{ "_id": "6ae384d93d0f299392dd1bd3", "Package": "deepSTRAPP", "Title": "Test for Differences in Diversification Rates over Time", "Version": "1.1.1", "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": "2026-10-29 10:36:26 UTC", "RemoteUrl": "https://github.com/maeldore/deepstrapp", "RemoteRef": "HEAD", "RemoteSha": "048beb26ea67cb260149964c7a5c61b67acb5488", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-29 17:14:52 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 ", "_user": "maeldore", "_type": "src", "_file": "deepSTRAPP_1.1.1.tar.gz", "_fileid": "https://r2.ropensci.org/4445c76315f85f357e07347a31883966168db7e4855b0ada46bb93513c63f8b5", "_filesize": 15638848, "_sha256": "4445c76315f85f357e07347a31883966168db7e4855b0ada46bb93513c63f8b5", "_expires": "2027-02-06T17:39:34.000Z", "_created": "2026-10-29T17:14:52.000Z", "_published": "2026-10-31T07:19:41.880Z", "_upstream": "https://github.com/maeldore/deepstrapp", "_status": "success", "_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" }, "_jobs": [ { "job": 123609005958, "time": 213, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12918330990" }, { "job": 123609005960, "time": 318, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12917452868" }, { "job": 123609006243, "time": 240, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12918101169" }, { "job": 123609005886, "time": 279, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12918136288" }, { "job": 123609006087, "time": 218, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12917094872" }, { "job": 123609005896, "time": 539, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12917398862" }, { "job": 123609006068, "time": 61, "config": "macos-release-arm64", "r": "", "check": "FAIL", "artifact": "" }, { "job": 123609005824, "time": 401, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12918875876" }, { "job": 123603109821, "time": 613, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12918155859" }, { "job": 123609005828, "time": 166, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12918440330" }, { "job": 123609006301, "time": 373, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12917767314" }, { "job": 123609006039, "time": 1199, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12918513191" }, { "job": 123609005981, "time": 1087, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12919580744" }, { "job": 123609005845, "time": 349, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12918590558" }, { "job": 123609005978, "time": 1162, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12919441381" } ], "_buildurl": "https://github.com/r-universe/maeldore/actions/runs/40917896805", "_commit": { "id": "048beb26ea67cb260149964c7a5c61b67acb5488", "author": "Maël DORÉ ", "committer": "Maël DORÉ ", "message": ":loudspeaker: Update comments to CRAN for v.1.1.1\n", "time": 1793270186 }, "_distro": "resolute", "_host": "GitHub-Actions", "_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": "rlang", "version": ">= 1.1.6", "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" }, { "package": "contsimmap", "version": ">= 0.1.0", "role": "Suggests" } ], "_owner": "maeldore", "_selfowned": true, "_usedby": 0, "_updates": [ { "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 }, { "week": "2026-26", "n": 2 }, { "week": "2026-27", "n": 8 }, { "week": "2026-34", "n": 13 }, { "week": "2026-35", "n": 89 }, { "week": "2026-36", "n": 28 }, { "week": "2026-37", "n": 53 }, { "week": "2026-38", "n": 5 }, { "week": "2026-39", "n": 1 }, { "week": "2026-40", "n": 1 }, { "week": "2026-41", "n": 4 }, { "week": "2026-42", "n": 2 }, { "week": "2026-43", "n": 3 }, { "week": "2026-44", "n": 3 } ], "_tags": [ { "name": "v1.0.0", "date": "2026-01-13" }, { "name": "v1.1.0", "date": "2026-09-28" } ], "_stars": 2, "_contributors": [ { "user": "maeldore", "count": 488, "uuid": 60143458 }, { "user": "bblaimer", "count": 14, "uuid": 233238098 } ], "_userbio": { "uuid": 60143458, "type": "user", "name": "Maël DORÉ", "followers": 10, "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": 394, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/deepSTRAPP" }, "_devurl": "https://github.com/maeldore/deepstrapp", "_pkgdown": "https://maeldore.github.io/deepSTRAPP/", "_searchresults": 34, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/deepSTRAPP.