This function calculates similarity between the GMYC and an alternative delimitation for assessment of accuracy. Two measures of similarity are available.
comp.delimit(obj, alt, method="EM")
a gmyc object obtained by
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
a character string specifying the method to measure similarity of delimitations; must be "EM" or "NMI"
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).
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.
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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
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