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build_ages()
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Get Age data from PBDB to pair to the tips of trees |
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custom_plots()
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Create treespace ordination including extra columns. |
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custom_treespace()
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Create treespace ordination including extra columns. |
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generate_fig_s1()
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Generate the S1 table of Wright and Lloyd 2019 |
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makeBoxplot()
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Create box plots of our data |
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makeViolins()
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Create violin plots of our data |
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make_strat_congruence()
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R script to perform strat congruence tests.
This R function runs statigraphic congruence tests on both a Bayesian posterior sample and a set of most parsimonious trees. Nothing is returned, but boxplots of these figures are saved to a results directory. |
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remove_missing_tips()
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Custom functions to filter datasets by completeness of tip sampling |
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remove_unreconciled()
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Custom functions to filter datasets down to those that do not have unreconciled taxa |
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summarize_medians()
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Process MIG score for all the files used in this study. |
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summary_stat()
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Generate the S1 table of Wright and Lloyd 2019 |