Enveomics collection

A toolbox for microbial genomics and metagenomics

RecPlot2.compareIdentities.R

Calculates the difference between identity distributions of two recruitment plots.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

§ Usage

RecPlot2.compareIdentities.R [opts] in_file in_file

§ Arguments

Method
 --method string  Distance method to use. This should be (an unambiguous abbreviation of) one of: 'hellinger' (Hellinger, 1090, doi:10.1515/crll.1909.136.210), 'bhattacharyya' (Bhattacharyya, 1943, Bull. Calcutta Math. Soc. 35), 'kl' or 'kullback–leibler' (Kullback & Leibler, 1951, doi:10.1214/aoms/1177729694), or 'euclidean'.
Pseudocounts
 --pseudocounts float  Smoothing parameter for Laplace smoothing. Use 0 for no smoothing, or 1 for add-one smoothing.
Max deviation
 --max-deviation float  Maximum mean deviation between identity breaks tolerated (as percent identity). Difference in number of id.breaks is never tolerated.
RecPlot A*
 in_file  File containing the R object `rp` for the first recruitment plot.
RecPlot B*
 in_file  File containing the R object `rp` for the second recruitment plot.
* Mandatory.