Guidance on the visualization of phylolm models
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Hi! I am a frequent user of phylolm
(currently I rely on version 2.6.4), and I regularly find myself stumped when it comes to visualizing the models. This is particularly so because I average PGLS models (MuMIn::dredge()
+ subset(delta <= threshold)
+ MuMIn::model.avg()
).
For instance, ggeffects::gpredict()
won't work with model-averaged phylolm
models (strengejacke/ggeffects#387). Another example is lack of compatiblity between phlyolm()
and visreg()
(#64), which does not show a confidence band.
Admitedly, one can use model coefficients to plot a line (https://stackoverflow.com/questions/43441467/plot-phylogenetic-logistic-regression-with-binary-response-variable), but this does not show uncertainty around the estimate, which is particularly important when visually assessing overlap among factor levels. As far as I can tell, phylolm
lacks a se.fit = TRUE
option for the predict()
method, which would be a very interesting feature.
Can anyone recommend a way to visualize model predictions, effects, marginal means? I am particularly interested in a way to show uncertainty around a prediction or estimated effect. If the solution also applies to model-averaged objects it would be best!
Thank you for your time, and congratulations for the great package!