entropart (version 1.1.3)

PhyloEntropy: Phylogenetic Entropy of a community

Description

Calculates the phylogenetic entropy of order $q$ of a probability vector.

Usage

PhyloEntropy(Ps, q, Tree, Normalize = TRUE, CheckArguments = TRUE)
bcPhyloEntropy(Ns, q, Tree, Normalize = TRUE, Correction = "Best", 
  CheckArguments = TRUE)
is.PhyloEntropy(x)
## S3 method for class 'PhyloEntropy':
summary(object, \dots)

Arguments

Ps

A probability vector, summing to 1.

Ns

A numeric vector containing species abundances.

q

A number.

Tree

An object of class hclust or phylog. The tree must be ultrametric.

Normalize

If TRUE (default), the Total entropy returned by the function is normalized by the height of the tree (it is the weighted average value of the entropy in each slice). If FALSE, it is the unnormalized weighted sum of

Correction

A string containing one of the possible corrections: "None" (no correction), "ChaoShen", "Grassberger", "Holste", "Bonachela" or "Best", the default value.

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 PhyloDiversity object to be summarized.

...

Additional arguments to be passed to the generic methods.

Value

• An object of class PhyloEntropy is a list:
• Distribution
  The distribution used to calculate entropy
• Function
  The function used to calculate entropy
• Tree
  The functional or phylogenetic tree used to calculate entropy
• Normalized
  Logical. Indicates whether phyloentropy is normalized or proportional to the height of the tree.
• Type
  The type of entropy ("alpha", "beta" or "gamma").
• Order
  The order of entropy $q$.
• Cuts
  A named vector containing values of neutral entropy along the tree. Names are cut ends, i.e. the ends of intervals (the first interval starts at 0 for leaves, the max value is the height of the tree).
• Total
  A value equal the total entropy multiplied by the tree height if Normalize is FALSE.
• is.PhyloEntropy returns TRUE if the object is of class PhyloEntropy. summary.PhyloEntropy returns a summary of the object's value. PhyloEntropy objects can be plotted by plot.PhyloValue because PhyloEntropy objects are also of class PhyloValue.

Details

The phylogenetic entropy is its generalization of HCDT entropy to unequal species distances (Pavoine et al., 2009). Calculation relies on Tsallis and PhyloApply. Intervals separate two cuts in a tree: no node is found at heights contained in an interval. Bias correction requires the number of individuals to estimate sample Coverage. Use bcPhyloEntropy and choose the Correction.

References

Marcon, E., Herault, B. (2014). Decomposing Phylodiversity. HAL hal-00946177(version 1). Pavoine, S., Love, M. S. and Bonsall, M. B. (2009). Hierarchical partitioning of evolutionary and ecological patterns in the organization of phylogenetically-structured species assemblages: Application to rockfish (genus: Sebastes) in the Southern California Bight. Ecology Letters 12(9): 898-908.

See Also

Tsallis, PhyloDiversity

Examples

# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest
  #      and their taxonomy)
  data(Paracou618)
  # Ps is the vector of probabilities
  Ps <- Paracou618.MC$Ps
  # Calculate the phylogenetic Shannon entropy of the plot
  summary(PhyloEntropy(Ps, 1, Paracou618.Taxonomy) -> e)
  plot(e)
  
  # Ns is the vector of abundances of the metacommunity
  Ns <- Paracou618.MC$Ns
  # Calculate the phylogenetic Shannon entropy of the plot
  summary(bcPhyloEntropy(Ns, 1, Paracou618.Taxonomy, Correction = "Best") -> e)
  plot(e)