AlphaDiversity {entropart} | R Documentation |
Calculates the eeduced-bias total alpha diversity of order q
of communities.
AlphaDiversity(MC, q = 1, Correction = "Best", Tree = NULL, Normalize = TRUE,
Z = NULL, CheckArguments = TRUE)
MC |
A |
q |
A number: the order of diversity. Default is 1 for Shannon diversity. |
Correction |
A string containing one of the possible corrections accepted by |
Tree |
An object of class |
Normalize |
If |
Z |
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. |
CheckArguments |
Logical; if |
Entropy is calculated by AlphaEntropy
and transformed into diversity.
An MCdiversity
object containing diversity values of each community and 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)
# Calculate Simpson alpha diversity
summary(AlphaDiversity(Paracou618.MC, 2))
# Compare without correction
summary(AlphaDiversity(Paracou618.MC, 2, Correction = "None"))
# Estimate phylogenetic Simpson alpha diversity
summary(AlphaDiversity(Paracou618.MC, 2, Tree = Paracou618.Taxonomy) -> e)
plot(e)