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.