 300
small, 303
spatial, 299, 302–303, 316, 347–348, 370,
383, 412
Scale-dependence, see Scale, dependence
Scaling, 153, 155–157, 159–161, 165, 168,
170, 173, 175, 178, 180, 185–188,
190, 191, 210–212, 214, 216–218,
224, 225, 231, 242, 243, 245, 246,
249, 251, 258–260, 350, 403
type 1, 153, 156, 157, 159, 160, 165, 168,
173, 175, 178, 185, 187, 190, 191,
211, 212, 214, 216–218, 224, 225,
231, 242, 243, 251, 258–260, 403
type 2, 153, 155, 157, 159–161, 168, 175,
178, 180, 186, 188, 210–212, 214,
216–218, 224, 245, 246, 249,
258–260
type 3, 157
Scalogram, 323, 324
Scores
site, 94, 157, 163, 164, 205, 210–214,
216–218, 224, 231, 257, 260, 269,
272, 281, 285, 286, 322
species, 157, 210, 211, 216, 250, 251,
256, 257, 260, 272, 291
Scree plot, 158, 176, 283
Selection
backward, 228
forward, 226–230, 235–237, 244, 247,
249, 260–262, 310, 320, 322, 324,
327, 329, 335, 340, 348
stepwise, 226
Semi-quantitative, 12, 21, 37, 170
Semivariance, 335
Shannon, 371, 373, 375, 380
Shapiro-Wilk test, see Test, Shapiro-Wilk
Shepard, 195
Silhouette
plot, 87–89, 102, 104, 142–144
width, 80–82
Sill, 358
Index
433