{ "_id": "6a1ed9d0b401979e7340f3ef", "Package": "deepSTRAPP", "Title": "Test for Differences in Diversification Rates over Time", "Version": "1.0.0", "Authors@R": "c(\nperson(\"Maël\", \"Doré\", , email = \"mael.dore@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-3242-9242\")),\nperson(\"Dan\", \"Rabosky\", role = \"ctb\"),\nperson(\"Mike\", \"Grundler\", role = \"ctb\"),\nperson(\"Huateng\", \"Huang\", role = \"ctb\"),\nperson(\"Pascal\", \"Title\", role = \"ctb\"),\nperson(\"Liam\", \"Revell\", role = \"ctb\"),\nperson(\"Nicholas J.\", \"Matzke\", role = \"ctb\"))", "Description": "Employ time-calibrated phylogenies and trait/range data to\ntest for differences in diversification rates over evolutionary\ntime. Extend the STRAPP test from\nBAMMtools::traitDependentBAMM() to any time step along\nphylogenies. See inst/COPYRIGHTS for details on third-party\ncode.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "URL": "https://github.com/MaelDore/deepSTRAPP,\nhttps://maeldore.github.io/deepSTRAPP/", "BugReports": "https://github.com/MaelDore/deepSTRAPP/issues", "LazyData": "true", "LazyDataCompression": "xz", "Additional_repositories": "https://maeldore.github.io/drat", "VignetteBuilder": "knitr", "Repository": "https://maeldore.r-universe.dev", "Date/Publication": "2026-01-13 16:19:41 UTC", "RemoteUrl": "https://github.com/maeldore/deepstrapp", "RemoteRef": "HEAD", "RemoteSha": "6f897d53fbce1e3acfae80307f2a05f0bcf3a0b2", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-20 09:09:28 UTC", "User": "root" }, "Author": "Maël Doré [aut, cre, cph] (ORCID:\n),\nDan Rabosky [ctb],\nMike Grundler [ctb],\nHuateng Huang [ctb],\nPascal Title [ctb],\nLiam Revell [ctb],\nNicholas J. Matzke [ctb]", "Maintainer": "Maël Doré ", "MD5sum": "a328c7ab64c790a9a5b25b32494f4a9d", "_user": "maeldore", "_type": "src", "_file": "deepSTRAPP_1.0.0.tar.gz", "_fileid": "d2213e21e6aa320d0873e27ed1d06402d2c2f9f23b807c68e8d2cb002824c08c", "_filesize": 12908740, "_sha256": "d2213e21e6aa320d0873e27ed1d06402d2c2f9f23b807c68e8d2cb002824c08c", "_created": "2026-05-20T09:09:28.000Z", "_published": "2026-06-02T13:25:36.934Z", "_distro": "noble", "_jobs": [ { "job": 79080798451, "time": 280, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7105952722" }, { "job": 79080798574, "time": 297, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7105959381" }, { "job": 79080798664, "time": 293, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7105957833" }, { "job": 79080797993, "time": 283, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7105954530" }, { "job": 79080798578, "time": 187, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7105912034" }, { "job": 79080798668, "time": 423, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7106000582" }, { "job": 79080798615, "time": 251, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7105931354" }, { "job": 79080798049, "time": 350, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7105971129" }, { "job": 79080798029, "time": 331, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7105847038" }, { "job": 79080796883, "time": 189, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7358940551" }, { "job": 79080797565, "time": 1101, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7106259774" }, { "job": 79080798151, "time": 1044, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7106239646" }, { "job": 79080798110, "time": 1123, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7106268064" } ], "_buildurl": "https://github.com/r-universe/maeldore/actions/runs/26152613455", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/maeldore/deepstrapp", "_commit": { "id": "6f897d53fbce1e3acfae80307f2a05f0bcf3a0b2", "author": "Maël DORÉ ", "committer": "Maël DORÉ ", "message": ":black_nib: Update comments to CRAN to answer enquiries\n", "time": 1768321181 }, "_maintainer": { "name": "Maël Doré", "email": "mael.dore@gmail.com", "login": "maeldore", "description": "I am a JSPS Fellow at Okinawa Institute