ade4: mjrochet – R documentation

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mjrochet

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)).

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)
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)
if (requireNamespace("adephylo", quietly = TRUE)) {
  adephylo::orthogram(tab0[,1], ortho = mjrochet.phy$Bscores)
}

ade4

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

v1.7-16

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.

Initial release