bomeara / missecomparison

Compare misse to other methods

missecomparison

Codes and data linked to the paper:

A flexible method for estimating tip diversification rates across a range of speciation and extinction scenarios

Thais Vasconcelos, Brian C. O’Meara, Jeremy M. Beaulieu

Empirical_example-Eucalypts

Tip-rate comparisons between plant height and net-turnover rates in Eucalypteae (Myrtaceae).

Data from:

Thornhill, A. H., Crisp, M. D., Külheim, C., Lam, K. E., Nelson, L. A., Yeates, D. K., & Miller, J. T. (2019). A dated molecular perspective of eucalypt taxonomy, evolution and diversification. Australian Systematic Botany, 32(1), 29-48. 10.1071/SB18015

EUCLID Eucalypts of Australia Edition 4 (2015, internet based, hosted by the Identic Pty Ltd, Brisbane.) link

Example_code-Lupinus_quick_run

A quick example of how MiSSE works using the genus Lupinus (Fabaceae).

Data from:

Drummond, C. S., Eastwood, R. J., Miotto, S. T., & Hughes, C. E. (2012). Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling. Systematic biology, 61(3), 443-460. 10.1093/sysbio/syr126

Simulation_study

Codes to compare MiSSE to other diversification methods based on trees from Title and Rabosky (2019) and Maliet et al. (2019).

Title, P. O., & Rabosky, D. L. (2019). Tip rates, phylogenies and diversification: what are we estimating, and how good are the estimates?. Methods in Ecology and Evolution, 10(6), 821-834. 10.1111/2041-210X.13153

Maliet, O., Hartig, F., & Morlon, H. (2019). A model with many small shifts for estimating species-specific diversification rates. Nature ecology & evolution, 3(7), 1086-1092. 10.1038/s41559-019-0908-0

missecomparison's Issues

Loop pascal rabosky trees

Downloaded the trees, removed the bamm output. Now just need to have script to pass trees into misse, calculate tip rates, then make table. Later, merge with table missecomparison/PascalRaboskyInfo/tipRates_dryad/dataFiles/trueTipRates.csv and missecomparison/PascalRaboskyInfo/tipRates_dryad/dataFiles/estimatedTipRates.csv