rarefied_disparity: Rarefied estimates of disparity/morphospace occupation

In fruciano/GeometricMorphometricsMix: Miscellaneous functions useful for geometric morphometrics

Rarefied estimates of disparity/morphospace occupation

Description

Computes rarefied estimates of multivariate variance (i.e., the trace of the covariance matrix) and the mean pairwise Euclidean distance

Usage

rarefied_disparity(Data, rep = 1000, samplesize, claramunt_pv = FALSE)

Arguments

Data	Matrix or data frame containing data (observations in rows, variables in columns).
rep	number of resamplings to obtain the rarefied estimate
samplesize	sample size to which the rarefaction procedure is carried out
claramunt_pv	if TRUE, compute an estimate of "Proper variance" (Claramunt 2010)

Details

The advantage of computing rarefied estimates of a parameter is to account for differences in sample sizes. This can be useful to compare estimates among groups.

This function is similar to the approaches implmented in the Matlab package MDA (Navarro 2003).

Examples of these approaches abound in the literature (e.g., Drake & Klingenberg 2010; Fruciano et al. 2014, 2016)

Optionally, the function also computes "Proper Variance" (Claramunt 2010) using linear shrinkage estimates of the covariance matrix.

Value

The function outputs a list with the following elements:

RarefiedSamplesEstimates

Estimates for each of the rarefied samples

Descriptives

Mean, standard deviation, median and 2.5% (Min) and 97.5% (Max) across the rarefied samples

Notice

the function does NOT perform GPA on each rarefied sample this may or may not make a difference in estimates. In many cases, it will probably not make much difference

If claramunt_pv=TRUE the package nlshrink should be installed. As this computation is based on linear shrinkage estimates of the covariance matrix it can be computational intensive. Please, also insure to check (and cite) the original publication (Claramunt 2010) to understand better this estimator.

References

Navarro N. 2003. MDA: a MATLAB-based program for morphospace-disparity analysis. Computers & Geosciences 29:655-664.

Drake AG, Klingenberg CP. 2010. Large-scale diversification of skull shape in domestic dogs: disparity and modularity. American Naturalist 175:289-301.

Claramunt S. 2010. Discovering exceptional diversifications at continental scales: the case of the endemic families of Neotropical Suboscine passerines. Evolution 64:2004-2019.

Fruciano C, Franchini P, Raffini F, Fan S, Meyer A. 2016. Are sympatrically speciating Midas cichlid fish special? Patterns of morphological and genetic variation in the closely related species Archocentrus centrarchus. Ecology and Evolution 6:4102-4114.

Fruciano C, Pappalardo AM, Tigano C, Ferrito V. 2014. Phylogeographical relationships of Sicilian brown trout and the effects of genetic introgression on morphospace occupation. Biological Journal of the Linnean Society 112:387-398.

See Also

rarefied_convex_hull, BTailTest

fruciano/GeometricMorphometricsMix documentation built on Jan. 31, 2024, 6:24 a.m.