{ "_id": "6a1fe7d1b401979e7343d56d", "Type": "Package", "Package": "PhaseTypeR", "Title": "General-Purpose Phase-Type Functions", "Version": "1.0.5.9000", "Authors@R": "c(\nperson(\"Iker\", \"Rivas-González\", , \"ikerrivas96@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0515-0628\")),\nperson(\"Asger\", \"Hobolth\", , \"asger@math.au.dk\", role = \"aut\"),\nperson(\"Lars Nørvang\", \"Andersen\", , \"larsa@math.au.dk\", role = \"aut\"),\nperson(\"Colin\", \"Guetemme\", , \"colin.guetemme@live.fr\", role = \"aut\")\n)", "Maintainer": "Iker Rivas-González ", "Description": "General implementation of core function from phase-type\ntheory. 'PhaseTypeR' can be used to model continuous and\ndiscrete phase-type distributions, both univariate and\nmultivariate. The package includes functions for outputting the\nmean and (co)variance of phase-type distributions; their\ndensity, probability and quantile functions; functions for\nrandom draws; functions for reward-transformation; and\nfunctions for plotting the distributions as networks. For more\ninformation on these functions please refer to Bladt and\nNielsen (2017, ISBN: 978-1-4939-8377-3) and Campillo Navarro\n(2019)\n.", "License": "GPL-3", "URL": "https://rivasiker.github.io/PhaseTypeR/,\nhttps://github.com/rivasiker/PhaseTypeR", "BugReports": "https://github.com/rivasiker/PhaseTypeR/issues", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://rivasiker.r-universe.dev", "Date/Publication": "2023-04-27 08:31:59 UTC", "RemoteUrl": "https://github.com/rivasiker/phasetyper", "RemoteRef": "HEAD", "RemoteSha": "a370d2070057985b69cf17483cd24888ca39b1e9", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 08:32:50 UTC", "User": "root" }, "Author": "Iker Rivas-González [aut, cre] (ORCID:\n),\nAsger Hobolth [aut],\nLars Nørvang Andersen [aut],\nColin Guetemme [aut]", "MD5sum": "89b5e3b16893bf6677cee2df984b2bba", "_user": "rivasiker", "_type": "src", "_file": "PhaseTypeR_1.0.5.9000.tar.gz", "_fileid": "a4b86e726c349bfd72d7887fae1c9876342de9e98a498db3852a81b12e19b3fb", "_filesize": 2767910, "_sha256": "a4b86e726c349bfd72d7887fae1c9876342de9e98a498db3852a81b12e19b3fb", "_created": "2026-06-03T08:32:50.000Z", "_published": "2026-06-03T08:37:37.632Z", "_distro": "noble", "_jobs": [ { "job": 79253741646, "time": 134, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7379602595" }, { "job": 79253741757, "time": 129, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7379600760" }, { "job": 79253741722, "time": 183, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7379617050" }, { "job": 79253741737, "time": 226, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7379628382" }, { "job": 79253041608, "time": 240, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7379554396" }, { "job": 79253741686, "time": 109, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7379594322" }, { "job": 79253741759, "time": 89, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7379587425" }, { "job": 79253741752, "time": 106, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7379593615" }, { "job": 79253741881, "time": 125, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7379599912" } ], "_buildurl": "https://github.com/r-universe/rivasiker/actions/runs/26873038770", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/rivasiker/phasetyper", "_commit": { "id": "a370d2070057985b69cf17483cd24888ca39b1e9", "author": "rivasiker ", "committer": "rivasiker ", "message": "Update citation\n", "time": 1682584319 }, "_maintainer": { "name": "Iker Rivas-González", "email": "ikerrivas96@gmail.com", "login": "rivasiker", "orcid": "0000-0002-0515-0628", "description": "Postdoctoral Researcher at Max Planck Institute of Evolutionary Anthropology ", "uuid": 54534843 }, "_registered": true, "_dependencies": [ { "package": "expm", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "partitions", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "rivasiker", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 2, "_contributors": [ { "user": "rivasiker", "count": 317, "uuid": 54534843 }, { "user": "colinguetemme", "count": 26, "uuid": 44171613 }, { "user": "larsnandersen", "count": 1, "uuid": 4065590 } ], "_userbio": { "uuid": 54534843, "type": "user", "name": "Iker Rivas-González", "description": "Postdoctoral Researcher at Max Planck Institute of Evolutionary Anthropology " }, "_downloads": { "count": 196, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PhaseTypeR" }, "_devurl": "https://github.com/rivasiker/phasetyper", "_pkgdown": "https://rivasiker.github.io/PhaseTypeR/", "_searchresults": 39, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/PhaseTypeR.