mjrochet: Phylogeny and quantitative traits of teleos fishes

In ade4: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

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)).

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. O?kos, 91, 255–270.

Examples

data(mjrochet)
mjrochet.phy <- newick2phylog(mjrochet$tre)
tab <- log((mjrochet$tab))
tab0 <- data.frame(scalewt(tab))
table.phylog(tab0, mjrochet.phy, csi = 2, clabel.r = 0.75)
orthogram(tab0[,1], ortho = mjrochet.phy$Bscores)

ade4 documentation built on May 2, 2019, 5:50 p.m.