entropart (version 1.1.3)

DivProfile: Diversity Profile of a metacommunity

Description

Calculate the diversity profiles (alpha, beta, gamma) of a metacommunity.

Usage

DivProfile(q.seq = seq(0, 2, 0.1), MC, Biased = TRUE, Correction = "Best", 
  Tree = NULL, Normalize = TRUE, CheckArguments = TRUE)
## S3 method for class 'DivProfile':
plot(x, \dots, main = NULL, xlab = "Order of Diversity",
  ylab = NULL, Which = "All")
## S3 method for class 'DivProfile':
summary(object, \dots)

Arguments

q.seq

A numeric vector.

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.

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.

main

The main title of the plot. Ignored if Which = "All".

xlab

The x axis label of the plots.

ylab

The y axis label of the plot. Ignored if Which = "All".

Which

May be "Communities", "Alpha", "Beta" or "Gamma" to respectively plot the alpha diversity of communities or the metacommunity's alpha, beta or gamma diversity. If "All" (default), all four p

object

A MCdiversity object to be summarized.

...

Additional arguments to be passed to the generic methods.

Value

• A DivProfile object. It is a list:
• MetaCommunity
  The name of the MetaCommunity object containing inventory data.
• Order
  A vector containing the values of q.
• Biased
  Logical. If FALSE, bias corrected values of diversity have been computed.
• Correction
  The estimation bias correction used to calculate diversity.
• 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.
• CommunityAlphaDiversities
  A matrix containing the alpha diversity of each community.
• TotalAlphaDiversity
  A vector containing the alpha diversity of communities for each order.
• BetaDiversity
  A vector containing the beta diversity of communities for each order.
• GammaDiversity
  A vector containing the gamma diversity of the metacommunity for each order.
• CommunityAlphaEntropies
  A matrix containing the alpha entropy of each community.
• TotalAlphaEntropy
  A vector containing the alpha entropy of communities for each order.
• BetaEntropy
  A vector containing the beta entropy of communities for each order.
• GammaEntropy
  A vector containing the gamma entropy of the metacommunity for each order.
• DivProfile objects can be summarized and plotted.

Details

If Tree is provided, the phylogenetic diversity is calculated. DivPart partitions the diversity of the metacommunity into alpha and beta components. It supports estimation-bias correction (Marcon et al., submitted). If Tree is provided, the phylogenetic diversity 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., 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. (2014). Decomposing Phylodiversity. HAL hal-00946177(version 1).

See Also

DivPart

Examples

# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest)
  data(Paracou618)
  # Estimate diversity.
  Profile <- DivProfile(q.seq = seq(0, 2, 0.1), Paracou618.MC, Biased = FALSE)
  plot(Profile)
  summary(Profile)