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/maeldore/deepstrapp", "_realowner": "maeldore", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2026-01-19" }, { "version": "1.1.0", "date": "2026-09-28" } ], "_exports": [ "aggregate_contMaps", "build_BAMM_object", "compute_STRAPP_test_for_focal_time", "convert_BSM_to_simmap", "convert_BSMs_to_simmaps", "convert_contsimmap_to_contMaps", "convert_simmaps_to_densityMaps", "cut_contMap_for_focal_time", "cut_contMaps_for_focal_time", "cut_densityMap_for_focal_time", "cut_densityMaps_for_focal_time", "cut_phylo_for_focal_time", "cut_simmap_for_focal_time", "cut_simmaps_for_focal_time", "extract_all_trait_values_for_focal_time", "extract_diversification_data_melted_df_for_focal_time", "extract_most_likely_trait_values_for_focal_time", "extract_trait_data_melted_df_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", "prune_BAMM_object", "run_deepSTRAPP_for_focal_time", "run_deepSTRAPP_over_time", "select_best_model_from_BioGeoBEARS", "select_best_trait_model_from_geiger", "subset_BAMM_object", "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 mammal 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": "aggregate_contMaps", "title": "Aggregate a list of contMaps into a unique mean/median contMap", "topics": [ "aggregate_contMaps" ] }, { "page": "BAMM_template_diversification", "title": "Template file for BAMM diversification analyses", "topics": [ "BAMM_template_diversification" ] }, { "page": "build_BAMM_object", "title": "Build a BAMM object for a deepSTRAPP run", "topics": [ "build_BAMM_object" ] }, { "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": "convert_BSM_to_simmap", "title": "Convert Biogeographic Stochastic Map (BSM) to phytools SIMMAP stochastic map (SM) format", "topics": [ "convert_BSMs_to_simmaps", "convert_BSM_to_simmap" ] }, { "page": "convert_contsimmap_to_contMaps", "title": "Convert a contsimmap object into a list of contMaps", "topics": [ "convert_contsimmap_to_contMaps" ] }, { "page": "convert_simmaps_to_densityMaps", "title": "Convert simmaps into densityMaps suitable for deepSTRAPP", "topics": [ "convert_simmaps_to_densityMaps" ] }, { "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_contMaps_for_focal_time", "title": "Cut the phylogenies and continuous trait mappings of a list of contMaps for a given focal time in the past", "topics": [ "cut_contMaps_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": "cut_simmap_for_focal_time", "title": "Cut the phylogeny and categorical trait/range mapping for a given focal time in the past", "topics": [ "cut_simmap_for_focal_time" ] }, { "page": "cut_simmaps_for_focal_time", "title": "Cut the phylogenies and categorical trait/range mappings of a list of simmaps for a given focal time in the past", "topics": [ "cut_simmaps_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_all_trait_values_for_focal_time", "title": "Extract all trait data from stochastic maps at a given time in the past", "topics": [ "extract_all_trait_values_for_focal_time" ] }, { "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_trait_values_for_focal_time", "title": "Extract most likely trait data mapped on a phylogeny at a given time in the past", "topics": [ "extract_most_likely_trait_values_for_focal_time" ] }, { "page": "extract_trait_data_melted_df_for_focal_time", "title": "Extract trait data from a trait_data