estimatePD: Computes phylogenetic diversity for specified values of...

In YanHanChen/iNEXTPD2: Interpolation and Extrapolation with Phylogenetic Diversity

Description

Function estimatePD computes Chao et al.’s (2010, 2016) phylogenetic diversity (PD, effective total branch lengths, for diversity order q = 0, 1 and 2) and mean phylogenetic diversity (meanPD, phylogenetic Hill numbers or the effective number of lineages, q = 0, 1 and 2) at specified values of sample coverage. See Chao et al. (2010, 2015) and Hsieh and Chao (2017) for formulas and interpretations. Use the function iNEXTPD to compute PD or meanPD for specified sample sizes.

Usage

estimatePD(
  data,
  nT,
  datatype = "abundance",
  tree,
  q = c(0, 1, 2),
  reftime = NULL,
  type = "PD",
  level = NULL,
  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 c(0,1,2).
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".
level	a positive value < 1 or sequence specifying particular values of sample coverage. If NULL, then level is set to be the minimum coverage value among all samples extrapolated up to double the reference sample sizes. Default is NULL.
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 the computed phylogenetic diversity (PD or meanPD) for specified/default diversity orders q and reference times for the user-specified values of sample coverage. The corresponding sample sizes and sample coverage values are also provided.

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.

Chao, A., Chiu C.-H. and Jost L. (2016). Phylogenetic diversity measures and their decomposition: a framework based on Hill numbers. pp. 141-172 in Pellens R. and Grandcolas P. (eds) Biodiversity Conservation and Phylogenetic Systematics: Preserving our Evolutionary Heritage in an Extinction Crisis, Springer.

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 <- estimatePD(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 <- estimatePD(data = data, nT = nT, datatype = "incidence_raw", tree = tree)
out

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