├── 1 - Klaus Schliep - Ape and Phangorn ├── ape_phangorn.Rmd ├── ape_phangorn.html ├── bibliography.bib ├── data │ └── seqfile.txt └── slides_workshop_Schliep_2019.pdf ├── 2 - Sam Price - Simulation ├── DiscreteModelfitting_ARDsimresults.txt ├── DiscreteModelfitting_ERsimresults.txt ├── ParrotfishSLlambdasim.csv ├── Price_Simulations.pdf ├── R packages needed ├── marsupialdiettree.nex ├── marsupialmass_diet.txt ├── parrotfishecology.txt ├── parrotfishesRawMorphology.txt ├── parrotfishtree.nex ├── simulationexercise_SSBworkshop.R └── sizedietoumboot1000.txt ├── 3 - April Wright - Teaching and resesarch with RevBayes ├── RB_MCMC_Discrete_Morph.Rmd ├── ResearchAndTeachingWithRevBayes.Rpres ├── data │ └── ants.nex ├── img │ ├── Fig5.png │ ├── Gamma.png │ ├── Mk_model.png │ ├── RB_tutorial.png │ ├── lnl.png │ └── tikz │ │ ├── Mk_model.pdf │ │ ├── Mk_model.png │ │ ├── Mk_model.tex │ │ ├── Normal.tex │ │ ├── Normal.tex.pdf │ │ ├── Normal.tex.png │ │ ├── constant_nodes.png │ │ ├── deterministic_node.tex.png │ │ ├── fbd_gm-eps-converted-to.png │ │ ├── graphical_model_legend.png │ │ ├── gtrg_graphical_model.pdf │ │ ├── gtrg_graphical_model.png │ │ ├── observed_node.tex.png │ │ └── stoch_nodes.png └── refs.bib ├── 4 - Luke Harmon - Treeplyr ├── Data │ ├── .Rhistory │ ├── sampleData.csv │ └── sampleTree.phy ├── treeplyr_harmon.Rmd ├── treeplyr_harmon.html └── workingRCode.R ├── 5 - Graeme Lloyd - Plotting trees against geologic time ├── Cullen data │ ├── Cullen_etal_2013a.nex │ ├── Cullen_etal_2013a.tre │ └── Cullenages.txt ├── Slides.pdf └── code.r ├── 6 - Tara Pelletier - Posterior Predictive Simulation ├── P2C2M.SNAPP_1.0.0.tar.gz ├── P2C2M_SNAPP_tutorial.Rmd ├── P2C2M_SNAPP_tutorial.html ├── PPS_Evolution2019.pdf ├── R packages to install ├── cluster_example_scripts │ ├── README.txt │ ├── masterscript │ └── pbs_template ├── example_mode1 │ ├── samples.txt │ ├── snap.log │ ├── snap.trees │ └── snapp.xml └── example_mode2 │ ├── intermediate.txt │ ├── samples.txt │ ├── simcoal_input_1.par │ ├── simcoal_input_1 │ ├── simcoal_input_1_1.arb │ ├── simcoal_input_1_1.simparam │ └── simcoal_input_1_1_1.arp │ ├── simcoal_input_10.par │ ├── simcoal_input_10 │ ├── simcoal_input_10_1.arb │ ├── simcoal_input_10_1.simparam │ └── simcoal_input_10_1_1.arp │ ├── simcoal_input_10_1_1.xml │ ├── simcoal_input_10_1_1_snap.log │ ├── simcoal_input_10_1_1_snap.trees │ ├── simcoal_input_1_1_1.xml │ ├── simcoal_input_1_1_1_snap.log │ ├── simcoal_input_1_1_1_snap.trees │ ├── simcoal_input_2.par │ ├── simcoal_input_2 │ ├── simcoal_input_2_1.arb │ ├── simcoal_input_2_1.simparam │ └── simcoal_input_2_1_1.arp │ ├── simcoal_input_2_1_1.xml │ ├── simcoal_input_2_1_1_snap.log │ ├── simcoal_input_2_1_1_snap.trees │ ├── simcoal_input_3.par │ ├── simcoal_input_3 │ ├── simcoal_input_3_1.arb │ ├── simcoal_input_3_1.simparam │ └── simcoal_input_3_1_1.arp │ ├── simcoal_input_3_1_1.xml │ ├── simcoal_input_3_1_1_snap.log │ ├── simcoal_input_3_1_1_snap.trees │ ├── simcoal_input_4.par │ ├── simcoal_input_4 │ ├── simcoal_input_4_1.arb │ ├── simcoal_input_4_1.simparam │ └── simcoal_input_4_1_1.arp │ ├── simcoal_input_4_1_1.xml │ ├── simcoal_input_4_1_1_snap.log │ ├── simcoal_input_4_1_1_snap.trees │ ├── simcoal_input_5.par │ ├── simcoal_input_5 │ ├── simcoal_input_5_1.arb │ ├── simcoal_input_5_1.simparam │ └── simcoal_input_5_1_1.arp │ ├── simcoal_input_5_1_1.xml │ ├── simcoal_input_5_1_1_snap.log │ ├── simcoal_input_5_1_1_snap.trees │ ├── simcoal_input_6.par │ ├── simcoal_input_6 │ ├── simcoal_input_6_1.arb │ ├── simcoal_input_6_1.simparam │ └── simcoal_input_6_1_1.arp │ ├── simcoal_input_6_1_1.xml │ ├── simcoal_input_6_1_1_snap.log │ ├── simcoal_input_6_1_1_snap.trees │ ├── simcoal_input_7.par │ ├── simcoal_input_7 │ ├── simcoal_input_7_1.arb │ ├── simcoal_input_7_1.simparam │ └── simcoal_input_7_1_1.arp │ ├── simcoal_input_7_1_1.xml │ ├── simcoal_input_7_1_1_snap.log │ ├── simcoal_input_7_1_1_snap.trees │ ├── simcoal_input_8.par │ ├── simcoal_input_8 │ ├── simcoal_input_8_1.arb │ ├── simcoal_input_8_1.simparam │ └── simcoal_input_8_1_1.arp │ ├── simcoal_input_8_1_1.xml │ ├── simcoal_input_8_1_1_snap.log │ ├── simcoal_input_8_1_1_snap.trees │ ├── simcoal_input_9.par │ ├── simcoal_input_9 │ ├── simcoal_input_9_1.arb │ ├── simcoal_input_9_1.simparam │ └── simcoal_input_9_1_1.arp │ ├── simcoal_input_9_1_1.xml │ ├── simcoal_input_9_1_1_snap.log │ ├── simcoal_input_9_1_1_snap.trees │ ├── snap.log │ ├── snap.trees │ └── snapp.xml ├── 7 - Dan Warren - MCMC convergence diagnostics using RWTY ├── .DS_Store ├── Intro to Convergence Diagnostics with RWTY.pptx ├── fungus trees │ ├── fungus1.p │ ├── fungus1.t │ ├── fungus2.p │ ├── fungus2.t │ ├── fungus3.p │ ├── fungus3.t │ ├── fungus4.p │ └── fungus4.t ├── loading-trees.Rmd ├── loading-trees.html ├── plot-comparisons.html └── rwty.html ├── 8 - Liam Revell - Discrete characters ├── ANOLIS.PHY ├── Discrete-character-data.Rmd ├── Discrete-character-data.html ├── Discrete-character-data.md ├── Enchelycore_schismatorhynchus.png ├── README.md ├── VERT.CSV ├── eel-picture.png ├── elopomorph.csv ├── elopomorph.tre ├── figure │ ├── unnamed-chunk-11-1.png │ ├── unnamed-chunk-12-1.png │ ├── unnamed-chunk-15-1.png │ ├── unnamed-chunk-16-1.png │ ├── unnamed-chunk-18-1.png │ ├── unnamed-chunk-19-1.png │ ├── unnamed-chunk-2-1.png │ ├── unnamed-chunk-20-1.png │ ├── unnamed-chunk-23-1.png │ ├── unnamed-chunk-3-1.png │ ├── unnamed-chunk-4-1.png │ ├── unnamed-chunk-6-1.png │ └── unnamed-chunk-7-1.png ├── other-code.R ├── polymorphic-data.csv ├── polymorphic-tree.phy ├── simulated-data.csv └── simulated-tree.tre ├── SSB Workshop.Rmd ├── SSB_Workshop.html ├── Setup.Rmd └── Setup.html /1 - 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