Dear experts in phylogenetic comparative methods, I am running the OUwie function to fit evolutionary models for traits. The help says for the input data frame: "The trait data.frame must have column entries in the following order: [,1] species names, [,2] current selective regime, and [,3] the continuous trait of interest".
However, I get different optima estimates when the second column (i.e. current selective regime) of the dataframe is set as the "factor" class compared to the "character" class. I am trying to figure this out because I have changed the order of the current trait states (as factor) by manually setting the level, while the node.label in the tree is still character. I have also tried changing the node.label to factor to follow the current level of regime in taxa, but the names in the estimated optima result are even stranger. I wonder if the column in the input dataframe should be mandatory factor and can only be ordered alphabetically? However, I would prefer to (pre-)order the level of the trait states, as this would make it easier to visualise and describe the results later. Thank you very much for your help and have a nice day! Best wishes Ting-Wen -- Ph.D. Ting-Wen Chen Animal Ecology (AG Scheu) J.F. Blumenbach Institute of Zoology and Anthropology Georg August Universität Göttingen Untere Karspüle 2 D-37073 Göttingen, Germany https://www.uni-goettingen.de/en/348915.html [[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/
