{ "_id": "6acb4fc5fe5cc25786e8dfa8", "Package": "nLTT", "Type": "Package", "Title": "Calculate the NLTT Statistic", "Version": "1.4.10", "Authors@R": "c(person(\"Thijs\",\"Janzen\", email = \"thijsjanzen@gmail.com\",role=c(\"aut\",\"cre\")),\nperson(\"Richèl J.C.\", \"Bilderbeek\", email = \"richel@richelbilderbeek.nl\", role = c(\"aut\"), comment = c(ORCID = \"0000-0003-1107-7049\")),\nperson(\"Pedro\", \"Neves\", email = \"p.m.santos.neves@rug.nl\", role = \"ctb\"))", "Description": "Provides functions to calculate the normalised\nLineage-Through- Time (nLTT) statistic, given two phylogenetic\ntrees. The nLTT statistic measures the difference between two\nLineage-Through-Time curves, where each curve is normalised\nboth in time and in number of lineages.", "License": "GPL-2", "NeedsCompilation": "no", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "URL": "https://github.com/thijsjanzen/nLTT", "BugReports": "https://github.com/thijsjanzen/nLTT/issues", "Repository": "https://thijsjanzen.r-universe.dev", "Date/Publication": "2025-05-06 12:32:58 UTC", "RemoteUrl": "https://github.com/thijsjanzen/nltt", "RemoteRef": "HEAD", "RemoteSha": "a70bad0bc10b829f8586d32dcc309daa6a2f28a2", "Packaged": { "Date": "2026-10-11 08:55:48 UTC", "User": "root" }, "Author": "Thijs Janzen [aut, cre],\nRichèl J.C. Bilderbeek [aut] (ORCID:\n),\nPedro Neves [ctb]", "Maintainer": "Thijs Janzen ", "_user": "thijsjanzen", "_type": "src", "_file": "nLTT_1.4.10.tar.gz", "_fileid": "https://r2.ropensci.org/ff1c3bb68c64d639a24ae5b7f035fa6a83ad7a613a410119a43b283ff9f39cb1", "_filesize": 1889320, "_sha256": "ff1c3bb68c64d639a24ae5b7f035fa6a83ad7a613a410119a43b283ff9f39cb1", "_expires": "2027-01-19T08:58:43.000Z", "_created": "2026-10-11T08:55:48.000Z", "_published": "2026-10-11T08:58:45.155Z", "_buildurl": "https://github.com/r-universe/thijsjanzen/actions/runs/38126301956", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 114432018018, "time": 144, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11697836864" }, { "job": 114432018064, "time": 138, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11697302896" }, { "job": 114432018054, "time": 107, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11697397645" }, { "job": 114432017974, "time": 96, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11697337822" }, { "job": 114431320505, "time": 243, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11697861576" }, { "job": 114432018010, "time": 139, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11697273128" }, { "job": 114432018035, "time": 103, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11697532336" }, { "job": 114432018040, "time": 107, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11697347656" }, { "job": 114432018060, "time": 115, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11697811046" } ], "_upstream": "https://github.com/thijsjanzen/nltt", "_commit": { "id": "a70bad0bc10b829f8586d32dcc309daa6a2f28a2", "author": "Thijs Janzen ", "committer": "Thijs Janzen ", "message": "further clean up\n", "time": 1746534778 }, "_maintainer": { "name": "Thijs Janzen", "email": "thijsjanzen@gmail.com", "login": "thijsjanzen", "bluesky": "@thijsjanzen.bsky.social", "twitter": "@thijsjanzen", "description": "Scientific programmer at University of Groningen", "uuid": 19486664 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "ape", "role": "Imports" }, { "package": "coda", "role": "Imports" }, { "package": "testit", "role": "Imports" }, { "package": "TreeSim", "role": "Suggests" }, { "package": "DDD", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "Hmisc", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "lintr", "role": "Suggests" }, { "package": "microbenchmark", "role": "Suggests" }, { "package": "plyr", "role": "Suggests" }, { "package": "reshape2", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "TESS", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "DAISIE", "role": "Suggests" } ], "_owner": "thijsjanzen", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "nltt", "nltt-statistic", "phylogenetic-trees", "phylogenetics" ], "_stars": 