stochasticity_rbr: Stochasticity by randomize_by_rows
In jfq3/QsNullModels: My null model functions

Description Usage Arguments Details Value Author(s) References

This function calculates stochasticity based on the Jaccard dissimilarity as defined in Zhou et al. (2014) by randomizing a binary community matrix using the function randomize_by_rows in this package.

1	stochasticity_rbr(com, w, n.reps=999)

`com`	A binary community matrix.
`w`	A vector of sampling wieghts.
`n.reps`	Number of replications.

The binary community matrix is randomized using the function randomize_by_rows in this package. This method maintains row (sample) totals.

The user must supply w, a vector of sampling weights. If w equals the column sums of com, the method corresponds to Ye Deng's gamma.method=sample (see reference). If w equals the column sums of a larger experiment matrix of which com is a sub-set, the method corresponds to gamma.method=total.

A vector of stochasticity values.

Johon Quensen

Zhou, J. Z., Y. Deng, P. Zhang, K. Xue, Y. T. Liang, J. D. Van Nostrand, Y. F. Yang, Z. L. He, L. Y. Wu, D. A. Stahl, T. C. Hazen, J. M. Tiedje, and A. P. Arkin. 2014. Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proceedings of the National Academy of Sciences of the United States of America 111:E836-E845.

jfq3/QsNullModels documentation built on April 6, 2020, 2:06 p.m.