of Science & Technologies. I am working on the Macroecology, Systematics, and Macroevolution of butterflies and ants.", "uuid": 60143458, "orcid": "0000-0003-3242-9242" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "ape", "version": ">= 5.8.0", "role": "Imports" }, { "package": "BAMMtools", "version": ">= 2.1.12", "role": "Imports" }, { "package": "cladoRcpp", "version": ">= 0.15.1", "role": "Imports" }, { "package": "coda", "version": ">= 0.19-4.1", "role": "Imports" }, { "package": "cowplot", "version": ">= 1.1.3", "role": "Imports" }, { "package": "dplyr", "version": ">= 1.1.4", "role": "Imports" }, { "package": "dunn.test", "version": ">= 1.3.6", "role": "Imports" }, { "package": "geiger", "version": ">= 2.0.11", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.5.0", "role": "Imports" }, { "package": "methods", "version": ">= 4.4.2", "role": "Imports" }, { "package": "phytools", "version": ">= 2.0.0", "role": "Imports" }, { "package": "plyr", "version": ">= 1.8.9", "role": "Imports" }, { "package": "purrr", "version": ">= 1.0.2", "role": "Imports" }, { "package": "qpdf", "version": ">= 1.4.1", "role": "Imports" }, { "package": "RColorBrewer", "version": ">= 1.1-3", "role": "Imports" }, { "package": "Rcpp", "version": ">= 1.0.14", "role": "Imports" }, { "package": "scales", "version": ">= 1.3.0", "role": "Imports" }, { "package": "stringr", "version": ">= 1.5.1", "role": "Imports" }, { "package": "tidyr", "version": ">= 1.3.1", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "maps", "version": ">= 3.4.2", "role": "Suggests" }, { "package": "parallel", "version": ">= 4.4.2", "role": "Suggests" }, { "package": "BioGeoBEARS", "version": ">= 1.1.3", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "maeldore", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-26", "n": 4 }, { "week": "2025-27", "n": 7 }, { "week": "2025-28", "n": 4 }, { "week": "2025-30", "n": 3 }, { "week": "2025-31", "n": 1 }, { "week": "2025-32", "n": 8 }, { "week": "2025-33", "n": 26 }, { "week": "2025-36", "n": 13 }, { "week": "2025-38", "n": 22 }, { "week": "2025-39", "n": 23 }, { "week": "2025-40", "n": 4 }, { "week": "2025-41", "n": 5 }, { "week": "2025-42", "n": 27 }, { "week": "2025-43", "n": 4 }, { "week": "2025-44", "n": 6 }, { "week": "2025-48", "n": 18 }, { "week": "2025-49", "n": 14 }, { "week": "2025-51", "n": 1 }, { "week": "2025-52", "n": 8 }, { "week": "2026-01", "n": 9 }, { "week": "2026-03", "n": 23 } ], "_tags": [ { "name": "v1.0.0", "date": "2026-01-13" } ], "_stars": 1, "_contributors": [ { "user": "maeldore", "count": 276, "uuid": 60143458 }, { "user": "bblaimer", "count": 14, "uuid": 233238098 } ], "_userbio": { "uuid": 60143458, "type": "user", "name": "Maël DORÉ", "description": "I am a JSPS Fellow at Okinawa Institute of Science & Technologies. I am working on the Macroecology, Systematics, and Macroevolution of butterflies and ants." }, "_downloads": { "count": 204, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/deepSTRAPP" }, "_devurl": "https://github.com/maeldore/deepstrapp", "_pkgdown": "https://maeldore.github.io/deepSTRAPP/", "_searchresults": 32, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/deepSTRAPP.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/maeldore/deepstrapp", "_realowner": "maeldore", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2026-01-19" } ], "_exports": [ "BSM_to_phytools_simmap", "compute_STRAPP_test_for_focal_time", "cut_contMap_for_focal_time", "cut_densityMap_for_focal_time", "cut_densityMaps_for_focal_time", "cut_phylo_for_focal_time", "extract_diversification_data_melted_df_for_focal_time", "extract_most_likely_ranges_from_densityMaps_for_focal_time", "extract_most_likely_states_from_densityMaps_for_focal_time", "extract_most_likely_trait_values_for_focal_time", "extract_most_likely_trait_values_from_contMap_for_focal_time", "is_dev_version", "plot_BAMM_rates", "plot_contMap", "plot_densityMaps_overlay", "plot_histogram_STRAPP_test_for_focal_time", "plot_histograms_STRAPP_tests_over_time", "plot_rates_through_time", "plot_rates_vs_trait_data_for_focal_time", "plot_rates_vs_trait_data_over_time", "plot_STRAPP_pvalues_over_time", "plot_traits_vs_rates_on_phylogeny_for_focal_time", "plot_traits_vs_rates_on_phylogeny_over_time", "prepare_diversification_data", "prepare_trait_data", "run_deepSTRAPP_for_focal_time", "run_deepSTRAPP_over_time", "select_best_model_from_BioGeoBEARS", "select_best_trait_model_from_geiger", "update_rates_and_regimes_for_focal_time" ], "_datasets": [ { "name": "BAMM_template_diversification", "title": "Template file for BAMM diversification analyses", "object": "BAMM_template_diversification", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "eel_biogeo_data", "title": "Data summarizing the evolution of geographic ranges in eels", "object": "eel_biogeo_data", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "eel_cat_3lvl_data", "title": "Data summarizing the evolution of feeding habits in eels using a 3-level factor as categorical trait", "object": "eel_cat_3lvl_data", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "mammals", "title": "Phylogeny and body mass data for extant and extinct mammals families/genera from Slater, 2013", "object": "mammals", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "Ponerinae_binary_range_table", "title": "Dataset providing biogeographic range data for extant ponerine ants", "object": "Ponerinae_binary_range_table", "class": [ "data.frame" ], "fields": [ "Taxa", "Afrotropics", "Australasia", "Indomalaya", "Nearctic", "Neotropics", "Eastern_Palearctic", "Western_Palearctic", "Old_World", "New_World" ], "rows": 1534, "table": true, "tojson": true }, { "name": "Ponerinae_biogeo_data_old_calib", "title": "Data summarizing the evolution of geographic ranges in Ponerinae ants using an old ill-calibrated phylogeny for illustrative purposes", "object": "Ponerinae_biogeo_data_old_calib", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "Ponerinae_cat_2lvl_data_old_calib", "title": "Data summarizing the evolution of fake size data in Ponerinae ants using a 2-level factor as categorical trait", "object": "Ponerinae_cat_2lvl_data_old_calib", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "Ponerinae_cat_3lvl_data_old_calib", "title": "Data summarizing the evolution of fake habitat data in Ponerinae ants using a 3-level factor as categorical trait", "object": "Ponerinae_cat_3lvl_data_old_calib", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "Ponerinae_trait_cont_tip_data_10My", "title": "Data summarizing the evolution of a fake continuous trait in Ponerinae ants extracted for 10 Mya", "object": "Ponerinae_trait_cont_tip_data_10My", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "Ponerinae_trait_tip_data", "title": "Dataset providing fake trait data for extant ponerine ants for illustrative purposes", "object": "Ponerinae_trait_tip_data", "class": [ "data.frame" ], "fields": [ "Taxa", "fake_cont_tip_data", "fake_cat_2lvl_tip_data", "fake_cat_3lvl_tip_data" ], "rows": 1534, "table": true, "tojson": true }, { "name": "Ponerinae_tree", "title": "Dataset providing the extensive time-calibrated phylogeny of extant ponerine ants", "object": "Ponerinae_tree", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "Ponerinae_tree_old_calib", "title": "Dataset providing the extensive time-calibrated phylogeny of extant ponerine ants using an old calibration for illustrative purposes", "object": "Ponerinae_tree_old_calib", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "whale_BAMM_object", "title": "Dataset summarizing 1000 posterior samples of BAMM for extant whales", "object": "whale_BAMM_object", "class": [ "bammdata" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "BAMM_template_diversification", "title": "Template file for BAMM diversification analyses", "topics": [ "BAMM_template_diversification" ] }, { "page": "BSM_to_phytools_simmap", "title": "Convert Biogeographic Stochastic Map (BSM) to phytools SIMMAP stochastic