6, "_contributors": [ { "user": "thijsjanzen", "count": 82, "uuid": 19486664 }, { "user": "neves-p", "count": 29, "uuid": 10762799 }, { "user": "richelbilderbeek", "count": 5, "uuid": 2098230 }, { "user": "maelle", "count": 1, "uuid": 8360597 }, { "user": "simongreenhill", "count": 1, "uuid": 220169 } ], "_userbio": { "uuid": 19486664, "type": "user", "name": "Thijs Janzen", "followers": 38, "description": "Scientific programmer at University of Groningen" }, "_downloads": { "count": 470, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/nLTT" }, "_mentions": 2, "_devurl": "https://github.com/thijsjanzen/nltt", "_searchresults": 68, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/nLTT.html", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/thijsjanzen/nltt", "_realowner": "thijsjanzen", "_cranurl": true, "_releases": [ { "version": "1.0", "date": "2015-01-19" }, { "version": "1.1", "date": "2015-04-21" }, { "version": "1.1.1", "date": "2015-12-07" }, { "version": "1.2", "date": "2016-04-26" }, { "version": "1.2.1", "date": "2016-06-06" }, { "version": "1.3", "date": "2016-10-07" }, { "version": "1.3.1", "date": "2016-10-11" }, { "version": "1.4", "date": "2018-04-18" }, { "version": "1.4.1", "date": "2019-05-19" }, { "version": "1.4.3", "date": "2020-01-13" }, { "version": "1.4.6", "date": "2022-02-18" }, { "version": "1.4.8", "date": "2022-05-24" }, { "version": "1.4.9", "date": "2023-08-21" }, { "version": "1.4.10", "date": "2025-05-06" } ], "_exports": [ "abc_smc_nltt", "check_input_event_times", "check_phylogenies", "check_step_type", "check_time_unit", "get_average_nltt_matrix", "get_branching_times", "get_n_lineages", "get_nltt_values", "get_norm_brts", "get_norm_n", "get_phylogeny_nltt_matrix", "mcmc_nltt", "nltt_diff", "nltt_diff_exact", "nltt_diff_exact_brts", "nltt_diff_exact_calc_extinct", "nltt_diff_exact_extinct", "nltt_diff_exact_norm_brts", "nltt_lines", "nltt_plot", "nltts_diff", "nltts_plot", "nLTTstat", "nLTTstat_exact", "stretch_nltt_matrix" ], "_datasets": [ { "name": "exampleTrees", "title": "example trees to test the functionality of the package", "object": "exampleTrees", "file": "exampleTrees.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": false } ], "_help": [ { "page": "nLTT-package", "title": "Package providing functions to visualize the normalized Lineage-Through-Time statistic, and calculate the difference between two nLTT curves", "topics": [ "nLTT-package", "nLTT" ] }, { "page": "abc_smc_nltt", "title": "A function to perform Approximate Bayesian Computation within a Sequential Markov Chain (ABC-SMC), for diversification analysis of phylogenetic trees.", "topics": [ "abc_smc_nltt" ] }, { "page": "check_input_event_times", "title": "Checks that event times are correct", "topics": [ "check_input_event_times" ] }, { "page": "check_phylogenies", "title": "Check if the input is a valid collection of one or more phylogenies", "topics": [ "check_phylogenies" ] }, { "page": "check_step_type", "title": "Check if the step type is valid", "topics": [ "check_step_type" ] }, { "page": "check_time_unit", "title": "Check if the time unit is valid", "topics": [ "check_time_unit" ] }, { "page": "default_params_doc", "title": "This function does nothing. It is intended to inherit is parameters' documentation.", "topics": [ "default_params_doc" ] }, { "page": "exampleTrees", "title": "example trees to test the functionality of the package", "topics": [ "exampleTrees" ] }, { "page": "get_average_nltt_matrix", "title": "Get the average nLTT from a collection of phylogenies", "topics": [ "get_average_nltt_matrix" ] }, { "page": "get_branching_times", "title": "Collect the branching times from the stem age", "topics": [ "get_branching_times" ] }, { "page": "get_n_lineages", "title": "Collect the number of lineages