object", "topics": [ "extract_trait_data_melted_df_for_focal_time" ] }, { "page": "mammals", "title": "Phylogeny and body mass data for extant and extinct mammal 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 mean 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": "prune_BAMM_object", "title": "Prune a BAMM object to a subset of tips", "topics": [ "prune_BAMM_object" ] }, { "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": "subset_BAMM_object", "title": "Subset a BAMM object before a deepSTRAPP run", "topics": [ "subset_BAMM_object" ] }, { "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": "2026-10-21 05:57:10", "commits": 9 }, { "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/ Handle uncertainty", "7/ Import external analyses", "8/ Cut phylogenies" ], "created": "2025-08-15 15:13:44", "modified": "2026-09-07 05:09:19", "commits": 13 }, { "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": "2026-10-21 05:57:10", "commits": 26 }, { "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": "2026-10-21 05:57:10", "commits": 21 }, { "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": "2026-10-21 05:57:10", "commits": 22 }, { "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": "2026-09-07 06:39:17", "commits": 8 }, { "source": "handle_uncertainty.Rmd", "filename": "handle_uncertainty.html", "title": "Handle uncertainty", "author": "Maël Doré", "engine": "knitr::rmarkdown", "headings": [], "created": "2026-08-24 09:44:50", "modified": "2026-09-07 06:39:17", "commits": 3 }, { "source": "import_external_analyses.Rmd", "filename": "import_external_analyses.html", "title": "Import external analyses", "author": "Maël Doré", "engine": "knitr::rmarkdown", "headings": [ "Plot pre-rendered graph" ], "created": "2026-08-24 09:45:25", "modified": "2026-10-12 00:28:31", "commits": 15 }, { "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": "2026-10-21 05:57:10", "commits": 19 }, { "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": "2026-09-07 06:39:17", "commits": 11 }, { "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": "2026-09-07 06:39:17", "commits": 9 }, { "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": "2026-09-09 03:51:25", "commits": 8 }, { "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": "2026-09-07 09:59:46", "commits": 9 }, { "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": "2026-09-07 06:39:17", "commits": 11 } ], "_score": 6.978636948384475, "_indexed": true, "_nocasepkg": "deepstrapp", "_universes": [ "maeldore" ], "_failure": { "version": "1.1.1.9000", "commit": { "id": "5f47fc664ef25f0dd6d0361ee85a07794f77589f", "author": "Maël DORÉ ", "committer": "Maël DORÉ ", "message": "Convert to dev version v.1.1.1.9000 - Update .rds datasets\n", "time": 1793322023 }, "buildurl": "https://github.com/r-universe/maeldore/actions/runs/40989871352", "date": "2026-10-31T07:19:41.875Z", "job": { "job": 124475116299, "time": 178, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "13035035374" } }, "_binaries": [ { "r": "4.6.1", "os": "mac", "version": "1.1.1", "date": "2026-10-29T11:05:07.000Z", "arch": "aarch64", "commit": "72a1c8a0083f8f496e30bce094a64b5774724804", "fileid": "https://r2.ropensci.org/2675d44757b1e413bd3918b6a86cc808b7ea604bf1e85a8eea68182f91c4b7da", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/40856994150" }, { "r": "4.7.0", "os": "linux", "version": "1.1.1", "date": "2026-10-29T17:17:43.000Z", "distro": "resolute", "arch": "aarch64", "commit": "048beb26ea67cb260149964c7a5c61b67acb5488", "fileid": "https://r2.ropensci.org/c81296dcbcc9bb6e48a787f41cda46f1b579c0a82573be4d141352f2ae6b5225", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/40917896805" }, { "r": "4.7.0", "os": "linux", "version": "1.1.1", "date": "2026-10-29T17:18:44.000Z", "distro": "resolute", "arch": "x86_64", "commit": "048beb26ea67cb260149964c7a5c61b