mjrochet: Phylogeny and quantitative traits of teleos fishes

mjrochetR Documentation

Phylogeny and quantitative traits of teleos fishes


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.




mjrochet is a list containing the 2 following objects :


is a character string giving the phylogenetic tree in Newick format.


is a data frame with 49 rows and 7 traits.


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)).


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


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.


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 documentation built on Feb. 16, 2023, 7:58 p.m.

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