# moranIdx: Computes Moran's index for a variable In adephylo: Exploratory Analyses for the Phylogenetic Comparative Method

 moran.idx R Documentation

## Computes Moran's index for a variable

### Description

This simple function computes Moran's index of autocorrelation given a variable and a matrix of proximities among observations.

### Usage

```moran.idx(x, prox, addInfo = FALSE)
```

### Arguments

 `x` a numeric vector whose autocorrelation is computed. `prox` a matrix of proximities between observations, as computed by the `proxTips`. Off-diagonal terms must be positive or null, while diagonal terms must all equal zero. `addInfo` a logical indicating whether supplementary info (null value, minimum and maximum values) should be returned (TRUE) or not (FALSE, default); if computed, these quantities are returned as attributes.

### Value

The numeric value of Moran's index.

### Author(s)

Thibaut Jombart tjombart@imperial.ac.uk

### References

Moran, P.A.P. (1948) The interpretation of statistical maps. Journal of the Royal Statistical Society, B 10, 243–251.

Moran, P.A.P. (1950) Notes on continuous stochastic phenomena. Biometrika, 37, 17–23.

de Jong, P. and Sprenger, C. and van Veen, F. (1984) On extreme values of Moran's I and Geary's c. Geographical Analysis, 16, 17–24.

`proxTips` which computes phylogenetic proximities between tips of a phylogeny.

### Examples

```
## Not run:
## use maples dataset
data(maples)
dom <- maples\$tab\$Dom
bif <- maples\$tab\$Bif

## get a proximity matrix between tips
W <- proxTips(tre, met="Abouheif")

## compute Moran's I for two traits (dom and bif)
moran.idx(dom, W)
moran.idx(bif, W)
moran.idx(rnorm(nTips(tre)), W)

## build a simple permutation test for 'bif'
sim <- replicate(499, moran.idx(sample(bif), W)) # permutations
sim <- c(moran.idx(bif, W), sim)

pval <- mean(sim>=sim[1]) # right-tail p-value
pval

hist(sim, col="grey", main="Moran's I Monte Carlo test for 'bif'") # plot
mtext("Histogram of permutations and observation (in red)")
abline(v=sim[1], col="red", lwd=3)

## End(Not run)
```

adephylo documentation built on Oct. 19, 2022, 5:15 p.m.