AlphaEntropy(MC, q = 1, Correction = "Best", Tree = NULL, Normalize = TRUE,
Z = NULL, CheckArguments = TRUE)
MetaCommunity
object."None"
or "Best"
, the default value.TRUE
(default), the entropy returned by the function is normalized by the height of the tree (it is the weighted average value of the entropy in each slice).
If FALSE
, it is the unnormalized weighted sum of the results.TRUE
, the function arguments are verified. Should be set to FALSE
to save time when the arguments have been checked elsewhere.MCentropy
object containing entropy values of each community and of the metacommunity.Tree
is not NULL
, then phylogenetic entropy is calculated by bcPhyloEntropy
; else, if Z
is not NULL
, then similarity-based entropy is calculated by bcHqz
; else, neutral entropy is calculated by bcTsallis
.
The alpha entropy of each community is calculated and summed according to community weights.
The possible corrections are detailed in Tsallis
.bcTsallis
# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest)
data(Paracou618)
# Calculate Simpson alpha entropy
summary(AlphaEntropy(Paracou618.MC, 2))
# Compare without correction
summary(AlphaEntropy(Paracou618.MC, 2, Correction = "None"))
# Estimate phylogenetic Simpson alpha entropy
summary(AlphaEntropy(Paracou618.MC, 2, Tree = Paracou618.Taxonomy) -> e)
plot(e)
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