my_rc: My Modification of Chase's Raup-Crick
In jfq3/QsNullModels: My null model functions

Description Usage Arguments Details Value Author(s) References Examples

Calculates a modified version of the Raup-Crick metric by Chase's method, but using a faster R script. Some of Chase's original options are omitted, and defaults are different.

1 2	my_rc(com, classic_metric = TRUE, split_ties = TRUE, nreps = 999, set_all_species_equal = FALSE)

`com`	A community matrix with samples as rows and species as columns.
`classic_metric`	A logical specifying whether or not the Raup-Crick metric should be standardized to the range -1 to 1 as Chase did. Defaults to TRuE.
`split_ties`	A logical specifying how ties are handled in calculating probabilities. Defaults to TRUE.
`nreps`	The number of replications used in calculating null expectations..
`set_all_species_equal`	A logical specifying sampling probablilites. Defaults to FALSE.

This function calculates a modified version of Raup-Crick using a null model approach. By default, it returns a distance matrix apppropriate for ordination. If classic_metric is set to FALSE, the metric is standardized as Chase preferred to range from -1 to 1 instead of 0 to 1. When this is done, values near -1 indicate that samples are more similar than expected by chance and values near 1 indicate that samples are less similar than expected by chance. If the result is to be used as a distance method, the metric should not be re-scaled (keep classic_metric set to TRUE, the default value). If ties are split (as Chase recommends) the dissimilarity matrix can be flipped by multiplying by -1 (for Chase's modification, which ranges from -1 to 1) or by subtracting the metric from 1 (for the classic metric which ranges from 0 to 1). If ties are not split (and there are ties between the observed and expected shared number of species) this conversion will not work. The argument nreps specifies the number of randomizations; a minimum of 999 is recommended. If the argument set_all_species_equal is set to TRUE, all species are weighted equally in the null model; this is not recommended. Chase's preferred method is to weight species by frequency of occupancy, as occurs when set_all_species_equal is left at the default value FALSE. Raup-Crick is calculated from a presence/absence communitiy matrix. If this function is given count data, it first converts it to presence/absence. The choice of how many plots (rows) to include has a real impact on the metric, as species and their occurrence frequencies across the set of plots is used to determine gamma and the frequency with which each species is drawn from the null model.

A Raup-Crick distance matrix.

With classic_metric=TRUE, returns a distance matrix that may be used for ordination or clustering. With classic_metric=FALSE, returns a matrix re-scaled to the interval -1 to 1.

John Quensen

Chase, J. M., N. J. B. Kraft, K. G. Smith, M. Vellend, and B. D. Inouye. 2011. Using null models to disentangle variation in community dissimilarity from variation in alpha-diversity. Ecosphere 2(2): Article 24. Raup, D. M. and R. E. Crick. 1979. Measurement of faunal similarity in paleontology. Journal of Paleontology 53:1213-1227.