Description Usage Arguments Value Author(s) References See Also Examples
View source: R/randtestEqRao.R
Permutation test for the third type of diversity decomposition (EqRao
).
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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.a |
option |
Rescaling type ("eq", "normed1" or "normed2"). |
wopt |
Site weighting type ("even", "speciesab"). Default is "even". |
level |
Level to test. Provide a number between 1 and 1+the number of columns in structures. The number is discarded if the parameter 'structures' is set to NULL. |
nrep |
The number of permutations. |
alter |
Alternative hypothesis type ("greater" (default), "less" or "two-sided"). |
tol |
A tolerance threshold (a value less than tol is considered equal to zero). |
metmean |
Mean type - "arithmetic" or "harmonic" (default). |
A list of class 'randtest', see randtest
.
Sandrine Pavoine, Eric Marcon, Carlo Ricotta.
Pavoine, S., Marcon, E. and 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | 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"]
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