DOI: 10.5061/dryad.6320t
title: Data from: Phylogenetic factor analysis

description: Phylogenetic comparative methods explore the relationships between
 quantitative traits adjusting for shared evolutionary history. This
 adjustment often occurs through a Brownian diffusion process along the
 branches of the phylogeny that generates model residuals or the traits
 themselves. For high-dimensional traits, inferring all pair-wise
 correlations within the multivariate diffusion is limiting. To circumvent
 this problem, we propose phylogenetic factor analysis (PFA) that assumes a
 small unknown number of independent evolutionary factors arise along the
 phylogeny and these factors generate clusters of dependent traits. Set in
 a Bayesian framework, PFA provides measures of uncertainty on the factor
 number and groupings, combines both continuous and discrete traits,
 integrates over missing measurements and incorporates phylogenetic
 uncertainty with the help of molecular sequences. We develop Gibbs
 samplers based on dynamic programming to estimate the PFA posterior
 distribution, over three-fold faster than for multivariate diffusion and a
 further order-of-magnitude more efficiently in the presence of latent
 traits. We further propose a novel marginal likelihood estimator for
 previously impractical models with discrete data and find that PFA also
 provides a better fit than multivariate diffusion in evolutionary
 questions in columbine flower development, placental reproduction
 transitions and triggerfish fin morphometry.
description: AquilegiaDiffusionXML which runs columbine flower examples under the latent multivariate Brownian diffusion modelAquilegiaFac2Runs the columbine flower example under the phylogenetic factor analysis model for 2 factors.AquilegiaDiffusionMLERuns the marginal likelihood estimator for the columbine flower example under the latent multivariate Brownian diffusion model.AquilegiaFacMLE1Runs the marginal likelihood estimator for the columbine flower example under the phylogenetic factor analysis model for 1 factor.AquilegiaFacMLE2Runs the marginal likelihood estimator for the columbine flower example under the phylogenetic factor analysis model for 2 factors.AquilegiaFacMLE3Runs the marginal likelihood estimator for the columbine flower example under the phylogenetic factor analysis model for 3 factors.AquilegiaSpeedDiffusionRuns the columbine flower example under the latent multivariate Brownian diffusion model. This file is designed to measure a speed comparison between models.AquilegiaSpeedFac2Runs the columbine flower example under the phylogenetic factor analysis model with 2 factors. This file is designed to measure a speed comparison between models.PoeciliidaeFac2Runs the poeciliidae example under the phylogenetic factor analysis model with 2 factors.PoeciliidaeFac3Runs the poeciliidae example under the phylogenetic factor analysis model with 3 factors.PoeciliidaeFac4Runs the poeciliidae example under the phylogenetic factor analysis model with 4 factors.PoeciliidaeFacMLE2Runs the marginal likelihood estimate for the poeciliidae example under the phylogenetic factor analysis model with 2 factors.PoeciliidaeFacMLE3Runs the marginal likelihood estimate for the poeciliidae example under the phylogenetic factor analysis model with 3 factors.PoeciliidaeFacMLE4Runs the marginal likelihood estimate for the poeciliidae example under the phylogenetic factor analysis model with 4 factors.PoeciliidaeFacMLE5Runs the marginal likelihood estimate for the poeciliidae example under the phylogenetic factor analysis model with 5 factors.PoeciliidaeDiffusionMLERuns the marginal likelihood estimate for the poeciliidae example under the latent multivariate Brownian diffusion model.PoeciliidaeDiffusionSpeedTestRuns the poeciliidae example under the latent multivariate Brownian diffusion model. This file is designed to measure a speed comparison between models.PoeciliidaeFac3SpeedTestRuns the poeciliidae example under the phylogenetic factor analysis model for 3 factors. This file is designed to measure a speed comparison between models.PoeciliidaeFac4speedTestRuns the poeciliidae example under the phylogenetic factor analysis model for 4 factors. This file is designed to measure a speed comparison between models.TriggerfishFac5Runs the triggerfish example under the phylogenetic factor analysis model for 5 factors.TriggerfishDiffusionMLERuns the marginal likelihood estimator for the triggerfish example under the multivariate Brownian diffusion model.TriggerfishFacMLE4Runs the marginal likelihood estimator for the triggerfish example under the phylogenetic factor analysis model for 4 factors.TriggerfishFacMLE5Runs the marginal likelihood estimator for the triggerfish example under the phylogenetic factor analysis model for 5 factors.TriggerfishFacMLE6Runs the marginal likelihood estimator for the triggerfish example under the phylogenetic factor analysis model for 6 factors.TriggerfishDiffusionSpeedRuns the triggerfish example under the multivariate Brownian diffusion model. This file is designed to measure a speed comparison between models.TriggerfishFac5SpeedRuns the triggerfish example under the phylogenetic factor analysis model for 5 factors. This file is designed to measure a speed comparison between models.Supplementary figures and tablesSupplementary figures and tables for the paper Phylogenetic Factor Analysis which were not included in the main text.supplementary_material_revised.pdf