Obs.link: Empirical diversity q profile

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

Description

Obs.link The estimated and empirical diversity of order q

Usage

Obs.link(
  data,
  diversity = "TD",
  q = seq(0, 2, 0.2),
  datatype = "abundance",
  nboot = 50,
  conf = 0.95,
  col.tree = NULL,
  row.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). Enter 0 to skip the bootstrap procedures. Default is 50.
datatype	data type of input data: individual-based abundance data (datatype = "abundance") or species by sampling-units incidence matrix (datatype = "incidence_raw").
conf	a positive number < 1 specifying the level of confidence interval. Default is 0.95.
col.tree	phylogenetic tree of column assemblage in interaction matrix
row.tree	phylogenetic tree of row assemblage in interaction matrix.

Value

a table of Empirical network diversity q profile

Examples

## Not run: 
## Example for abundance-based data
## Ex.1
data(Norfolk)
out1 <- Obs.link(Norfolk, diversity = 'TD', datatype = "abundance", nboot = 30)
ggObs.link(out1)
## Ex.2
data(puerto.rico)
out2 <- Obs.link(data = puerto.rico$data, diversity = 'PD', datatype = "abundance",
ggObs.link(out2)

## End(Not run)

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