Description Usage Format Details Note Source References Examples
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.
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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$tab
are the following ones : tm (age at
maturity (years)), lm (length at maturity (cm)), l05 (length at 5 per
cent survival (cm)), t05 (time to 5 per cent survival (years)), fb
(slope of the log-log fecundity-length relationship), fm (fecundity the
year of maturity), egg (volume of eggs (mm^3)).
This dataset replaces the former version in ade4.
Data taken from:
Summary of data - Clupeiformes : http://www.ifremer.fr/maerha/clupe.html
Summary of data - Argentiniformes : http://www.ifremer.fr/maerha/argentin.html
Summary of data - Salmoniformes : http://www.ifremer.fr/maerha/salmon.html
Summary of data - Gadiformes : http://www.ifremer.fr/maerha/gadi.html
Summary of data - Lophiiformes : http://www.ifremer.fr/maerha/loph.html
Summary of data - Atheriniformes : http://www.ifremer.fr/maerha/ather.html
Summary of data - Perciformes : http://www.ifremer.fr/maerha/perci.html
Summary of data - Pleuronectiformes : http://www.ifremer.fr/maerha/pleuro.html
Summary of data - Scorpaeniformes : http://www.ifremer.fr/maerha/scorpa.html
Phylogenetic tree : http://www.ifremer.fr/maerha/life_history.html
Rochet, M. J., Cornillon, P-A., Sabatier, R. and Pontier, D. (2000) Comparative analysis of phylogenic and fishing effects in life history patterns of teleos fishes. Oïkos, 91, 255–270.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ## Not run:
if(require(ape) && require(phylobase)){
data(mjrochet)
tre <- read.tree(text=mjrochet$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
}
## End(Not run)
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