Data from: Phylogenetic factor analysis

Tolkoff MR, Alfaro ME, Baele G, Lemey P, Suchard MA

Date Published: August 3, 2017

DOI: http://dx.doi.org/10.5061/dryad.6320t

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title AquilegiaDiffusion
Downloaded 7 times
Description XML which runs columbine flower examples under the latent multivariate Brownian diffusion model
Download AquilegiaDiffusion.xml (18.12 Kb)
Details View File Details
Title AquilegiaFac2
Downloaded 8 times
Description Runs the columbine flower example under the phylogenetic factor analysis model for 2 factors.
Download AquilegiaFac2.xml (19.90 Kb)
Details View File Details
Title AquilegiaDiffusionMLE
Downloaded 3 times
Description Runs the marginal likelihood estimator for the columbine flower example under the latent multivariate Brownian diffusion model.
Download AquilegiaDiffusionMLE.xml (19.05 Kb)
Details View File Details
Title AquilegiaFacMLE1
Downloaded 5 times
Description Runs the marginal likelihood estimator for the columbine flower example under the phylogenetic factor analysis model for 1 factor.
Download AquilegiaFacMLE1.xml (20.57 Kb)
Details View File Details
Title AquilegiaFacMLE2
Downloaded 3 times
Description Runs the marginal likelihood estimator for the columbine flower example under the phylogenetic factor analysis model for 2 factors.
Download AquilegiaFacMLE2.xml (21.61 Kb)
Details View File Details
Title AquilegiaFacMLE3
Downloaded 3 times
Description Runs the marginal likelihood estimator for the columbine flower example under the phylogenetic factor analysis model for 3 factors.
Download AquilegiaFacMLE3.xml (20.93 Kb)
Details View File Details
Title AquilegiaSpeedDiffusion
Downloaded 8 times
Description Runs the columbine flower example under the latent multivariate Brownian diffusion model. This file is designed to measure a speed comparison between models.
Download AquilegiaSpeedDiffusion.xml (17.95 Kb)
Details View File Details
Title AquilegiaSpeedFac2
Downloaded 5 times
Description Runs the columbine flower example under the phylogenetic factor analysis model with 2 factors. This file is designed to measure a speed comparison between models.
Download AquilegiaSpeedFac2.xml (21.14 Kb)
Details View File Details
Title PoeciliidaeFac2
Downloaded 6 times
Description Runs the poeciliidae example under the phylogenetic factor analysis model with 2 factors.
Download PoeciliidaeFac2.xml (44.26 Kb)
Details View File Details
Title PoeciliidaeFac3
Downloaded 4 times
Description Runs the poeciliidae example under the phylogenetic factor analysis model with 3 factors.
Download PoeciliidaeFac3.xml (44.39 Kb)
Details View File Details
Title PoeciliidaeFac4
Downloaded 6 times
Description Runs the poeciliidae example under the phylogenetic factor analysis model with 4 factors.
Download PoeciliidaeFac4.xml (44.61 Kb)
Details View File Details
Title PoeciliidaeFacMLE2
Downloaded 5 times
Description Runs the marginal likelihood estimate for the poeciliidae example under the phylogenetic factor analysis model with 2 factors.
Download PoeciliidaeFacMLE2.xml (45.23 Kb)
Details View File Details
Title PoeciliidaeFacMLE3
Downloaded 3 times
Description Runs the marginal likelihood estimate for the poeciliidae example under the phylogenetic factor analysis model with 3 factors.
Download PoeciliidaeFacMLE3.xml (45.45 Kb)
Details View File Details
Title PoeciliidaeFacMLE4
Downloaded 5 times
Description Runs the marginal likelihood estimate for the poeciliidae example under the phylogenetic factor analysis model with 4 factors.
Download PoeciliidaeFacMLE4.xml (45.59 Kb)
Details View File Details
Title PoeciliidaeFacMLE5
Downloaded 3 times
Description Runs the marginal likelihood estimate for the poeciliidae example under the phylogenetic factor analysis model with 5 factors.
