├── .gitignore ├── COMADRE-UserGuide └── README.md ├── COMPADRE-UserGuide └── README.md ├── Functions └── README.md ├── GeneratePhylogeny ├── BackboneTrees │ └── PhytoPhylo.tre ├── Code │ ├── GenerateCompadrePhylogeny.R │ └── S.PhyloMaker.R ├── Data │ ├── COMPADRE_Species_TPL_append.csv │ ├── example.splist.csv │ └── nodes.csv ├── GeneratedTrees │ ├── 20180728_compadrePhylogeny.RData │ ├── 20180728_compadrePhylogeny.nex │ └── 20180728_compadrePhylogeny.tre └── README.md ├── LICENSE ├── Mage ├── .Rbuildignore └── README.md ├── OldDBVersions ├── COMADRE_v.1.0.0.RData ├── COMADRE_v.2.0.0.RData ├── COMADRE_v.2.0.1.RData ├── COMADRE_v.3.0.0.RData ├── COMADRE_v.3.0.1.RData ├── COMPADRE_v.3.0.0.RData ├── COMPADRE_v.3.2.0.RData ├── COMPADRE_v.3.2.1.RData ├── COMPADRE_v.4.0.0.RData ├── COMPADRE_v.4.0.1.RData ├── COMPADRE_v.5.0.0.RData ├── COMPADRE_v.5.0.1.RData └── readme.md ├── Phylogeny ├── COMPADRE-COMADRE_Phylo_June_16_2019.tre ├── COMPADRE_Phylogeny_July_20_2014.nex ├── COMPADRE_Phylogeny_July_20_2014.tre └── README.md ├── Protocol └── README.md ├── README.md ├── Scripts ├── AgeFromStage.R ├── COMADRE_Author_Citations.R ├── COMADRE_Check_Taxonomy.R ├── COMPADRE_Author_Citations.R ├── COMPADRE_Update_Taxonomy_TPL.R ├── ConvergenceToQSD.Rmd ├── Plot_LifeCycle_Diagram.R ├── README.md ├── subsettingCOMADRE.R ├── subsettingCOMPADRE.R └── ternaryPlots.R ├── Workshop ├── AgeFromStage.Rmd ├── AgeFromStage.pdf ├── CheckingTaxonomy.Rmd ├── CheckingTaxonomy.pdf ├── GeographicDistribution.Rmd ├── GeographicDistribution.html ├── GeographicDistribution.pdf ├── Obtaining an MPM.Rmd ├── ObtainingReferences.Rmd ├── ObtainingReferences.pdf ├── Obtaining_an_MPM.html ├── Obtaining_an_MPM.pdf ├── PlotALifeCycleDiagram.Rmd ├── PlotALifeCycleDiagram.html ├── PlotALifeCycleDiagram.pdf ├── Presentations │ ├── COMADRE-Workshop-EvoDemoS-Structure.pdf │ ├── COMPADRE-Workshop-BES2015.pdf │ └── Salguero-Gomez EvoDemoS 2015 reduced.pdf ├── README.md ├── SimpleOutputs.Rmd ├── SimpleOutputs.html ├── SimpleOutputs.pdf ├── TernaryPlots.Rmd ├── TernaryPlots.pdf ├── ThePapers │ ├── COMADRE - Salguero-Gomez_et_al-2016-Journal_of_Animal_Ecology.pdf │ └── COMPADRE - Salguero-Gomez_et_al-2015-Journal_of_Ecology.pdf ├── images │ ├── Logo_COMADRE_Vertical_Color.png │ └── Logo_COMPADRE_Vertical_Color.png ├── phyloexample.Rmd ├── phyloexample.html └── phyloexample.pdf └── oldWorkshopMaterials ├── BES2015 ├── COMPADRE-Workshop-BES2015.pdf ├── CheckingTaxonomy.Rmd ├── CheckingTaxonomy.pdf ├── GeographicDistribution.Rmd ├── GeographicDistribution.pdf ├── Obtaining an MPM.Rmd ├── ObtainingReferences.Rmd ├── ObtainingReferences.pdf ├── Obtaining_an_MPM.pdf ├── PlotALifeCycleDiagram.Rmd ├── PlotALifeCycleDiagram.pdf ├── README.md ├── SimpleOutputs.Rmd ├── SimpleOutputs.pdf ├── TernaryPlots.Rmd ├── TernaryPlots.pdf ├── ThePapers │ ├── COMADRE-BIORXIV-2015-027821v1-Salguero Gomez.pdf │ └── COMPADRE-jec12334.pdf └── images │ ├── Logo_COMADRE_Vertical_Color.png │ └── Logo_COMPADRE_Vertical_Color.png ├── EvoDemoS2015 ├── AgeFromStage.Rmd ├── AgeFromStage.pdf ├── COMADRE-Workshop-EvoDemoS-Structure.pdf ├── CheckingTaxonomy.Rmd ├── CheckingTaxonomy.pdf ├── GeographicDistribution.Rmd ├── GeographicDistribution.pdf ├── ObtainingReferences.Rmd ├── ObtainingReferences.pdf ├── PlotALifeCycleDiagram.Rmd ├── PlotALifeCycleDiagram.pdf ├── README.md ├── Salguero-Gomez EvoDemoS 2015 reduced.pdf ├── SimpleOutputs.Rmd ├── SimpleOutputs.pdf ├── TernaryPlots.Rmd ├── TernaryPlots.pdf └── images │ ├── Logo_COMADRE_Vertical_Color.png │ └── Logo_COMPADRE_Vertical_Color.png └── UQ2015 ├── AgeFromStage.Rmd ├── AgeFromStage.pdf ├── COMADRE-Workshop-EvoDemoS-Structure.pdf ├── CheckingTaxonomy.Rmd ├── CheckingTaxonomy.pdf ├── ChoosingMatrices.Rmd ├── ChoosingMatrices.pdf ├── GeographicDistribution.Rmd ├── GeographicDistribution.pdf ├── ObtainingReferences.Rmd ├── ObtainingReferences.pdf ├── PlotALifeCycleDiagram.Rmd ├── PlotALifeCycleDiagram.pdf ├── README.md ├── 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