Hi all, I'm using the caper package to run some pgls regressions, with the goal of understanding if growth in aerobic conditions has any effect on growth in anaerobic conditions (Anaerobic ~ Aerobic). I've been able to do the pgls, but we are interested in looking for outliers that may be a sign of more of an effect in either direction.
Does anyone have any recommendations on how to go about that? I've tried looking for outliers using the method mentioned here: https://duke.atlassian.net/wiki/spaces/AnthroTree/pages/15926335/7.5.1+PGLS+in+R+caper (see code below) modelo_res <- residuals(modelo_pgls_AnaexAer, phylo = TRUE) modelo_res <- modelo_res/sqrt(var(modelo_res))[1] rownames(modelo_res)<-rownames(modelo_pgls_AnaexAer$residuals) rownames(modelo_res)[(abs(modelo_res)>3)] But what it outputs doesn't necessarily make biological sense because those values are in the "cluster" of our growth rates, while other strains are much farther from the cluster. Maybe I'm misinterpreting? Happy to share any information needed to get some help with this. Thank you! Kind regards, Jaime Jaime A. Cordova Jr. Pronouns: he/him/his/�l Genetics PhD Candidate, Perna Lab University of Wisconsin, Madison NASA/JPL Solar System Ambassador I tend to work at irregular hours, but I never expect others to do the same. If I email you outside of your working hours, please do not feel obligated to respond until you are comfortable doing so. [[alternative HTML version deleted]]
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