Comparing the GMYC delimitation with an alternative clustering

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Description

This function calculates similarity between the GMYC and an alternative delimitation for assessment of accuracy. Two measures of similarity are available.

Usage

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comp.delimit(obj, alt, method="EM")

Arguments

obj

a gmyc object obtained by gmyc

alt

a data frame of associations between samples and species representing a delimitation. The first column must be species identifiers and the second column must be samples

method

a character string specifying the method to measure similarity of delimitations; must be "EM" or "NMI"

Details

The function measures partitioning similarity between the GMYC delimitation and an user specified grouping (eg. taxonomic species). The available measures of partitioning distance is following:

  • "EM": This counts the number of species which have exact match (EM) between the GMYC and alternative delimitation used in Fujisawa & Barraclough (2013) paper.

  • "NMI": This calculates the normalized mutual information (NMI) between the GMYC and an alternative delimitation. The method is described in Vinh et al.(2010).

Author(s)

Tomochika Fujisawa t.fujisawa05@gmail.com and Jiajie Zhang Jiajie.Zhang@h-its.org

References

Fujisawa, T. & Barraclough, TG. 2013. Delimiting species using single-locus data and the generalized mixed Yule coalescent (GMYC) approach: A revised method and evaluation on simulated datasets. Systematic Biology. 62(5): 707-724.

Vinh, NX., Epps, J. & Bailey, J. 2010. Information theoretic measures for clustering comparison: variants, properties, normalization and correction for chance. Journal of Machne Learning Research. 11: 2837-2854.

Examples

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data(test.tr)
test <- gmyc(test.tr, method="single")

#true species names
truesp <- sapply(strsplit(test.tr$tip.label, "\\."), head, 1) 
truesp <- data.frame(truesp, test.tr$tip.label)

#compare 
comp.delimit(test, truesp, method="EM") #count exact match
comp.delimit(test, truesp, method="NMI") #calculate NMI