diverclust | R Documentation |
Function forms hierarchic clustering so that each fusion minimizes beta deiversity or gamma diversity.
diverclust(
x,
renyi = 1,
equalize = TRUE,
beta = TRUE,
hill = FALSE,
trace = TRUE
)
x |
Community data. |
renyi |
The scale of Renyi diversity index as defined in
|
equalize |
Equalize data rows so that they can be meaningfully
pooled and averaged. If this is |
beta |
Use beta diversities: the average alpha diversity of
cluster members is subtracted from the pooled diversity. If this is
|
hill |
Use Hill numbers instead of Renyi diversity (see
|
trace |
Trace calculations. Either logical or an integer:
|
The function forms clusters so that pooled diversity or its change to the baseline alpha diversity is minimized at each level of clustering. The change of pooled diversity with respect to the baseline alpha diversity is called beta diversity, and the overall diversity is called gamma diversity. For beta diversity, the clustering implies an additive partitioning.
Function returns an hclust
object.
Jari Oksanen.
hclust
for cluster analysis and its support
methods, renyi
for estimating Renyi
diversities and Hill numbers, and adipart
for
related additive partitioning of beta diversity.
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