map (SM) format", "topics": [ "BSMs_to_phytools_simmaps", "BSM_to_phytools_simmap" ] }, { "page": "compute_STRAPP_test_for_focal_time", "title": "Compute STRAPP to test for a relationship between diversification rates and trait data", "topics": [ "compute_STRAPP_test_for_focal_time" ] }, { "page": "cut_contMap_for_focal_time", "title": "Cut the phylogeny and continuous trait mapping for a given focal time in the past", "topics": [ "cut_contMap_for_focal_time" ] }, { "page": "cut_densityMap_for_focal_time", "title": "Cut the phylogeny and posterior probability mapping of a categorical trait for a given focal time in the past", "topics": [ "cut_densityMap_for_focal_time" ] }, { "page": "cut_densityMaps_for_focal_time", "title": "Cut phylogenies and posterior probability mapping of each state for a given focal time in the past", "topics": [ "cut_densityMaps_for_focal_time" ] }, { "page": "cut_phylo_for_focal_time", "title": "Cut the phylogeny for a given time in the past", "topics": [ "cut_phylo_for_focal_time" ] }, { "page": "eel_biogeo_data", "title": "Data summarizing the evolution of geographic ranges in eels", "topics": [ "eel_biogeo_data" ] }, { "page": "eel_cat_3lvl_data", "title": "Data summarizing the evolution of feeding habits in eels using a 3-level factor as categorical trait", "topics": [ "eel_cat_3lvl_data" ] }, { "page": "extract_diversification_data_melted_df_for_focal_time", "title": "Extract diversification data from a BAMM_object", "topics": [ "extract_diversification_data_melted_df_for_focal_time" ] }, { "page": "extract_most_likely_ranges_from_densityMaps_for_focal_time", "title": "Extract biogeographic range data mapped on a phylogeny at a given time in the past", "topics": [ "extract_most_likely_ranges_from_densityMaps_for_focal_time" ] }, { "page": "extract_most_likely_states_from_densityMaps_for_focal_time", "title": "Extract categorical trait data mapped on a phylogeny at a given time in the past", "topics": [ "extract_most_likely_states_from_densityMaps_for_focal_time" ] }, { "page": "extract_most_likely_trait_values_for_focal_time", "title": "Extract trait data mapped on a phylogeny at a given time in the past", "topics": [ "extract_most_likely_trait_values_for_focal_time" ] }, { "page": "extract_most_likely_trait_values_from_contMap_for_focal_time", "title": "Extract continuous trait data mapped on a phylogeny at a given time in the past", "topics": [ "extract_most_likely_trait_values_from_contMap_for_focal_time" ] }, { "page": "is_dev_version", "title": "Check whether deepSTRAPP is a development version", "topics": [ "is_dev_version" ] }, { "page": "mammals", "title": "Phylogeny and body mass data for extant and extinct mammals families/genera from Slater, 2013", "topics": [ "mammals" ] }, { "page": "plot_BAMM_rates", "title": "Plot diversification rates and regime shifts from BAMM on phylogeny", "topics": [ "plot_BAMM_rates" ] }, { "page": "plot_contMap", "title": "Plot continuous trait evolution on the tree", "topics": [ "plot_contMap" ] }, { "page": "plot_densityMaps_overlay", "title": "Plot posterior probabilities of states/ranges on phylogeny from densityMaps", "topics": [ "plot_densityMaps_overlay" ] }, { "page": "plot_histogram_STRAPP_test_for_focal_time", "title": "Plot histogram of STRAPP test statistics to assess results", "topics": [ "plot_histogram_STRAPP_test_for_focal_time" ] }, { "page": "plot_histograms_STRAPP_tests_over_time", "title": "Plot multiple histograms of STRAPP test statistics over time-steps", "topics": [ "plot_histograms_STRAPP_tests_over_time" ] }, { "page": "plot_rates_through_time", "title": "Plot evolution of diversification rates in relation to trait values over time", "topics": [ "plot_rates_through_time" ] }, { "page": "plot_rates_vs_trait_data_for_focal_time", "title": "Plot rates vs. trait data for a given focal time", "topics": [ "plot_rates_vs_trait_data_for_focal_time" ] }, { "page": "plot_rates_vs_trait_data_over_time", "title": "Plot rates vs. trait data over