It seems the function was masked from some other package: This works: require(geiger) geo <- get(data(geospiza)) lphy <- geiger::rescale(geo$phy, "lambda", 0.9) # transform tree in one fell swoop
Thanks again, 2014-05-16 15:49 GMT-03:00 Agus Camacho <[email protected]>: > Thank you both, > > However, > > > geo <- get(data(geospiza)) > > lphy <- rescale(geo$phy, "lambda", 0.5) # transform tree in one fell > swoop > Error in colMeans(x, na.rm = TRUE) : 'x' must be numeric > > I got this error also for simulated and other real trees. > > > 2014-05-16 15:24 GMT-03:00 Liam J. Revell <[email protected]>: > > It looks like transform.phylo has been deprecated. Use rescale.phylo. >> >> All the best, Liam >> >> Liam J. Revell, Assistant Professor of Biology >> University of Massachusetts Boston >> web: http://faculty.umb.edu/liam.revell/ >> email: [email protected] >> blog: http://blog.phytools.org >> >> >> On 5/16/2014 2:20 PM, Agus Camacho wrote: >> >>> Dear list users, >>> >>> Im trying to show what happens when we apply lambda transformations to a >>> tree. >>> >>> For that, I was following swenson's book explanations: >>> >>> library(geiger) >>> lambda.phylo=transform(tree,1) >>> >>> however, I got the following errors: >>> >>> lambda.phylo=transform(tree,"lambda") >>>> >>> Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors >>> = >>> stringsAsFactors) : cannot coerce class ""phylo"" to a data.frame >>> >>> lambda.phylo=geiger::transform(tree,"lambda") >>>> >>> Error: 'transform' is not an exported object from 'namespace:geiger' >>> >>> Any one would point to a workaround for branch transformation and >>> posterior >>> visualization of the tree? >>> >>> Thanks in advance. >>> Agus >>> >>> >>> >>> _______________________________________________ >>> R-sig-phylo mailing list - [email protected] >>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>> Searchable archive at http://www.mail-archive.com/r- >>> [email protected]/ >>> >>> > > > -- > Agustín Camacho Guerrero. > Doutor em Zoologia. > Laboratório de Herpetologia, Departamento de Zoologia, Instituto de > Biociências, USP. > Rua do Matão, trav. 14, nº 321, Cidade Universitária, > São Paulo - SP, CEP: 05508-090, Brasil. > -- Agustín Camacho Guerrero. Doutor em Zoologia. Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, USP. Rua do Matão, trav. 14, nº 321, Cidade Universitária, São Paulo - SP, CEP: 05508-090, Brasil. [[alternative HTML version deleted]]
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