PhyloApply {entropart} | R Documentation |
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.
PhyloApply(Tree, FUN, NorP, Normalize = TRUE, dfArgs = NULL,
..., CheckArguments = TRUE)
Tree |
An object of class |
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 |
dfArgs |
A dataframe. Columns are arguments for |
... |
Further arguments to pass to |
CheckArguments |
Logical; if |
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.
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 |
Total |
The total value, multiplied by the tree height if |
Marcon, E., Herault, B. (2015). Decomposing Phylodiversity. Methods in Ecology and Evolution 6(3): 333-339.
# 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))