Asy.link: Asymptotic diversity q profile

In Chunger-Lo/iNEXT.link: Network diversity iNterpolation/Extrapolation Estimation

Description

Asy.link The estimated and empirical diversity of order q

Usage

Asy.link(
  data,
  diversity = "TD",
  q = seq(0, 2, 0.2),
  datatype = "abundance",
  nboot = 30,
  conf = 0.95,
  row.tree = NULL,
  col.tree = 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). Abundance data: a species-by-site matrix/data.frame of species abundances. The row (species) names of data must match the species names in the phylogenetic tree and thus cannot be missing. Incidence raw data: species-by-site raw incidence matrix/data.frame. When there are N assemblages and thus N matrices, users must first merge the N matrices by species identity to obtain a large merged incidence matrix, where the rows of the matrix refer to all species presented in the merged data. The row (species) names of data must match the species names in the phylogenetic tree and thus cannot be missing.
diversity	a choice of three-level diversity: 'TD' = 'Taxonomic', 'PD' = 'Phylogenetic', and 'FD' = 'Functional' under certain threshold.
q	a nonnegative value or sequence specifying the diversity order. Default is c(0,1,2).
datatype	data type of input data: individual-based abundance data (datatype = "abundance") or species by sampling-units incidence matrix (datatype = "incidence_raw").
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

Value

a table of Asymptotic network diversity q profile

Examples

## Not run: 
## Ex.1
data(Norfolk)
out1 <- Asy.link(Norfolk, diversity = 'TD', datatype = "abundance", nboot = 10)
ggAsy.link(out1)
## Ex.2
data(puerto.rico)
out2 <- Asy.link(puerto.rico$data, diversity = 'PD', datatype = "abundance", nboot = 10,
row.tree = puerto.rico$row.tree, col.tree = puerto.rico$col.tree)
ggAsy.link(out2)

## End(Not run)

Chunger-Lo/iNEXT.link documentation built on Dec. 17, 2021, 2:05 p.m.