PhyloApply {entropart}

Apply a Function over a Phylogenetic Tree

Description

Cuts the tree into slices separated by nodes, applies the function to each slice and returns the weighted (by slice lengths) sum of the results.

Usage

PhyloApply(Tree, FUN, NorP, Normalize = TRUE, dfArgs = NULL,
           ..., CheckArguments = TRUE)

Arguments

Tree

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

FUN

The function to be applied to each interval of the tree.

NorP

A numeric vector or a two-column matrix. Contains either abundances or probabilities. Two-column matrices should contain the observed abundances (or probabilities) in the first column and the expected ones in the second column, to allow using beta diversity functions.

Normalize

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

dfArgs

A dataframe. Columns are arguments for FUN: their names are those of valid arguments. Values will be passed to FUN in each slice of the tree, starting from the tips. The number of lines must equal the number of slices.

...

Further arguments to pass to Function.

CheckArguments

Logical; if TRUE, the function arguments are verified. Should be set to FALSE to save time when the arguments have been checked elsewhere.

Details

This funtion is generally not used directly. It is a tool to calculate PhyloEntropy and PhyloDiversity.

Intervals (slices) separate two cuts (nodes) in a tree: no node is found at heights contained in an interval.

Objects of class PPtree are returned by Preprocess.Tree.

... allow passing arguments to the function but they can't change along the tree. If necessary, dfArgs allow passing a different value for each slice of the tree.

Value

An object of class PhyloValue. It is a list:

Distribution

The distribution used to calculate the value

Function

The function used to calculate the value

Tree

The functional or phylogenetic tree used to calculate the value

Normalized

Logical. Indicates whether phylovalue is normalized or proportional to the height of the tree.

Cuts

A named vector containing values 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).

Corrections

A named vector containing the correction used by FUN to obtain each value of Cuts. Names are those of Cuts.

Total

The total value, multiplied by the tree height if Normalize is FALSE.

References

Marcon, E., Herault, B. (2015). Decomposing Phylodiversity. Methods in Ecology and Evolution 6(3): 333-339.

See Also

Preprocess.Tree

Examples

# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest
#      and their taxonomy)
data(Paracou618)
# Plot the taxonomy
plot(Paracou618.Taxonomy, type="fan", show.tip.label=FALSE)
# Calculate the mean number of trees (individuals) per species 
# (Cuts are 1=species, 2=genus, 3=family)
summary(PhyloApply(Paracou618.Taxonomy, mean, Paracou618.MC$Ns, TRUE))