wapqe: Rao’s apportionment of the quadratic entropy (APQE).

In vmikk/phylonest: Equivalent numbers for biodiversity in a nested hierarchy of multiple scales.

Description

The hierarchical apportionment of quadratic entropy defined by Rao (1982) wich allows biodiversity to be considered in terms of equivalent number of species, sites, regions, etc., in a nested hierarchy of multiple scales.

Usage

wapqe(
  df,
  dis = NULL,
  structures = NULL,
  formula = c("QE", "EDI"),
  wopt = c("even", "speciesab"),
  tol = 1e-08
)

Arguments

df	Dataframe or matrix with sites as rows and species as columns. Entries are abundances of species within sites.
dis	Dissimilarity among species (NULL or class 'dist').
structures	Data frame that contains the name of the group (row) of an level (column) to which the site belongs. Sites in structures should be in the same order as in df. Default is NULL.
formula	Quadratic entropy formula ("QE", "EDI"). "QE" is default.
wopt	Site weighting type ("even", "speciesab"). Default is "even".
tol	A tolerance threshold (a value less than tol is considered equal to zero).

Details

For the associated permutation test see randtestapqe.

Value

A data frame with each component of the selected diversity decomposition.

Author(s)

Sandrine Pavoine, Eric Marcon, Carlo Ricotta.

References

Pavoine S., Marcon E., Ricotta, C. (2016) ‘Equivalent numbers’ for species, phylogenetic or functional diversity in a nested hierarchy of multiple scales. Methods Ecol Evol, 7: 1152-1163. DOI:10.1111/2041-210X.12591

Rao, C.R. (1982) Diversity: its measurement, decomposition, apportionment and analysis. Sankhya: The Indian Journal of Statistics, A44, 1-22.

Pavoine S., Dolédec S. (2005) The apportionment of quadratic entropy: a useful alternative for partitioning diversity in ecological data. Environmental and Ecological Statistics, 12, 125-138. DOI:10.1007/s10651-005-1037-2

See Also

randtestEqRSintra, EqRS, EqRao, apqe in ade4.

Examples

data(macroloire)
# Taxonomic dissimilarities among species:
dTaxo <- dist.taxo(macroloire$taxo)^2/2
dTaxo <- dTaxo/max(dTaxo)
# Size-based dissimilarities among species
dSize <- dist.prop(macroloire$traits[ ,1:4], method = 2)
# Dissimilarities among species in terms of feeding categories
dFeed <- dist.prop(macroloire$traits[ ,5:11], method = 2)
# Dissimilarities among species in terms of both size and feeding categories
dSF <- (dSize+dFeed)/2

# Table with sites as rows (stations), species as columns and abundances as entries
ab <- as.data.frame(t(macroloire$fau))
# Table with sites as rows and one column only. Entries indicate the geological region associated with each site
stru <- macroloire$envir["Morphoregion"]

wapqe(ab, , stru, formula = "QE")
wapqe(ab, dTaxo, stru, formula = "QE")
wapqe(ab, dSize, stru, formula = "QE")
wapqe(ab, dFeed, stru, formula = "QE")
wapqe(ab, dSF, stru, formula = "QE")

vmikk/phylonest documentation built on Nov. 20, 2019, 4:17 p.m.