{ "_id": "6a101a7facfb0bcc41c868e3", "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. 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"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", "description": "Scientific programmer at University of Groningen" }, "_downloads": { "count": 686, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/nLTT" }, "_mentions": 2, "_devurl": "https://github.com/thijsjanzen/nltt", "_searchresults": 61, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/nLTT.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_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 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