Extrapolation Estimation

Description Usage Arguments Value Examples

estimateD.link computes species diversity (Hill numbers with q = 0, 1 and 2) with a particular user-specified level of sample size or sample coverage.

estimateD.link(
  data,
  diversity = "TD",
  q = c(0, 1, 2),
  datatype = "abundance",
  base = "size",
  level = NULL,
  nboot = 50,
  conf = 0.95,
  row.tree = NULL,
  col.tree = NULL
)

`data`	a `matrix`, `data.frame` (species by assemblages), or `list` of species abundance/incidence raw data.
`diversity`	a choice of three-level diversity: 'TD' = 'Taxonomic', 'PD' = 'Phylogenetic', and 'FD' = 'Functional' under certain threshold. Besides,'AUC' is the fourth choice which integrates several threshold functional diversity to get diversity.
`q`	a numerical vector of the order of Hill number.
`datatype`	data type of input data: individual-based abundance data (`datatype = "abundance"`) or species by sampling-units incidence matrix (`datatype = "incidence_raw"`).
`base`	comparison base: sample-size-based (`base="size"`) or coverage-based (`base="coverage"`).
`level`	a sequence specifying the particular sample sizes or sample coverages(between 0 and 1). If `base="size"` and `level=NULL`, then this function computes the diversity estimates for the minimum sample size among all sites extrapolated to double reference sizes. If `base="coverage"` and `level=NULL`, then this function computes the diversity estimates for the minimum sample coverage among all sites extrapolated to double reference sizes.
`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.
`row.tree`	phylogenetic tree of row assemblage in interaction matrix.
`col.tree`	phylogenetic tree of column assemblage in interaction matrix

a data.frame of species diversity table including the sample size, sample coverage, method (rarefaction or extrapolation), and diversity estimates with q = 0, 1, and 2 for the user-specified sample size or sample coverage.

## Not run: 
data(Norfolk)
out1 <- estimateD.link(Norfolk, diversity = 'TD',datatype="abundance",
                       base="coverage", level=0.7, nboot = 30)
out2 <- estimateD.link(Norfolk, diversity = 'TD',datatype="abundance",
                       base="size", level=0.7, nboot = 30)

## End(Not run)