Hi Emmanuel, Thank you for your reply. I see, that gives me some peace of mind when interpreting the results. I did recently notice that the issue only comes up when the input file had polytomies, which I then removed when converting to treeshapes using as.treeshape(x, model="yule") before calculating beta. Maybe that is causing the issue whith the condition tests.
Best, Pedro > Subject: Re: [R-sig-phylo] Warnings when calculating beta in apTreeshape > To: pedro.santos.ne...@outlook.com; r-sig-phylo@r-project.org > From: emmanuel.para...@ird.fr > Date: Tue, 2 Feb 2016 09:02:32 +0100 > > Hi Pedro, > > It's an issue in the design of the package. The condition tests should > be something like: > > if (inherits(phylo, "treeshape")) .... > if (inherits(phylo, "phylo")) .... > > But if the output makes sense, you should not worry about it since, > apparently, this is just to transform the tree in the appropriate class. > > Best, > > Emmanuel > > Le 01/02/2016 18:15, Pedro Neves a �crit : > > Hello, > > > > I'm trying to use the function maxlik.betasplit from the apTreeshape > > package in some phylogenetic trees. I previously converted the trees to the > > treeshape format and removed polytomies. > > However, each time I run the command, I get several warnings, usually more > > than 50, all with the same text: > > > > > > > > > > > > > > > > 49: In if > > (class(phylo) == "treeshape") bal <- bbalance(as.phylo(phylo)) : > > > > the condition has length > 1 and only the > > first element will be used > > > > > > 50: In if > > (class(phylo) == "phylo") bal <- bbalance(phylo) : > > > > the condition has length > 1 and only the > > first element will be used > > Despite getting the results I need, I'm not sure what these warnings mean > > and so don't really trust the data I'm getting. Is it something I can > > ignore? > > Thanks in advance!Pedro > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-sig-phylo mailing list - R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ > > > > > > Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : > > http://f.security-mail.net/807il6XNqbK > > > > > [[alternative HTML version deleted]]
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