PhdObs: Computes observed phylogenetic diversity and phylogenetic...

In YanHanChen/iNEXTPD2: Interpolation and Extrapolation with Phylogenetic Diversity

Description

Function PhdObs computes empirical or observed phylogenetic diversity (PD) and phylogenetic Hill numbers (meanPD, mean phylogenetic diversity) for specified/default order q and reference time specified in the argument reftime. See Chao et al. (2010) for details of PD and meanPD.

Usage

PhdObs(
  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 empirical (observed) phylogenetic diversity (type = "PD") or phylogenetic Hill number (type= "meanPD") for specified/default order q and reference time.

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.

Examples

# Datatype: abundance data
data(data.abu)
data <- data.abu$data
tree <- data.abu$tree
out <- PhdObs(data = data, datatype = "abundance", tree = tree,
q = seq(0, 2, by = 0.25))
out

# Datatype: incidence_raw data
data(data.inc)
data <- data.inc$data
tree <- data.inc$tree
nT <- data.inc$nT
out <- PhdObs(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.