DataInfo3D: Data Information for three diversity.

In KaiHsiangHu/iNEXT3D: Interpolation and Extrapolation for Species Diversity in three dimensions

Description

DataInfo3D Exhibit basic data information

Usage

DataInfo3D(
  data,
  diversity = "TD",
  datatype = "abundance",
  nT,
  PDtree,
  PDreftime = NULL,
  FDdistM,
  FDtype,
  FDtau = NULL
)

Arguments

data	a matrix, data.frame (species by sites), or list of species abundance/incidence frequencies. If datatype = "incidence_freq", then the first entry of the input data must be total number of sampling units in each column or list.
diversity	selection of diversity type: 'TD' = Taxonomic diversity, 'PD' = Phylogenetic diversity, and 'FD' = Functional diversity.
datatype	data type of input data: individual-based abundance data (datatype = "abundance"), sampling-unit-based incidence frequencies data (datatype = "incidence_freq") or species by sampling-units incidence matrix (datatype = "incidence_raw").
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. It is necessary when diversity = 'PD' and datatype = "incidence_raw".
PDtree	a phylo object describing the phylogenetic tree in Newick format for all observed species in the pooled assemblage. It is necessary when diversity = 'PD'.
PDreftime	Select several reference time points for diversity = 'PD'. Default is NULL.
FDdistM	a pair wise distance matrix for all pairs of observed species in the pooled assemblage. It will be use when diversity = 'FD'.
FDtype	a binary selection for FD. FDtype = "tau_values" computes diversity under certain threshold values. FDtype = "AUC" computes an overall FD which integrates all threshold values between zero and one. Default is "AUC".
FDtau	a sequence between 0 and 1 specifying tau. If NULL, threshold = dmean. Default is NULL. It will be use when diversity = 'FD' and FDtype = "tau_values".

Value

a data.frame of basic data information including sample size, observed species richness, sample coverage estimate, and the first ten abundance/incidence frequency counts.

Examples

## example for abundance-based data
# diversity = 'TD'
data(spider)
DataInfo3D(spider, diversity = 'TD', datatype = "abundance")

# diversity = 'PD'
data(data.abu)
data <- data.abu$data
tree <- data.abu$tree
DataInfo3D(data, diversity = 'PD', datatype = "abundance", PDtree = tree)

# diversity = 'FD' & FDtype = 'tau_values'
data(FunDdata.abu)
data <- FunDdata.abu$data
distM <-  FunDdata.abu$dij
DataInfo3D(data, diversity = 'FD', datatype = "abundance", FDdistM = distM, FDtype = 'tau_values')

# diversity = 'FD' & FDtype = 'AUC'
data(FunDdata.abu)
data <- FunDdata.abu$data
distM <-  FunDdata.abu$dij
DataInfo3D(data, diversity = 'FD', datatype = "abundance", FDdistM = distM, FDtype = 'AUC')

## example for incidence-based data
# diversity = 'TD'
data(ant)
DataInfo3D(ant, diversity = 'TD', datatype = "incidence_freq")

# diversity = 'PD'
data(data.inc)
data <- data.inc$data
tree <- data.inc$tree
nT <- data.inc$nT
DataInfo3D(data, diversity = 'PD', datatype = "incidence_raw", nT = nT, PDtree = tree)

# diversity = 'FD' & FDtype = 'tau_values'
data(FunDdata.inc)
data <- FunDdata.inc$data
distM <-  FunDdata.inc$dij
DataInfo3D(data, diversity = 'FD', datatype = "incidence_freq", FDdistM = distM, FDtype = 'tau_values')

# diversity = 'FD' & FDtype = 'AUC'
data(FunDdata.inc)
data <- FunDdata.inc$data
distM <-  FunDdata.inc$dij
DataInfo3D(data, diversity = 'FD', datatype = "incidence_freq", FDdistM = distM, FDtype = 'AUC')

KaiHsiangHu/iNEXT3D documentation built on July 18, 2021, 8:11 p.m.