Description Usage Arguments Details Value References

This function computes Local Indicator of Phylogenetic Association (local Moran's I) for each tip of a tree. Tests are based on permutations.

1 2 |

`p4d` |
a |

`trait` |
the traits in the |

`reps` |
a numeric value. Number of repetitions for the estimation of p.values with randomization. |

`alternative` |
a character string specifying the alternative hypothesis for the tests.
Must be one of |

`prox.phylo` |
a matrix of phylogenetic proximities or a character string specifying a method to compute it. See Details. |

`as.p4d` |
logical. Should the results returned as a |

If "`prox.phylo`

" is a character string,
the phylogenetic proximity matrix is computed internally
using the function `proxTips`

from the package adephylo.
Different methods are available:
"`patristic`

","`nNodes`

","`Abouheif`

" and "`sumDD`

".
See `proxTips`

for details about the methods.

If `as.p4d`

is `FALSE`

(default), the function returns a list:

- lipa
A matrix of LIPA indices computed for each tip of the tree and each trait.

- p.value
A matrix of p-values (tests of LIPA indices)

- reps
Number of permutations for the tests

- alternative
Alternative hypothesis for the tests

If `as.p4d`

is `TRUE`

, the function returns a `phylo4d`

object
with LIPA values as tips associated data.

Anselin L. (1995) Local Indicators of Spatial Association-LISA. Geographical Analysis 27, 93-115.

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