Download PoeciliidaeFacMLE5.xml (46.30 Kb)
Details View File Details
Title PoeciliidaeDiffusionMLE
Downloaded 3 times
Description Runs the marginal likelihood estimate for the poeciliidae example under the latent multivariate Brownian diffusion model.
Download PoeciliidaeDiffusionMLE.xml (40.75 Kb)
Details View File Details
Title PoeciliidaeDiffusionSpeedTest
Downloaded 6 times
Description Runs the poeciliidae example under the latent multivariate Brownian diffusion model. This file is designed to measure a speed comparison between models.
Download PoeciliidaeDiffusionSpeedTest.xml (39.42 Kb)
Details View File Details
Title PoeciliidaeFac3SpeedTest
Downloaded 3 times
Description Runs the poeciliidae example under the phylogenetic factor analysis model for 3 factors. This file is designed to measure a speed comparison between models.
Download PoeciliidaeFac3SpeedTest.xml (45.41 Kb)
Details View File Details
Title PoeciliidaeFac4speedTest
Downloaded 3 times
Description Runs the poeciliidae example under the phylogenetic factor analysis model for 4 factors. This file is designed to measure a speed comparison between models.
Download PoeciliidaeFac4speedTest.xml (45.40 Kb)
Details View File Details
Title TriggerfishFac5
Downloaded 5 times
Description Runs the triggerfish example under the phylogenetic factor analysis model for 5 factors.
Download TriggerfishFac5.xml (149.1 Kb)
Details View File Details
Title TriggerfishDiffusionMLE
Downloaded 7 times
Description Runs the marginal likelihood estimator for the triggerfish example under the multivariate Brownian diffusion model.
Download TriggerfishDiffusionMLE.xml (142.1 Kb)
Details View File Details
Title TriggerfishFacMLE4
Downloaded 6 times
Description Runs the marginal likelihood estimator for the triggerfish example under the phylogenetic factor analysis model for 4 factors.
Download TriggerfishFacMLE4.xml (150.3 Kb)
Details View File Details
Title TriggerfishFacMLE5
Downloaded 5 times
Description Runs the marginal likelihood estimator for the triggerfish example under the phylogenetic factor analysis model for 5 factors.
Download TriggerfishFacMLE5.xml (150.9 Kb)
Details View File Details
Title TriggerfishFacMLE6
Downloaded 4 times
Description Runs the marginal likelihood estimator for the triggerfish example under the phylogenetic factor analysis model for 6 factors.
Download TriggerfishFacMLE6.xml (151.5 Kb)
Details View File Details
Title TriggerfishDiffusionSpeed
Downloaded 3 times
Description Runs the triggerfish example under the multivariate Brownian diffusion model. This file is designed to measure a speed comparison between models.
Download TriggerfishDiffusionSpeed.xml (139.0 Kb)
Details View File Details
Title TriggerfishFac5Speed
Downloaded 4 times
Description Runs the triggerfish example under the phylogenetic factor analysis model for 5 factors. This file is designed to measure a speed comparison between models.
Download TriggerfishFac5Speed.xml (150.0 Kb)
Details View File Details
Title Supplementary figures and tables
Downloaded 21 times
Description Supplementary figures and tables for the paper Phylogenetic Factor Analysis which were not included in the main text.
Download supplementary_material_revised.pdf (2.626 Mb)
Details View File Details

When using this data, please cite the original publication:

Tolkoff MR, Alfaro ME, Baele G, Lemey P, Suchard MA (2017) Phylogenetic factor analysis. Systematic Biology, online in advance of print. http://dx.doi.org/10.1093/sysbio/syx066

Additionally, please cite the Dryad data package:

Tolkoff MR, Alfaro ME, Baele G, Lemey P, Suchard MA (2017) Data from: Phylogenetic factor analysis. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.6320t
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: