Hello all, I have been trying to get something to work in a number of different packages and with a number of different approaches today that I couldn't get to run in a believable way. Before I spend another day on this, I was wondering what people think about the idea in general.
I have a dataset of disease prevalence across ~100 species. There are ~2000 individuals total across the dataset, with >4 individuals per species. Prevalence per individual is coded as 0 or 1. I am interested in the phylogenetic signal of disease prevalence across the species. One approach that works is to simply calculate prevalence as the species-specific mean, i.e. if 3 individuals of 6 for a species had the disease, the prevalence would be 3/6 = 0.5. Then one can use these values with e.g. phylosig() (I arcsin sqrt transformed these proportions here). Like the few other published tests of phylogenetic signal in disease prevalence, there is little signal here. I could leave it at that, because in general there are very low detections in this dataset and it's probably not ideally suited to address this question anyhow. That aside however, because not all individuals of a given species always have the disease, I wanted to incorporate "measurement error". So, based on the calculation for SE for binary data from the site: http://www.researchgate.net/post/Can_standard_deviation_and_standard_error_be_calculated_for_a_binary_variable, I also calculated a species-specific SEs as the sqrt(mean(prevalence)*((1- mean(prevalence))/individuals)). What do people think about this? It's hardly measurement error in the sense we normally mean it. On the other hand, I think it would be neat if there were some way to account for variation among individuals in prevalence, and the influence this has on phylogenetic signal. Cheers, Eliot [[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/
