PDInfo: Summarizes phylogenetic data information.

In YanHanChen/iNEXTPD2: Interpolation and Extrapolation with Phylogenetic Diversity

Description

Function PDInfo summarizes phylogenetic data statistics for specified/default reference time.

Usage

PDInfo(data, nT, datatype = "abundance", tree, reftime = NULL)

Arguments

data	a matrix/data.frame of species abundances (for abundance data) or species-by-site incidence raw matrix/data.frame (for incidence data). See the function iNEXTPD for details.
nT	needed only when datatype = "incidence_raw", a sequence of named nonnegative integers specifying the number of sampling units in each assemblage. If names(nT) = NULL, then assemblage are automatically named as "assemblage1", "assemblage2",..., etc. Ignored if datatype = "abundance".
datatype	data type of input data: individual-based abundance data (datatype = "abundance"), or species-by-site raw incidence matrix (datatype = "incidence_raw"). Default is "abundance".
tree	a phylo object describing the phylogenetic tree in Newick format for all observed species in the pooled assemblage.
reftime	a positive value or sequence specifying the reference times for diversity computation. If NULL, then reftime is set to be the tree depth of the phylogenetic tree, which is spanned by all the observed species in the pooled assemblage. Default is NULL.

Value

Returns a table of phylogenetic data information, including reference sample size (n), number of sampling units (nT), number of observed species (S.obs), observed total branch length, i.e., Faith’s PD (PD.obs), the first two rare species frequency counts and their branch length sums, at specified/default reference time specified in the argument reftime. See Chao et al. (2010, 2015) and Hsieh and Chao (2017) for formulas and interpretations.

References

Chao, A., Chiu C.-H. and Jost, L. (2010). Phylogenetic diversity measures based on Hill numbers. Philosophical Transactions of the Royal Society B., 365, 3599-3609.

Chao, A., Chiu, C.-H., Hsieh, T. C., Davis, T., Nipperess, D., and Faith, D. (2015). Rarefaction and extrapolation of phylogenetic diversity. Methods in Ecology and Evolution, 6, 380-388.

Hsieh, T. C. and Chao, A. (2017). Rarefaction and extrapolation: making fair comparison of abundance-sensitive phylogenetic diversity among multiple assemblages. Systematic Biology, 66, 100-111.

Examples

# Datatype: abundance data
data(data.abu)
data <- data.abu$data
tree <- data.abu$tree
out <- PDInfo(data = data, datatype = "abundance", tree = tree)
out

# Datatype: incidence_raw data
data(data.inc)
data <- data.inc$data
tree <- data.inc$tree
nT <- data.inc$nT
out <- PDInfo(data = data, nT = nT, datatype = "incidence_raw", tree = tree)
out

YanHanChen/iNEXTPD2 documentation built on Aug. 24, 2020, 4:15 a.m.