The function calculates parametric indices of species' rarity and functional or phylogenetic distinctiveness and effective originality according to Pavoine and Ricotta (2021).
distinctAb(comm, disORtree, method = c("Q", "KY", "KstarI"), palpha = 2,
option = c("asymmetric", "symmetric"), tol = 1e-10)If palpha <= 1, then, the function returns a list of four objects of class data.frame (with communities as rows and species as columns):
TotContr provides for each species in each community the effective originality multiplied by the relative abundance;
EffOriPres provides for each species present in each community the effective originality; NA for absent species;
DistinctPres provides for each species present in each community the distinctiveness; NA for absent species;
Rarity provides for each species in each community the rarity (maximum rarity for absent species).
Else, the function returns a list with the three objects of class data.frame presented above and two additional objects also of class data.frame:
EffOriAll provides for each species its effective originality compared with the composition of each community; even absent species have a value considering they have zero abundance so maximum rarity and considering their functional dissimilarity or phylogenetic dissimilarity with all species present in each community;
DistinctAll provides for each species its effective originality compared with the composition of each community; even absent species have a value considering they have zero abundance so maximum rarity and considering their functional dissimilarity or phylogenetic dissimilarity with all species present in each community.
a data frame or a matrix typically with communities as rows, species as columns and abundance as entry. Species should be labelled as in object disORtree.
an object inheriting the class dist, giving the FP-dissimilarities between species, or inheriting the class phylo (see package ape), phylo4 (see package phylobase), or hclust, where species are tips.
a string either "Q" for the quadratic entropy, "KY" for index \(^{\alpha}K\) (if disORtree is of class dist) or \(^{\alpha}Y\) if disORtree is of class phylo, phylo4 or hclust; or "KstarI" for index \(^{\alpha}K*\) (if disORtree is of class dist) or \(^{\alpha}I\) if disORtree is of class phylo, phylo4 or hclust. If several values are given, only the first one is considered.
a numeric, nonnegative value for parameter \(\alpha\). palpha is ignored if method = "Q".
a string either "asymmetric", or"symmetric" The parameter option is only used if disORtree is of class phylo, phylo4 or hclust If option="symmetric", the distance between two tips on a tree is defined as half the sum of branch length on the smallest path that connects the two species; while if option="asymmetric" the distance between a tip i and a tip j on a tree is defined as the sum of branch lengths between tip i and its most recent ancestor with tip j. If the tree is ultrametric, the two options are equivalent.
numeric tolerance threshold: values between -tol and tol are considered equal to zero.
Sandrine Pavoine sandrine.pavoine@mnhn.fr
Pavoine, S., Ricotta, C. (2021) On the relationships between rarity, uniqueness, distinctiveness, originality and functional/phylogenetic diversity. BiorXiv. tools:::Rd_expr_doi("10.1101/2021.08.09.455640")
distinctDis, distinctTopo, distinctTree, distinctUltra
if (FALSE) {
if(require(ape) && require(adephylo) && require(phylobase)){
data(batcomm)
phy <- read.tree(text=batcomm$tre2)
disAb <- distinctAb(batcomm$ab2, phy, method="Q")
U.4d <- phylo4d(phy, t(disAb[[2]]))
dotp4d(U.4d, center = FALSE, scale = FALSE, data.xlim = range(t(disAb[[2]]), na.rm=TRUE),
tree.ratio = 0.20, dot.cex=2)
title("Effective originality associated with quadratic entropy (diversity)")
}
}
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