time-steps", "topics": [ "plot_rates_vs_trait_data_over_time" ] }, { "page": "plot_STRAPP_pvalues_over_time", "title": "Plot evolution of p-values of STRAPP tests over time", "topics": [ "plot_STRAPP_pvalues_over_time" ] }, { "page": "plot_traits_vs_rates_on_phylogeny_for_focal_time", "title": "Plot trait/range evolution vs. diversification rates and regime shifts on phylogeny", "topics": [ "plot_traits_vs_rates_on_phylogeny_for_focal_time" ] }, { "page": "plot_traits_vs_rates_on_phylogeny_over_time", "title": "Plot multiple mapped phylogenies of trait/range evolution vs. diversification rates and regime shifts over time-steps", "topics": [ "plot_traits_vs_rates_on_phylogeny_over_time" ] }, { "page": "Ponerinae_binary_range_table", "title": "Dataset providing biogeographic range data for extant ponerine ants", "topics": [ "Ponerinae_binary_range_table" ] }, { "page": "Ponerinae_biogeo_data_old_calib", "title": "Data summarizing the evolution of geographic ranges in Ponerinae ants using an old ill-calibrated phylogeny for illustrative purposes", "topics": [ "Ponerinae_biogeo_data_old_calib" ] }, { "page": "Ponerinae_cat_2lvl_data_old_calib", "title": "Data summarizing the evolution of fake size data in Ponerinae ants using a 2-level factor as categorical trait", "topics": [ "Ponerinae_cat_2lvl_data_old_calib" ] }, { "page": "Ponerinae_cat_3lvl_data_old_calib", "title": "Data summarizing the evolution of fake habitat data in Ponerinae ants using a 3-level factor as categorical trait", "topics": [ "Ponerinae_cat_3lvl_data_old_calib" ] }, { "page": "Ponerinae_trait_cont_tip_data_10My", "title": "Data summarizing the evolution of a fake continuous trait in Ponerinae ants extracted for 10 Mya", "topics": [ "Ponerinae_trait_cont_tip_data_10My" ] }, { "page": "Ponerinae_trait_tip_data", "title": "Dataset providing fake trait data for extant ponerine ants for illustrative purposes", "topics": [ "Ponerinae_trait_tip_data" ] }, { "page": "Ponerinae_tree", "title": "Dataset providing the extensive time-calibrated phylogeny of extant ponerine ants", "topics": [ "Ponerinae_tree" ] }, { "page": "Ponerinae_tree_old_calib", "title": "Dataset providing the extensive time-calibrated phylogeny of extant ponerine ants using an old calibration for illustrative purposes", "topics": [ "Ponerinae_tree_old_calib" ] }, { "page": "prepare_diversification_data", "title": "Run a full BAMM (Bayesian Analysis of Macroevolutionary Mixtures) workflow", "topics": [ "prepare_diversification_data" ] }, { "page": "prepare_trait_data", "title": "Map trait evolution on a time-calibrated phylogeny", "topics": [ "prepare_trait_data" ] }, { "page": "run_deepSTRAPP_for_focal_time", "title": "Run deepSTRAPP to test for a relationship between diversification rates and trait data at a given focal time", "topics": [ "run_deepSTRAPP_for_focal_time" ] }, { "page": "run_deepSTRAPP_over_time", "title": "Run deepSTRAPP to test for a relationship between diversification rates and trait data over multiple time steps", "topics": [ "run_deepSTRAPP_over_time" ] }, { "page": "select_best_model_from_BioGeoBEARS", "title": "Compare model fits with AICc and Akaike's weights", "topics": [ "select_best_model_from_BioGeoBEARS" ] }, { "page": "select_best_trait_model_from_geiger", "title": "Compare trait evolutionary model fits with AICc and Akaike's weights", "topics": [ "select_best_trait_model_from_geiger" ] }, { "page": "update_rates_and_regimes_for_focal_time", "title": "Update diversification rates/regimes mapped on a phylogeny up to a given time in the past", "topics": [ "update_rates_and_regimes_for_focal_time" ] }, { "page": "whale_BAMM_object", "title": "Dataset summarizing 1000 posterior samples of BAMM for extant whales", "topics": [ "whale_BAMM_object" ] } ], "_pkglogo": "https://github.com/maeldore/deepstrapp/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/maeldore/deepstrapp/raw/HEAD/README.md", "_rundeps": [ "ape", "askpass", "BAMMtools", "bitops", "caTools", "cladoRcpp", "cli", "clusterGeneration", "coda", "codetools", "colorspace", "combinat", "cowplot", "cpp11", "curl", "DEoptim", "deSolve", "digest", "doParallel", "dplyr", "dunn.test", "expm", "farver", "fastmatch", "foreach", "geiger", "generics", "ggplot2", "glue", "gplots", "gtable", "gtools", "igraph", "isoband", "iterators", "KernSmooth", "labeling", "lattice", "lifecycle", "magrittr", "maps", "MASS", "Matrix", "mnormt", "mvtnorm", "ncbit", "nlme", "numDeriv", "optimParallel", "phangorn", "phytools", "pillar", "pkgconfig", "plyr", "purrr", "qpdf", "quadprog", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "rlang", "S7", "scales", "scatterplot3d", "stringi", "stringr", "subplex", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "cut_phylogenies.Rmd", "filename": "cut_phylogenies.html", "title": "Cut phylogenies", "author": "Maël Doré", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-08-15 15:13:44", "modified": "2026-01-13 13:32:24", "commits": 6 }, { "source": "deepSTRAPP.Rmd", "filename": "deepSTRAPP.html", "title": "deepSTRAPP: All tutorials", "author": "Maël Doré", "engine": "knitr::rmarkdown", "headings": [ "Main tutorial", "Quick-to-run example", "Advanced uses / tutorials", "1/ Full deepSTRAPP workflows on different types of data", "2/ Explore options for trait evolution", "3/ Explore options for BAMM", "4/ Explore the STRAPP test options", "5/ Plot rates through time (RTT)", "6/ Cut phylogenies" ], "created": "2025-08-15 15:13:44", "modified": "2025-10-17 08:29:53", "commits": 11 }, { "source": "deepSTRAPP_biogeographic_data.Rmd", "filename": "deepSTRAPP_biogeographic_data.html", "title": "deepSTRAPP: Biogeographic range data", "author": "Maël Doré", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-08-15 15:13:44", "modified": "2026-01-13 13:32:24", "commits": 19 }, { "source": "deepSTRAPP_categorical_data.Rmd", "filename": "deepSTRAPP_categorical_data.html", "title": "deepSTRAPP: Categorical trait data", "author": "Maël Doré", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-08-15 15:13:44", "modified": "2026-01-13 13:32:24", "commits": 15 }, { "source": "deepSTRAPP_continuous_data.Rmd", "filename": "deepSTRAPP_continuous_data.html", "title": "deepSTRAPP: Continuous trait data", "author": "Maël Doré", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-08-15 15:13:44", "modified": "2026-01-13 13:32:24", "commits": 16 }, { "source": "explore_STRAPP_test_types.Rmd", "filename": "explore_STRAPP_test_types.html", "title": "Explore STRAPP test options", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-08-15 15:13:44", "modified": "2025-12-22 15:22:56", "commits": 5 }, { "source": "main_tutorial.Rmd", "filename": "main_tutorial.html", "title": "Main tutorial", "author": "Maël Doré", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-09-01 09:46:51", "modified": "2026-01-13 13:32:24", "commits": 13 }, { "source": "model_biogeographic_range_evolution.Rmd", "filename": "model_biogeographic_range_evolution.html", "title": "Model biogeographic range evolution", "author": "Maël Doré", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-08-15 15:13:44", "modified": "2026-01-13 10:47:40", "commits": 8 }, { "source": "model_categorical_trait_evolution.Rmd", "filename": "model_categorical_trait_evolution.html", "title": "Model categorical trait evolution", "author": "Maël Doré", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-08-15 15:13:44", "modified": "2025-12-29 16:33:22", "commits": 6 }, { "source": "model_continuous_trait_evolution.Rmd", "filename": "model_continuous_trait_evolution.html", "title": "Model continuous trait evolution", "author": "Maël Doré", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-09-18 13:40:15", "modified": "2025-12-29 16:33:22", "commits": 4 }, { "source": "model_diversification_dynamics.Rmd", "filename": "model_diversification_dynamics.html", "title": "Model diversification dynamics", "author": "Maël Doré", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-08-15 