Data from 'The impact of fossil stratigraphic ranges on tip-calibration, and the accuracy and precision of divergence time estimates'
datasetposted on 12.11.2019, 10:00 by Hans P. Püschel, Joseph E. O'Reilly, Davide Pisani, Philip C. J. Donoghue
This data package is composed of three components: 1. Appendices: appendices 1-5 which are supplementary figures and tables 2. R scripts: R scripts 1-4 used for our different simulation strategies: "1_Data_simulation_tree1_stem__Mk_MaxFoss_v2" This R script allows you to generate the 100 replicates simulation Nexus files for tree 1 (fossils in the stem group) using the parameters described in the article. "2_Data_simulation_tree2_crown_Mk_MaxFoss_v2" This R script allows you to generate the 100 replicates simulation Nexus files for tree 2 (fossils in the crown group) using the parameters described in the article. "3_Extract_ages_simulation_results" This R script allows to extract from the .p and .t files of MrBayes all the ages of the nodes from the posterior of 100 replicates in the tree for each calibration approach. It results in 5 .csv files. It can be used for both trees (1 stem and 2 crown) "4_Extract_ages_empirical_Ursidae" This R script allows to extract all the node ages from the the .p and .t files of MrBayes 3. Bear Molecular Clock analyses: composed of five folders with each calibration approach called "Maximum", "Minimum", "Minimum-maximum", "Min-max_95CI_max" and "Min-max_95CI_min". Inside these folders you have the nexus files necessary to run the empirical analyses in MrBayes and the output files after running the analyses.
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