For a while, I have been working on the R-package sensiPhy, together with the amazing Gustavo Paterno and Caterina Penone. This package is now available for download through CRAN.
SensiPhy allows users to easily and quickly check perform sensitivity analyses when using phylogenetic comparative methods, in order to test the robustness of their results to uncertainty in the underlying data, phylogeny or species sampling. It uses simulation and rarefaction approaches and implements accessible summary statistics and visual outputs for various forms of sensitivity analysis.
Currently, the package implements functions to analyse sensitivity to uncertainty in phylogenetic regressions, but we aim to develop sensiPhy into a general platform for sensitivity analysis of phylogenetic comparative methods. We will submit a manuscript describing sensiPhy in more detail soon. In the mean time, try our package our by downloading from CRAN, or Github and let me know what you think! You can also see the slides of a presentation I recently gave about the package here.
If you are interested in contributing to a future expansion of sensiPhy, for instance to include more types of comparative methods or types of uncertainty, we would be very interested to hear! Fork the package from Github to contribute, or send me an email.