15:13:44", "modified": "2025-12-29 16:33:22", "commits": 5 }, { "source": "plot_rates_through_time.Rmd", "filename": "plot_rates_through_time.html", "title": "Plot rates through time", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-08-15 15:13:44", "modified": "2025-12-29 16:33:22", "commits": 7 } ], "_score": 6.605520523437469, "_indexed": true, "_nocasepkg": "deepstrapp", "_universes": [ "maeldore" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-05-20T09:13:22.000Z", "distro": "noble", "arch": "aarch64", "commit": "6f897d53fbce1e3acfae80307f2a05f0bcf3a0b2", "fileid": "e958dd6ffd149e23991b88ee5ef4434f7a1efb63122bfb673f8c2259d6188c7a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/26152613455" }, { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-05-20T09:13:28.000Z", "distro": "noble", "arch": "x86_64", "commit": "6f897d53fbce1e3acfae80307f2a05f0bcf3a0b2", "fileid": "420a717861acdc3b5eceaf02818a0ef9d97d50948bfeb36b673378f9edacb883", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/26152613455" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-05-20T09:13:38.000Z", "distro": "noble", "arch": "aarch64", "commit": "6f897d53fbce1e3acfae80307f2a05f0bcf3a0b2", "fileid": "a16d1c946f1a3e22ce791e297c2a004d8717f181d078e692e7e2a66b39969ac4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/26152613455" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-05-20T09:13:21.000Z", "distro": "noble", "arch": "x86_64", "commit": "6f897d53fbce1e3acfae80307f2a05f0bcf3a0b2", "fileid": "696e8bd29e81fac15b90eefa2c2c5cced07b2a1b1eae574a707cdfc93b91e1a8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/26152613455" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-05-20T09:12:05.000Z", "arch": "aarch64", "commit": "6f897d53fbce1e3acfae80307f2a05f0bcf3a0b2", "fileid": "70946ed20a5251b0cfba793b495909e9a1ec5f2029ff0e01e4db6615f9f2a664", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/26152613455" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-05-20T09:13:35.000Z", "arch": "x86_64", "commit": "6f897d53fbce1e3acfae80307f2a05f0bcf3a0b2", "fileid": "f14b3e0b6edabf9519adeeb30fd91fadcdfea13793ba0f379c070826dccc0474", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/26152613455" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-05-20T09:12:23.000Z", "arch": "aarch64", "commit": "6f897d53fbce1e3acfae80307f2a05f0bcf3a0b2", "fileid": "29c101fd86811d9c8b7dc9c55e87076a67311cae2af48efda5ad0cf1bd27aa65", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/26152613455" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-05-20T09:13:28.000Z", "arch": "x86_64", "commit": "6f897d53fbce1e3acfae80307f2a05f0bcf3a0b2", "fileid": "e8e5dca9498bc244fba8eb6d00cdaa632340e0460d001944d0b36ca3d529b7c3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/26152613455" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-05-20T09:26:27.000Z", "arch": "x86_64", "commit": "6f897d53fbce1e3acfae80307f2a05f0bcf3a0b2", "fileid": "4cf8acc369ad12e50d45ce48ff3a0c5b4607c42f730daa6f8ef6aa77baa62e0e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/26152613455" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-05-20T09:25:46.000Z", "arch": "x86_64", "commit": "6f897d53fbce1e3acfae80307f2a05f0bcf3a0b2", "fileid": "469d920aa056069c0d27a28df3df0ebee1ca4b874b70a283bf98e8611c5e8b11", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/26152613455" }, { "r": "4.6.0", "os": "win", "version": "1.0.0", "date": "2026-05-20T09:27:05.000Z", "arch": "x86_64", "commit": "6f897d53fbce1e3acfae80307f2a05f0bcf3a0b2", "fileid": "3fb14dff25a642a9f5eaa2e358096b06345c9e4415a4188a39685fffbc91895f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/26152613455" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-06-02T13:24:34.000Z", "arch": "emscripten", "commit": "6f897d53fbce1e3acfae80307f2a05f0bcf3a0b2", "fileid": "cc13116ca1bcceea47d95a5c0c42edf30b11a8e0c8fbd801234d4e9a496a5fd3", "status": "success", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/26152613455" } ] }