Data from: Magnuson-Ford, K., and S. Otto. 2012. Linking the investigations of character evolution and species diversification. American Naturalist. BiSSE-ness was developed and all analyses were carried out using the R program diversitree (v.0.6-1; http://www.zoology.ubc.ca/prog/diversitree/). To use BiSSE-ness, we recommend that users download the latest version of diversitree, which contains BiSSE-ness as an option (as of v.0.9-1; http://www.zoology.ubc.ca/prog/diversitree/; courtesy of R. FitzJohn). Example Analysis folder: An illustration of the method using the latest version of BiSSE-ness as incorporated into diversitree (v.0.9-1), for users who wish to perform a similar analysis. BiSSE-ness Model folder: Files containing the BiSSE-ness model code for implementation in R with diversitree. This code was used to analyse the simulated data and the primate data reported in the paper (see next folders), using diversitree v.0.6-1. The code in this folder also works with versions of diversitree up to v.0.7-2, but not with more recent versions (see "Sample Analyses folder" for running the most recent version). Simulation Analyses: All files concerning the simulation analyses can be found in the Simulations folder. The Simulation_Analyses_ReadMe.R files provides the script we used to carry out all simulations and subsequent analyses. The .RData files contain the simulated trees as well as the ML analyses output. Primate Analyses: Included in the Primates folder are both the input data (the phylogenies: primate_trees.nex, the trait information: primate_traits.csv) as well as a script outlining how the maximum likelihood and Bayesian analyses were carried out (Primate_Analyses_ReadMe.R). Output of the ML analyses using BiSSE and the BiSSE-ness models are found in Primates_1_2.csv, Primates_3.csv, and Primates_4. Two files, AICscores.R and LikelihoodRatioTests.R provide the code used to analyse the ML primate output. Output of the mcmc analyses the full, 10-parameter BiSSE-ness model are found in Primates_MCMC.csv.