mjrochet {adephylo}R Documentation

Phylogeny and quantitative traits of teleos fishes

Description

This data set describes the phylogeny of 49 teleos fishes as reported by Rochet et al. (2000). It also gives life-history traits corresponding to these 49 species.

Usage

data(mjrochet)

Format

mjrochet is a list containing the 2 following objects :

tre
is a character string giving the phylogenetic tree in Newick format.
tab
is a data frame with 49 rows and 7 traits.

Details

Variables of mjrochet$tab are the following ones : tm (age at maturity (years)), lm (length at maturity (cm)), l05 (length at 5 per cent survival (cm)), t05 (time to 5 per cent survival (years)), fb (slope of the log-log fecundity-length relationship), fm (fecundity the year of maturity), egg (volume of eggs (mm^3)).

Note

This dataset replaces the former version in ade4.

Source

Data taken from:
Summary of data - Clupeiformes : http://www.ifremer.fr/maerha/clupe.html
Summary of data - Argentiniformes : http://www.ifremer.fr/maerha/argentin.html
Summary of data - Salmoniformes : http://www.ifremer.fr/maerha/salmon.html
Summary of data - Gadiformes : http://www.ifremer.fr/maerha/gadi.html
Summary of data - Lophiiformes : http://www.ifremer.fr/maerha/loph.html
Summary of data - Atheriniformes : http://www.ifremer.fr/maerha/ather.html
Summary of data - Perciformes : http://www.ifremer.fr/maerha/perci.html
Summary of data - Pleuronectiformes : http://www.ifremer.fr/maerha/pleuro.html
Summary of data - Scorpaeniformes : http://www.ifremer.fr/maerha/scorpa.html
Phylogenetic tree : http://www.ifremer.fr/maerha/life_history.html

References

Rochet, M. J., Cornillon, P-A., Sabatier, R. and Pontier, D. (2000) Comparative analysis of phylogenic and fishing effects in life history patterns of teleos fishes. Oïkos, 91, 255–270.

Examples

data(mjrochet)
tre <- read.tree(text=mjrochet$tre) # make a tree
traits <- log((mjrochet$tab))

## build a phylo4d
mjr <- phylo4d(tre, traits)

## see data
table.phylo4d(mjr,cex.lab=.5,show.node=FALSE,symb="square")

## perform Abouheif's test for each trait
mjr.tests <- abouheif.moran(mjr, nrep=499)
mjr.tests
plot(mjr.tests)


[Package adephylo version 1.0-2 Index]