from the stem age", "topics": [ "get_n_lineages" ] }, { "page": "get_nltt_values", "title": "Get the nLTT values in time", "topics": [ "get_nltt_values" ] }, { "page": "get_norm_brts", "title": "Collect the normalized branching times from the stem age", "topics": [ "get_norm_brts" ] }, { "page": "get_norm_n", "title": "Collect the normalized number of lineages from the stem age", "topics": [ "get_norm_n" ] }, { "page": "get_phylogeny_nltt_matrix", "title": "Extract the nLTT matrix from a phylogeny", "topics": [ "get_phylogeny_nltt_matrix" ] }, { "page": "mcmc_nltt", "title": "function, using a Monte Carlo Markov Chain", "topics": [ "mcmc_nltt" ] }, { "page": "nltt_diff", "title": "Calculates the exact difference between the lineage through time curves of tree1 & tree2 (normalized in time and for the number of lineages)", "topics": [ "nltt_diff" ] }, { "page": "nltt_diff_exact", "title": "Calculates the exact, difference between the lineage through time curves of tree1 & tree2 (normalized in time and for the number of lineages)", "topics": [ "nltt_diff_exact" ] }, { "page": "nltt_diff_exact_brts", "title": "Calculates the exact difference between the nLTT curves of the branching times", "topics": [ "nltt_diff_exact_brts" ] }, { "page": "nltt_diff_exact_calc_extinct", "title": "Calculates the exact difference between the nLTT curves of the event times. This includes extinction events.", "topics": [ "nltt_diff_exact_calc_extinct" ] }, { "page": "nltt_diff_exact_extinct", "title": "Calculates the exact difference between the nLTT curves of the event times. This includes extinction events.", "topics": [ "nltt_diff_exact_extinct" ] }, { "page": "nltt_diff_exact_norm_brts", "title": "Calculates the exact difference between the nLTT curves of the branching times", "topics": [ "nltt_diff_exact_norm_brts" ] }, { "page": "nltt_lines", "title": "Normalized version of the ape function ltt.lines.", "topics": [ "nltt_lines" ] }, { "page": "nltt_plot", "title": "Normalized version of the ape function ltt.plot", "topics": [ "nltt_plot" ] }, { "page": "nltts_diff", "title": "Calculates the nLTT statistic between each phylogeny in a collection compared to a same focal/reference tree", "topics": [ "nltts_diff" ] }, { "page": "nltts_plot", "title": "Get the average nLTT from a collection of phylogenies", "topics": [ "nltts_plot" ] }, { "page": "nLTTstat", "title": "Calculate the difference between two normalized Lineage-Through-Time curves, given two phylogenetic trees.", "topics": [ "nLTTstat" ] }, { "page": "nLTTstat_exact", "title": "Calculate the exact difference between two normalized Lineage-Through-Time curves, given two phylogenetic trees.", "topics": [ "nLTTstat_exact" ] }, { "page": "stretch_nltt_matrix", "title": "Stretch matrix 'm' with a timestep resolution of 'dt'.", "topics": [ "stretch_nltt_matrix" ] } ], "_readme": "https://github.com/thijsjanzen/nltt/raw/HEAD/README.md", "_rundeps": [ "ape", "coda", "digest", "lattice", "nlme", "Rcpp", "testit" ], "_vignettes": [ { "source": "nltts_plot.Rmd", "filename": "nltts_plot.html", "title": "How to plot multiple nLTTs and their average", "author": "Richel Bilderbeek", "engine": "knitr::rmarkdown", "headings": [ "Example: Easy trees", "Example: Harder trees" ], "created": "2017-01-24 07:20:47", "modified": "2017-01-24 07:20:47", "commits": 1 }, { "source": "stretch_nltt_matrix.Rmd", "filename": "stretch_nltt_matrix.html", "title": "How to stretch an nLTT timepoints matrix", "author": "Richel Bilderbeek", "engine": "knitr::rmarkdown", "headings": [ "Examples", "Example: Easy tree", "Example: Tree that has two branching events at the same time", "Example: Complex tree" ], "created": "2017-01-24 07:20:47", "modified": "2022-05-23 09:16:29", "commits": 2 }, { "source": "get_nltt_values.Rmd", "filename": "get_nltt_values.html", "title": "How to visualize nLTT values distributions", "author": "Richel Bilderbeek", "engine": "knitr::rmarkdown", "headings": [ "Example: