View source: R/estConnectivity.R

diffMantel | R Documentation |

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).

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

`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. |

`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.

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.

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