diffMantel {MigConnectivity}

Pairwise differences between two or more independent Mantel correlation estimates

Description

Estimates mean (and median) differences in Mantel correlations (rM), and includes measures of uncertainty (SE and CI). For those measures of uncertainty to be accurate, only apply this function to rM estimates where all data sources are independent (e.g., different species).

Usage

diffMantel(estimates, nSamples = 1e+05, alpha = 0.05, returnSamples = FALSE)

diffCorr(estimates, nSamples = 1e+05, alpha = 0.05, returnSamples = FALSE)

Arguments

estimates

List of at least two Mantel correlation estimates, provided by either the estMC or the estMantel functions. If this is a named list (recommended), the function will use these names in labeling the differences.

nSamples

A positive integer, number of samples (with replacement) to draw from each pair of MC estimates (default 100000). If set to NULL, compares all Mantel correlation samples from each pair.

alpha

Level for confidence/credible intervals provided.

returnSamples

Should the function return all the sampled differences? Defaults to FALSE to reduce storage requirements. Change to TRUE to compute your own summary statistics.

Value

diffMantel returns a list with elements:

meanDiff, medianDiff

Vectors with mean and medians of sampled differences for each pairwise comparison. Estimates of difference between rM values incorporating parametric uncertainty.

seDiff

Vector with standard errors of rM differences for each pairwise comparison, estimated from SD of sampled differences.

simpleCI

Matrix of 1 - alpha confidence intervals for rM differences, estimated as alpha/2 and 1 - alpha/2 quantiles of sampleCorr.

bcCI

Matrix of bias-corrected 1 - alpha confidence intervals for rM differences for each pairwise comparison. Preferable to simpleCI when meanDiff is the best estimate of the rM difference. simpleCI is preferred when medianDiff is a better estimator. When meanDiff==medianDiff, these should be identical. Estimated as the pnorm(2 * z0 + qnorm(alpha / 2)) and pnorm(2 * z0 + qnorm(1 - alpha / 2)) quantiles of sampled differences, where z0 is the proportion of sampleDiff < meanDiff.

sampleDiff

Only provided if returnSamples is TRUE. List of sampled values for each pairwise rM difference.

References

Cohen, E. B., C. S. Rushing, F. R. Moore, M. T. Hallworth, J. A. Hostetler, M. Gutierrez Ramirez, and P. P. Marra. 2019. The strength of migratory connectivity for birds en route to breeding through the Gulf of Mexico.