PhdAsy: Computes asymptotic estimates for phylogenetic diversity and...

In YanHanChen/iNEXTPD2: Interpolation and Extrapolation with Phylogenetic Diversity

Description

Function PhdAsy computes asymptotic phylogenetic diversity estimates with respect to specified/default diversity order q and reference time to infer true phylogenetic diversity (PD) or phylogenetic Hill numbers (meanPD). See Chao et al. (2015) and Hsieh and Chao (2017) for the statistical estimation detail.

Usage

PhdAsy(
  data,
  nT,
  datatype = "abundance",
  tree,
  q = seq(0, 2, by = 0.25),
  reftime = NULL,
  type = "PD",
  nboot = 50,
  conf = 0.95
)

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.
q	a nonnegative value or sequence specifying the diversity order. Default is seq(0, 2, by = 0.25).
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.
type	desired diversity type: type = "PD" for Chao et al. (2010) phylogenetic diversity and type = "meanPD" for mean phylogenetic diversity (phylogenetic Hill number). Default is "PD".
nboot	a positive integer specifying the number of bootstrap replications when assessing sampling uncertainty and constructing confidence intervals. Enter 0 to skip the bootstrap procedures. Default is 50.
conf	a positive number < 1 specifying the level of confidence interval. Default is 0.95.

Value

Returns a table of estimated asymptotic phylogenetic diversity estimates (type = "PD") or phylogenetic Hill numbers (type = "meanPD") with respect to specified/default order q and reference time specified in the argument reftime.

References

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 <- PhdAsy(data = data, datatype = "abundance", tree = tree,
q = seq(0, 2, by = 0.25), nboot = 30)
out

# Datatype: incidence_raw data
data(data.inc)
data <- data.inc$data
tree <- data.inc$tree
nT <- data.inc$nT
out <- PhdAsy(data = data, nT = nT, datatype = "incidence_raw",
tree = tree, q = seq(0, 2, by = 0.25))
out

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