DivPart: Diversity Partition of a metacommunity

In entropart: Entropy Partitioning to Measure Diversity

Diversity Partition of a metacommunity

Description

Partitions the diversity of a metacommunity into alpha and beta components.

Usage

DivPart(q = 1, MC, Biased = TRUE, Correction = "Best", Tree = NULL,
  Normalize = TRUE, Z = NULL, CheckArguments = TRUE)
is.DivPart(x)
## S3 method for class 'DivPart'
plot(x, ...)
## S3 method for class 'DivPart'
autoplot(object, col = ggplot2::GeomRect$default_aes$fill, 
  border = ggplot2::GeomRect$default_aes$colour, ...)
## S3 method for class 'DivPart'
summary(object, ...)

Arguments

q	A number: the order of diversity. Default is 1.
MC	A MetaCommunity object.
Biased	Logical; if FALSE, a bias correction is appplied.
Correction	A string containing one of the possible corrections. The correction must be accepted by AlphaEntropy, BetaEntropy and GammaEntropy. "Best" is the default value.
Tree	An object of class hclust, "phylo" (see read.tree), phylog or PPtree. The tree must be ultrametric.
Normalize	If TRUE (default), diversity is not affected by the height of the tree. If FALSE, diversity is proportional to the height of the tree.
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 TRUE, the function arguments are verified. Should be set to FALSE to save time when the arguments have been checked elsewhere.
x	An object to be tested or plotted.
object	A MCdiversity object to be summarized or plotted.
col	The color used to fill the bars. See "Color Specification" in par.
border	The color of the borders around the bars. See rect.
...	Additional arguments to be passed to the generic methods.

Details

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.

Value

A DivPart object. It is a list:

MetaCommunity	The name of the MetaCommunity object containing inventory data.
Order	The value of q.
Biased	Logical. If FALSE, bias corrected values of diversity have been computed.
Correction	The estimation bias correction used to calculate diversity.
Method	The method used to calculate entropy ("HCDT", "Similarity-based").
Tree	The phylogenetic or functional tree used to calculate phylodiversity.
Normalized	Logical. Indicates whether phylodiversity is normalized or proportional to the height of the tree.
Z	The matrix used to calculate similarity-based entropy.
TotalAlphaDiversity	The alpha diversity of communities.
TotalBetaDiversity	The beta diversity of communities.
GammaDiversity	The gamma diversity of the metacommunity.
CommunityAlphaDiversities	A vector containing the alpha diversity of each community.
TotalAlphaEntropy	The alpha entropy of communities.
TotalBetaEntropy	The beta entropy of communities.
GammaEntropy	The gamma entropy of the metacommunity.
CommunityAlphaEntropies	A vector containing the alpha entropy of each community.

DivPart objects can be summarized and plotted.

Author(s)

Eric Marcon <[e-mail]>, Bruno Herault <[e-mail]>

References

Marcon, E., Herault, B., Baraloto, C. and Lang, G. (2012). The Decomposition of Shannon's Entropy and a Confidence Interval for Beta Diversity. Oikos 121(4): 516-522.

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).

See Also

DivProfile

Examples

# 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)

entropart documentation built on Sept. 11, 2024, 6:20 p.m.