# Phylogenetic correlogram

### Description

This function computes a phylogenetic correlogram.

### Usage

1 2 | ```
phyloCorrelogram(p4d, trait = names(tdata(p4d)), dist.phylo = "patristic",
sigma = NULL, n.points = 100, ci.bs = 1000, ci.conf = 0.95)
``` |

### Arguments

`p4d` |
a |

`trait` |
the traits in the |

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

`sigma` |
a numeric value giving the standard deviation of the normal distribution used
to compute the matrix of phylogenetic weights. If |

`n.points` |
an integer giving the number of points at which to compute the correlogram's statistics. |

`ci.bs` |
an integer giving the number of bootstrap replicates for confidence interval estimation. |

`ci.conf` |
a value between 0 and 1 giving the confidence level of the confidence interval. |

### Details

This function computes a correlogram on a continuous scale of phylogenetic distance.
This is achieved by using a collection of specific phylogenetic weights matrices generated
with the "`lag-norm`

" method of `phyloWeights`

and different values of "`mu`

".

The confidence envelope is computed by bootstrapping. At each iteration, the autocorrelation is re-estimated after re-standardization of the matrix of phylogenetic weights. The nonparametric confidence intervals are computed at each lag by first order normal approximation. Intervals are constrained between 0 and 1.

If there is one trait, the function computes Moran's I. If there is more than one trait, the function computes the Mantel's statistic (Oden and Sokal 1986).

If "`dist.phylo`

" is a character string,
the phylogenetic distance matrix is computed internally
using the function `distTips`

from the package adephylo.
See `distTips`

for details about the methods.

### Value

An object of class "`phylocorrelogram`

".

### References

Oden N.L. & Sokal R.R. (1986) Directional Autocorrelation: An Extension of Spatial Correlograms to Two Dimensions. Systematic Zoology 35, 608-617.

### See Also

`plot.phylocorrelogram`

,
`correlogram.formula`

in ape for correlograms based on taxonomic levels.

### Examples

1 2 3 4 5 6 | ```
## Not run:
data(navic)
pc <- phyloCorrelogram(navic)
plot(pc)
## End(Not run)
``` |

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