ape: correlogram.formula – R documentation

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ape

correlogram.formula

Phylogenetic Correlogram

Description

This function computes a correlogram from taxonomic levels.

Usage

correlogram.formula(formula, data = NULL, use = "all.obs")

Arguments

`formula`	a formula of the type `y1+..+yn ~ g1/../gn`, where the `y`'s are the data to analyse and the `g`'s are the taxonomic levels.
`data`	a data frame containing the variables specified in the formula. If `NULL`, the variables are sought in the user's workspace.
`use`	a character string specifying how to handle missing values (i.e., `NA`). This must be one of "all.obs", "complete.obs", or "pairwise.complete.obs", or any unambiguous abbrevation of these. In the first case, the presence of missing values produces an error. In the second case, all rows with missing values will be removed before computation. In the last case, missing values are removed on a case-by-case basis.

Details

See the vignette in R: vignette("MoranI").

Value

An object of class correlogram which is a data frame with three columns:

`obs`	the computed Moran's I
`p.values`	the corresponding P-values
`labels`	the names of each level

or an object of class correlogramList containing a list of objects of class correlogram if several variables are given as response in formula.

Author(s)

Julien Dutheil dutheil@evolbio.mpg.de and Emmanuel Paradis

Examples

data(carnivora)
### Using the formula interface:
co <- correlogram.formula(SW ~ Order/SuperFamily/Family/Genus,
      data=carnivora)
co
plot(co)
### Several correlograms on the same plot:
cos <- correlogram.formula(SW + FW ~ Order/SuperFamily/Family/Genus,
      data=carnivora)
cos
plot(cos)

ape

Analyses of Phylogenetics and Evolution

v5.5

GPL-2 | GPL-3

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24