Data from: How reliably can we infer diversity-dependent diversification from phylogenies?

Etienne RS, Pigot AL, Phillimore A

Date Published: April 27, 2016

DOI: http://dx.doi.org/10.5061/dryad.tg37f

 

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 Simulations under CR and DD models - part 2
Downloaded 23 times
Description Second batch of .RData files of the tree simulations under the CR and DD models.
Download biastestCRDD_sims2.zip (1.045 Gb)
Details View File Details
Title Simulations under CR and DD models - part 1
Downloaded 25 times
Description First of two batches of .RData files of the trees simulation under the CR and DD models and the R-script that generated both batches.
Download biastestCRDD_sims1.zip (984.4 Mb)
Details View File Details
Title Maximum likelihood results under CR model
Downloaded 13 times
Description RData files with maximum likelihoods and corresponding parameter estimates under the constant-rate (CR) model, and the R-script that generated them.
Download biastestCR_LL.zip (6.959 Mb)
Details View File Details
Title Maximum likelihood results under DD model - 1
Downloaded 17 times
Description RData files with maximum likelihoods and corresponding parameter estimates under the diversity-dependent model, and the R-script that generated them. The starting values of the optimization are the simulation values.
Download biastestDD_LL1.zip (7.331 Mb)
Details View File Details
Title Maximum likelihood results under DD model - 2
Downloaded 18 times
Description RData files with maximum likelihoods and corresponding parameter estimates under the diversity-dependent model, and the R-script that generated them. The starting values of the optimization are the results from the CR models fits with a large but finite carrying capacity..
Download biastestDD_LL2.zip (6.900 Mb)
Details View File Details
Title R-script to make plots from results
Downloaded 13 times
Description R-script to make plots from simulation results
Download plot_params.R (23.00 Kb)
Details View File Details
Title Bootstrap likelihood ratio test results of the Dendroica case study
Downloaded 13 times
Description RData file of the bootstrap likelihood ratio test results of the Dendroica case study.
Download DendroicaLRtestresults.RData (1.941 Mb)
Details View File Details

When using this data, please cite the original publication:

Etienne RS, Pigot AL, Phillimore A (2016) How reliably can we infer diversity-dependent diversification from phylogenies? Methods in Ecology and Evolution 7(9): 1092–1099. http://dx.doi.org/10.1111/2041-210X.12565

Additionally, please cite the Dryad data package:

Etienne RS, Pigot AL, Phillimore A (2016) Data from: How reliably can we infer diversity-dependent diversification from phylogenies? Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.tg37f
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: