mjrochet {ade4}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)).

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)

Worked out examples


> library(ade4)
> ### Name: mjrochet
> ### Title: Phylogeny and quantitative traits of teleos fishes
> ### Aliases: mjrochet
> ### Keywords: datasets
> 
> ### ** 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$Bscores)
class: krandtest 
Monte-Carlo tests
Call: orthogram(x = tab0[, 1], orthobas = mjrochet.phy$Bscores)

Test number:   4 
Permutation number:   999 
   Test        Obs   Std.Obs     Alter Pvalue
1 R2Max  0.1501481  1.023525   greater  0.135
2 SkR2k 14.7098590 -3.555577      less  0.002
3  Dmax  0.3519553  3.894789 two-sided  0.002
4   SCE  2.5268895  7.417595   greater  0.003

other elements: NULL
> 
> 
> 
> 

[Package ade4 Index]