├── .Rbuildignore ├── .directory ├── .gitignore ├── .travis.yml ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── DESCRIPTION ├── ISSUE_TEMPLATE.md ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── .Rapp.history ├── clade_Discrete.R ├── clade_continuous.R ├── clade_phyglm.R ├── clade_phylm.R ├── clade_physig.R ├── document-data.R ├── influ_Discrete.R ├── influ_continuous.R ├── influ_phyglm.R ├── influ_phylm.R ├── influ_physig.R ├── intra_clade_phyglm.R ├── intra_clade_phylm.R ├── intra_influ_phyglm.R ├── intra_influ_phylm.R ├── intra_phyglm.R ├── intra_phylm.R ├── intra_physig.R ├── intra_samp_phyglm.R ├── intra_samp_phylm.R ├── match_dataphy.R ├── miss.phylo.d.R ├── print_methods.R ├── samp_Discrete.R ├── samp_continuous.R ├── samp_phyglm.R ├── samp_phylm.R ├── samp_physig.R ├── sensiPhy.R ├── sensi_plot.R ├── sensi_plot.clade.physig.R ├── sensi_plot.influ.physig.R ├── sensi_plot.samp.physig.R ├── sensi_plot.sensiClade.R ├── sensi_plot.sensiINTER_Clade.R ├── sensi_plot.sensiINTER_Influ.R ├── sensi_plot.sensiINTER_Samp.R ├── sensi_plot.sensiInflu.R ├── sensi_plot.sensiIntra.sensiTree.R ├── sensi_plot.sensiSamp.R ├── sensi_plot.tree.bd.R ├── sensi_plot.tree.physig.R ├── summary_methods.R ├── tree_Discrete.R ├── tree_bd.R ├── tree_clade_phyglm.R ├── tree_clade_phylm.R ├── tree_continuous.R ├── tree_influ_phyglm.R ├── tree_influ_phylm.R ├── tree_intra_phyglm.R ├── tree_intra_phylm.R ├── tree_phyglm.R ├── tree_phylm.R ├── tree_physig.R ├── tree_samp_phyglm.R ├── tree_samp_phylm.R ├── utils_internal.R └── utils_plot.R ├── README.md ├── _config.yml ├── _pkgdown.yml ├── cran-comments.md ├── data-raw ├── alienMammals.tre ├── alienMammals.txt ├── gather_alienMammals.R ├── gather_panTHERIA.R ├── pantheria.csv └── pantheria.tre ├── data ├── alien.data.rda ├── alien.phy.rda ├── alien.rda ├── primates.data.rda ├── primates.phy.rda └── primates.rda ├── docs ├── 404.html ├── CODE_OF_CONDUCT.html ├── CONTRIBUTING.html ├── ISSUE_TEMPLATE.html ├── LICENSE-text.html ├── articles │ ├── index.html │ ├── sensiPhy_vignette.html │ └── sensiPhy_workflow_functions.png ├── authors.html ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml └── reference │ ├── alien.data.html │ ├── alien.html │ ├── alien.phy.html │ ├── clade_continuous.html │ ├── clade_discrete.html │ ├── clade_phyglm.html │ ├── clade_phylm.html │ ├── clade_physig-1.png │ ├── clade_physig-2.png │ ├── clade_physig.html │ ├── index.html │ ├── influ_continuous.html │ ├── influ_discrete.html │ ├── influ_phyglm-1.png │ ├── influ_phyglm.html │ ├── influ_phylm-1.png │ ├── influ_phylm-2.png │ ├── influ_phylm.html │ ├── influ_physig.html │ ├── intra_clade_phyglm-1.png │ ├── intra_clade_phyglm.html │ ├── intra_clade_phylm.html │ ├── intra_influ_phyglm-1.png │ ├── intra_influ_phyglm.html │ ├── intra_influ_phylm-1.png │ ├── intra_influ_phylm.html │ ├── intra_phyglm-1.png │ ├── intra_phyglm.html │ ├── intra_phylm-1.png │ ├── intra_phylm.html │ ├── intra_physig.html │ ├── intra_samp_phyglm-1.png │ ├── intra_samp_phyglm.html │ ├── intra_samp_phylm.html │ ├── match_dataphy.html │ ├── miss.phylo.d-1.png │ ├── miss.phylo.d-2.png │ ├── miss.phylo.d.html │ ├── primates.data.html │ ├── primates.html │ ├── primates.phy.html │ ├── samp_continuous.html │ ├── samp_discrete.html │ ├── samp_phyglm.html │ ├── samp_phylm.html │ ├── samp_physig-1.png │ ├── samp_physig-2.png │ ├── samp_physig-3.png │ ├── samp_physig.html │ ├── sensiPhy.html │ ├── sensi_plot.clade.physig.html │ ├── sensi_plot.html │ ├── sensi_plot.influ.physig.html │ ├── sensi_plot.intra.physig.html │ ├── sensi_plot.samp.physig.html │ ├── sensi_plot.sensiClade.TraitEvol.html │ ├── sensi_plot.sensiClade.html │ ├── sensi_plot.sensiInflu.TraitEvol.html │ ├── sensi_plot.sensiInflu.html │ ├── sensi_plot.sensiIntra.html │ ├── sensi_plot.sensiIntra_Clade.html │ ├── sensi_plot.sensiIntra_Influ.html │ ├── sensi_plot.sensiIntra_Samp.html │ ├── sensi_plot.sensiSamp.TraitEvol.html │ ├── sensi_plot.sensiSamp.html │ ├── sensi_plot.sensiTree.TraitEvol.html │ ├── sensi_plot.sensiTree.html │ ├── sensi_plot.sensiTree_Clade.html │ ├── sensi_plot.sensiTree_Influ.html │ ├── sensi_plot.sensiTree_Intra.html │ ├── sensi_plot.sensiTree_Samp.html │ ├── sensi_plot.tree.bd.html │ ├── sensi_plot.tree.physig.html │ ├── tree_bd-1.png │ ├── tree_bd-2.png │ ├── tree_bd.html │ ├── tree_clade_phyglm-1.png │ ├── tree_clade_phyglm.html │ ├── tree_clade_phylm.html │ ├── tree_continuous.html │ ├── tree_discrete.html │ ├── tree_influ_phyglm.html │ ├── tree_influ_phylm.html │ ├── tree_intra_phyglm-1.png │ ├── tree_intra_phyglm.html │ ├── tree_intra_phylm-1.png │ ├── tree_intra_phylm.html │ ├── tree_phyglm-1.png │ ├── tree_phyglm.html │ ├── tree_phylm-1.png │ ├── tree_phylm-2.png │ ├── tree_phylm.html │ ├── tree_physig-1.png │ ├── tree_physig-2.png │ ├── tree_physig-3.png │ ├── tree_physig.html │ ├── tree_samp_phyglm.html │ ├── tree_samp_phylm-1.png │ └── tree_samp_phylm.html ├── inst └── CITATION ├── man ├── alien.Rd ├── alien.data.Rd ├── alien.phy.Rd ├── clade_continuous.Rd ├── clade_discrete.Rd ├── clade_phyglm.Rd ├── clade_phylm.Rd ├── clade_physig.Rd ├── influ_continuous.Rd ├── influ_discrete.Rd ├── influ_phyglm.Rd ├── influ_phylm.Rd ├── influ_physig.Rd ├── intra_clade_phyglm.Rd ├── intra_clade_phylm.Rd ├── intra_influ_phyglm.Rd ├── intra_influ_phylm.Rd ├── intra_phyglm.Rd ├── intra_phylm.Rd ├── intra_physig.Rd ├── intra_samp_phyglm.Rd ├── intra_samp_phylm.Rd ├── match_dataphy.Rd ├── miss.phylo.d.Rd ├── primates.Rd ├── primates.data.Rd ├── primates.phy.Rd ├── samp_continuous.Rd ├── samp_discrete.Rd ├── samp_phyglm.Rd ├── samp_phylm.Rd ├── samp_physig.Rd ├── sensiPhy.Rd ├── sensi_plot.Rd ├── sensi_plot.clade.physig.Rd ├── sensi_plot.influ.physig.Rd ├── sensi_plot.intra.physig.Rd ├── sensi_plot.samp.physig.Rd ├── sensi_plot.sensiClade.Rd ├── sensi_plot.sensiClade.TraitEvol.Rd ├── sensi_plot.sensiInflu.Rd ├── sensi_plot.sensiInflu.TraitEvol.Rd ├── sensi_plot.sensiIntra.Rd ├── sensi_plot.sensiIntra_Clade.Rd ├── sensi_plot.sensiIntra_Influ.Rd ├── sensi_plot.sensiIntra_Samp.Rd ├── sensi_plot.sensiSamp.Rd ├── sensi_plot.sensiSamp.TraitEvol.Rd ├── sensi_plot.sensiTree.Rd ├── sensi_plot.sensiTree.TraitEvol.Rd ├── sensi_plot.sensiTree_Clade.Rd ├── sensi_plot.sensiTree_Influ.Rd ├── sensi_plot.sensiTree_Intra.Rd ├── sensi_plot.sensiTree_Samp.Rd ├── sensi_plot.tree.bd.Rd ├── sensi_plot.tree.physig.Rd ├── tree_bd.Rd ├── tree_clade_phyglm.Rd ├── tree_clade_phylm.Rd ├── tree_continuous.Rd ├── tree_discrete.Rd ├── tree_influ_phyglm.Rd ├── tree_influ_phylm.Rd ├── tree_intra_phyglm.Rd ├── tree_intra_phylm.Rd ├── tree_phyglm.Rd ├── tree_phylm.Rd ├── tree_physig.Rd ├── tree_samp_phyglm.Rd └── tree_samp_phylm.Rd └── vignettes ├── sensiPhy_vignette.Rmd └── sensiPhy_workflow_functions.png /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/paternogbc/sensiPhy/HEAD/.Rbuildignore 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