Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie)

Hi Rafael. > Also, I realized that this has the effect of making the mserr of > species with sample size of 1 equal to the pooled standard deviation. Yes. This makes sense because our uncertainty about that observation of the mean should be exactly equal to the population dispersion around the

Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie)

Hi again Liam, Do you mind having a quick look at the piece of code below to see if I'm interpreting your suggestion correctly? Also, I realized that this has the effect of making the mserr of species with sample size of 1 equal to the pooled standard deviation. Is this what you had in mind? Tha

Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie)

Hi Liam, Great, thank you! I'll definitely try that. Do you know of any references describing that approach in detail, or using it in practice? Thank you, *--* *Rafael Sobral Marcondes* PhD Candidate (Systematics, Ecology and Evolution/Ornithology) Museum of Natural Science

Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie)

Another possibility is to do a regression to predict variance for species with a single observation. Or even do a phylogenetic regression so species nearer the ones with missing data matter more. But all this stuff is minor tweaks: it's great you're incorporating measurement error at all, and I ho

Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie)

Hi Santiago. This is identical to my suggestion, except that the pooled variance is a weighted mean in which weights (for better or worse) are proportional to the sample size of each species. If the variances are indeed homogeneous, this should be preferred because it gives greater weight to

Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie)

Hi Rafael, Your method would underestimate the error associated with values derived from single specimens because those values would have the highest errors, not average errors. What I have done in such cases is to estimate an average standard deviation across species and use that average stand

Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie)

Hi Rafael. What I would recommend in the case where you have relatively small samples per species is to compute a pooled within-species variance (https://en.wikipedia.org/wiki/Pooled_variance). This is effectively equivalent to assuming that the within-species variances are relatively homogen

[R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie)

Hi all, I’m using OUwie to fit multi-optima OU models and I have a question about incorporating measurement error into my analyses. I’m running my models with known measurement error (mserr=‘known’) and using the standard error (std.error()) as an estimate of it, as recommended by Ives et al (200