DivPart(q = 1, MC, Biased = TRUE, Correction = "Best", Tree = NULL, Normalize = TRUE, Z = NULL, CheckArguments = TRUE)
is.DivPart(x)
"plot"(x, ...)
"summary"(object, ...)
MetaCommunity
object.
FALSE
, a bias correction is appplied.
AlphaEntropy
, BetaEntropy
and GammaEntropy
. "Best"
is the default value.
TRUE
(default), diversity is not affected by the height of the tree.
If FALSE
, diversity is proportional to the height of the tree.
TRUE
, the function arguments are verified. Should be set to FALSE
to save time when the arguments have been checked elsewhere.
MCdiversity
object to be summarized.
DivPart
object. It is a list:DivPart
objects can be summarized and plotted.
DivPart
partitions the diversity of the metacommunity into alpha and beta components. It supports estimation-bias correction.
If Tree
is provided, the phylogenetic diversity is calculated else if Z
is not NULL
, then similarity-based entropy is calculated.
Beta diversity/entropy is calculated from Gamma and Alpha when bias correction is required, so community values are not available.
Marcon, E., Zhang, Z. and Herault, B. (2014). The decomposition of similarity-based diversity and its bias correction. HAL hal-00989454(version 1).
DivProfile
# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest)
data(Paracou618)
# Estimate Shannon diversity.
summary(DivPart(q = 1, Paracou618.MC, Biased = FALSE) -> dp)
plot(dp)
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