entropart (version 1.4-4)

DivPart: 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, \dots)
## S3 method for class 'DivPart':
summary(object, \dots)

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

Tree

An object of class hclust or phylog. 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.

...

Additional arguments to be passed to the generic methods.

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.

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.

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 1).

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)