BetaDiversity.RdCalculates the reduced-bias beta diversity of order \(q\) between communities.
BetaDiversity(MC, q = 1, Correction = "Best", Tree = NULL, Normalize = TRUE,
Z = NULL, CheckArguments = TRUE)A MetaCommunity object.
A number: the order of diversity. Default is 1 for Shannon diversity.
A string containing one of the possible corrections accepted by bcTsallisBeta or "None" or "Best", the default value.
An object of class hclust, phylo, phylog or PPtree. The tree must be ultrametric.
If TRUE (default), diversity is not affected by the height of the tree.
If FALSE, diversity is proportional to the height of the tree.
A relatedness matrix, i.e. a square matrix whose terms are all positive, strictly positive on the diagonal. Generally, the matrix is a similarity matrix, i.e. the diagonal terms equal 1 and other terms are between 0 and 1.
Logical; if TRUE, the function arguments are verified. Should be set to FALSE to save time when the arguments have been checked elsewhere.
Entropy is calculated by BetaEntropy and transformed into diversity.
Diversity values of communities are not defined: community entropies are averaged to obtain the metacommunity entropy wich is transformed into diversity (Marcon et al., 2014).
An MCdiversity object containing diversity value of the metacommunity.
Marcon, E., Scotti, I., Herault, B., Rossi, V. and Lang, G. (2014). Generalization of the partitioning of Shannon diversity. PLOS One 9(3): e90289.
Marcon, E., Herault, B. (2015). Decomposing Phylodiversity. Methods in Ecology and Evolution 6(3): 333-339.
Marcon, E., Zhang, Z. and Herault, B. (2014). The decomposition of similarity-based diversity and its bias correction. HAL hal-00989454(version 3).
# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest)
data(Paracou618)
# Estimate Shannon beta diversity
summary(BetaDiversity(Paracou618.MC, 1))
#> Neutral beta diversity of order 1 of metaCommunity Paracou618.MC
#> with correction: Best
#>
#> Average diversity of the communities:
#> [1] 1.436039
# Compare without correction
summary(BetaDiversity(Paracou618.MC, 1, Correction = "None"))
#> Neutral beta diversity of order 1 of metaCommunity Paracou618.MC
#> with correction: None
#>
#> Average diversity of the communities:
#> [1] 1.563888
# Estimate phylogenetic Shannon beta diversity
summary(BetaDiversity(Paracou618.MC, 1, Tree = Paracou618.Taxonomy) -> e)
#> HCDT beta diversity of order 1 of metaCommunity Paracou618.MC with correction:
#> Best
#>
#> Phylogenetic or functional diversity was calculated according to the tree
#> Paracou618.Taxonomy
#>
#> Diversity is normalized
#>
#> Average diversity of the communities:
#> [1] 1.289993