67acb5488", "fileid": "https://r2.ropensci.org/9652616d602a8f1d84409fb87af3b690d4c7580359c0e8c10c5f0156bab99da5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/40917896805" }, { "r": "4.6.1", "os": "linux", "version": "1.1.1", "date": "2026-10-29T17:18:21.000Z", "distro": "resolute", "arch": "aarch64", "commit": "048beb26ea67cb260149964c7a5c61b67acb5488", "fileid": "https://r2.ropensci.org/483b4482efaafb9f430819a20ca48df80289bffd4f0a246dca48221afc542dd0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/40917896805" }, { "r": "4.6.1", "os": "linux", "version": "1.1.1", "date": "2026-10-29T17:18:25.000Z", "distro": "resolute", "arch": "x86_64", "commit": "048beb26ea67cb260149964c7a5c61b67acb5488", "fileid": "https://r2.ropensci.org/03de2bda91dd649d29250f82480528fdb75c17113b96aedc7dd5fc71de9ba20d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/40917896805" }, { "r": "4.5.3", "os": "mac", "version": "1.1.1", "date": "2026-10-29T17:30:53.000Z", "arch": "aarch64", "commit": "048beb26ea67cb260149964c7a5c61b67acb5488", "fileid": "https://r2.ropensci.org/9d2b709f79eeeb8cf5c61e6cd5a938c8f4408cd08926018aa77a8898323feded", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/40917896805" }, { "r": "4.5.3", "os": "mac", "version": "1.1.1", "date": "2026-10-29T17:20:53.000Z", "arch": "x86_64", "commit": "048beb26ea67cb260149964c7a5c61b67acb5488", "fileid": "https://r2.ropensci.org/98a77cc0f0f676129fb699f9ebcac1668a921c9db91bfd60917bd0195298d187", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/40917896805" }, { "r": "4.6.1", "os": "mac", "version": "1.1.1", "date": "2026-10-29T17:25:57.000Z", "arch": "x86_64", "commit": "048beb26ea67cb260149964c7a5c61b67acb5488", "fileid": "https://r2.ropensci.org/ab29bd9d041452f0b044178dd7e0c224dfe759218735f7fabe49b24cff7f4d9c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/40917896805" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.1", "date": "2026-10-29T17:18:19.000Z", "arch": "emscripten", "commit": "048beb26ea67cb260149964c7a5c61b67acb5488", "fileid": "https://r2.ropensci.org/9c182a2d9e584ec823e2e4f6e7e198df3beeed38c96248ae40026823ad135ce2", "status": "success", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/40917896805" }, { "r": "4.7.0", "os": "win", "version": "1.1.1", "date": "2026-10-29T17:19:47.000Z", "arch": "aarch64", "commit": "048beb26ea67cb260149964c7a5c61b67acb5488", "fileid": "https://r2.ropensci.org/0b4e3f8076e90855d348d2d414fcbad6496250af8ce124d5077bf3cfaf2556dc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/40917896805" }, { "r": "4.7.0", "os": "win", "version": "1.1.1", "date": "2026-10-29T17:32:47.000Z", "arch": "x86_64", "commit": "048beb26ea67cb260149964c7a5c61b67acb5488", "fileid": "https://r2.ropensci.org/76e23d3cad6ba80f6e029c319e924b02f0560217c0f346c78ef9596cac39cd5d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/40917896805" }, { "r": "4.5.3", "os": "win", "version": "1.1.1", "date": "2026-10-29T17:31:43.000Z", "arch": "x86_64", "commit": "048beb26ea67cb260149964c7a5c61b67acb5488", "fileid": "https://r2.ropensci.org/52506b6aaba8ff10aaa948edd502e88dad684e03b71779e35a7ddd743fe28865", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/40917896805" }, { "r": "4.6.1", "os": "win", "version": "1.1.1", "date": "2026-10-29T17:19:35.000Z", "arch": "aarch64", "commit": "048beb26ea67cb260149964c7a5c61b67acb5488", "fileid": "https://r2.ropensci.org/a6c077806d8bf12c91fa1a0eb3929fe6ad4386531af097139588ce7d6119b0c0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/40917896805" }, { "r": "4.6.1", "os": "win", "version": "1.1.1", "date": "2026-10-29T17:33:01.000Z", "arch": "x86_64", "commit": "048beb26ea67cb260149964c7a5c61b67acb5488", "fileid": "https://r2.ropensci.org/c8cffbcb059a80399ff597afbb746ffedd562d697637ffa04eac2af8c4c7ae5d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/maeldore/actions/runs/40917896805" } ] }