Easy trees", "Example: Harder trees", "Example: Five random trees" ], "created": "2017-01-24 07:20:47", "modified": "2022-05-23 09:16:29", "commits": 4 }, { "source": "nltt_diff.Rmd", "filename": "nltt_diff.html", "title": "nltt_diff functions", "author": "Richel Bilderbeek", "engine": "knitr::rmarkdown", "headings": [ "Close to polytomies, easier to eyeball", "Two pylogenies", "Two LTT plots", "Two nLTT plots" ], "created": "2017-01-23 17:29:38", "modified": "2022-05-08 10:57:32", "commits": 21 }, { "source": "trees_with_root_edge.Rmd", "filename": "trees_with_root_edge.html", "title": "Trees with a root edge", "author": "Richel Bilderbeek", "engine": "knitr::rmarkdown", "headings": [], "created": "2016-08-03 12:14:23", "modified": "2018-04-13 15:32:17", "commits": 8 }, { "source": "walkthrough.Rmd", "filename": "walkthrough.html", "title": "Walkthrough using the nLTT package", "author": "Thijs Janzen", "engine": "knitr::rmarkdown", "headings": [ "nLTT statistic & nLTT plot", "Average nLTT matrix & Average nLTT plot" ], "created": "2016-10-06 13:00:22", "modified": "2022-05-13 07:52:50", "commits": 11 } ], "_score": 6.990871404801486, "_indexed": true, "_nocasepkg": "nltt", "_universes": [ "thijsjanzen" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.4.10", "date": "2026-10-11T08:58:10.000Z", "distro": "resolute", "commit": "a70bad0bc10b829f8586d32dcc309daa6a2f28a2", "fileid": "https://r2.ropensci.org/2886f368be36f96642d38b0bbd5e9e59f8188271b93e9eb717334b6b7e3d33eb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thijsjanzen/actions/runs/38126301956" }, { "r": "4.6.1", "os": "linux", "version": "1.4.10", "date": "2026-10-11T08:58:06.000Z", "distro": "resolute", "commit": "a70bad0bc10b829f8586d32dcc309daa6a2f28a2", "fileid": "https://r2.ropensci.org/6524354901e551ee37b8c89b705421ecdbcf34308fa909535644d554a994f1e1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thijsjanzen/actions/runs/38126301956" }, { "r": "4.5.3", "os": "mac", "version": "1.4.10", "date": "2026-10-11T08:58:13.000Z", "commit": "a70bad0bc10b829f8586d32dcc309daa6a2f28a2", "fileid": "https://r2.ropensci.org/611c7ab9e0fa33d5bf454c8f5b87045635cc2d11b40182c054cd0cf7764c3971", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thijsjanzen/actions/runs/38126301956" }, { "r": "4.6.1", "os": "mac", "version": "1.4.10", "date": "2026-10-11T08:57:57.000Z", "commit": "a70bad0bc10b829f8586d32dcc309daa6a2f28a2", "fileid": "https://r2.ropensci.org/152a0bef0987f84a928a4070b6b3f280d6caeee5cd3ea68451149113909c909d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thijsjanzen/actions/runs/38126301956" }, { "r": "4.6.0", "os": "wasm", "version": "1.4.10", "date": "2026-10-11T08:58:20.000Z", "commit": "a70bad0bc10b829f8586d32dcc309daa6a2f28a2", "fileid": "https://r2.ropensci.org/ce205a8cc8461def8ed11ffff006a7ab317184162f74c297bff666dd32808f6f", "status": "success", "buildurl": "https://github.com/r-universe/thijsjanzen/actions/runs/38126301956" }, { "r": "4.7.0", "os": "win", "version": "1.4.10", "date": "2026-10-11T08:57:20.000Z", "commit": "a70bad0bc10b829f8586d32dcc309daa6a2f28a2", "fileid": "https://r2.ropensci.org/771d1b352ddd818836397cef3b549a4b51b1e129b82d2d5eb8a68a3b5961afb5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thijsjanzen/actions/runs/38126301956" }, { "r": "4.5.3", "os": "win", "version": "1.4.10", "date": "2026-10-11T08:57:30.000Z", "commit": "a70bad0bc10b829f8586d32dcc309daa6a2f28a2", "fileid": "https://r2.ropensci.org/d8e73a9bc1be8203a9c7d43660dc88d27b093caa54245c97e5f01964b672f946", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thijsjanzen/actions/runs/38126301956" }, { "r": "4.6.1", "os": "win", "version": "1.4.10", "date": "2026-10-11T08:57:35.000Z", "commit": "a70bad0bc10b829f8586d32dcc309daa6a2f28a2", "fileid": "https://r2.ropensci.org/82c9032afff352e30147976b821e1c02b22c2b6b20cdb04f57f4ce7428154e88", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thijsjanzen/actions/runs/38126301956" } ] }