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/rivasiker/phasetyper", "_realowner": "rivasiker", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2021-11-30" }, { "version": "1.0.1", "date": "2021-12-06" }, { "version": "1.0.2", "date": "2022-02-10" }, { "version": "1.0.3", "date": "2022-07-14" }, { "version": "1.0.4", "date": "2022-07-21" } ], "_exports": [ "dDPH", "dMDPH", "dMPH", "dPH", "DPH", "MDPH", "MPH", "pDPH", "PH", "phase_type_to_network", "pMDPH", "pMPH", "pPH", "qDPH", "qMDPH", "qMPH", "qPH", "rDPH", "reward_phase_type", "rFullDPH", "rFullMDPH", "rFullMPH", "rFullPH", "rMDPH", "rMPH", "rPH", "var" ], "_help": [ { "page": "DPH_functions", "title": "The Univariate Discrete Phase-Type Distribution", "topics": [ "dDPH", "DPH_functions", "pDPH", "qDPH", "rDPH", "rFullDPH" ] }, { "page": "generator_functions", "title": "The phase-type distribution", "topics": [ "DPH", "generator_functions", "MDPH", "MPH", "PH" ] }, { "page": "MDPH_functions", "title": "The Multivariate Discrete Phase-Type Distribution", "topics": [ "dMDPH", "MDPH_functions", "pMDPH", "qMDPH", "rFullMDPH", "rMDPH" ] }, { "page": "mean", "title": "Mean of Phase-Type Distributions", "topics": [ "mean", "mean.cont_phase_type", "mean.disc_phase_type", "mean.mult_cont_phase_type", "mean.mult_disc_phase_type" ] }, { "page": "MPH_functions", "title": "The Multivariate Continuous Phase-Type Distribution", "topics": [ "dMPH", "MPH_functions", "pMPH", "qMPH", "rFullMPH", "rMPH" ] }, { "page": "PH_functions", "title": "The Univariate Continuous Phase-Type Distribution", "topics": [ "dPH", "PH_functions", "pPH", "qPH", "rFullPH", "rPH" ] }, { "page": "phase_type_to_network", "title": "Phase-type distribution to network", "topics": [ "phase_type_to_network" ] }, { "page": "print.cont_phase_type", "title": "Print method for phase-type objects", "topics": [ "print.cont_phase_type", "print.disc_phase_type", "print.mult_cont_phase_type", "print.mult_disc_phase_type" ] }, { "page": "reward_phase_type", "title": "Transformation of Phase-Type Distributions via Rewards", "topics": [ "reward_phase_type" ] }, { "page": "summary.cont_phase_type", "title": "Pretty summary of the 'cont_phase_type' class.", "topics": [ "summary.cont_phase_type" ] }, { "page": "summary.disc_phase_type", "title": "Pretty summary of the 'disc_phase_type' class.", "topics": [ "summary.disc_phase_type" ] }, { "page": "summary.mult_cont_phase_type", "title": "Pretty summary of the 'mult_cont_phase_type' class.", "topics": [ "summary.mult_cont_phase_type" ] }, { "page": "summary.mult_disc_phase_type", "title": "Pretty summary of the 'mult_dist_phase_type' class.", "topics": [ "summary.mult_disc_phase_type" ] }, { "page": "var", "title": "Variance and Covariance of Phase-Type Distributions", "topics": [ "var", "var.cont_phase_type", "var.disc_phase_type", "var.mult_cont_phase_type", "var.mult_disc_phase_type" ] } ], "_readme": "https://github.com/rivasiker/phasetyper/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "expm", "glue", "igraph", "lattice", "lifecycle", "magrittr", "Matrix", "pkgconfig", "rlang", "vctrs" ], "_vignettes": [ { "source": "PhaseTypeR.Rmd", "filename": "PhaseTypeR.html", "title": "PhaseTypeR", "engine": "knitr::rmarkdown", "headings": [ "Preface", "1. Introduction", "2. The phase-type objects", "3. Univariate phase-type distributions", "3.1. The continuous univariate phase-type", "3.2. The discrete univariate phase-type", "4. Reward transformations", "4.1 Strictly positive rewards for continuous phase-type distribution", "4.2. Strictly positive integer-valued rewards for the discrete phase-type distribution", "4.3. Non-negative reward transformation for continuous phase-type distribution", "4.4. Non-negative integer valued reward transformation for discrete phase-type distribution", "5. Multivariate phase-type distributions", "5.1. The multivariate continuous phase-type", "5.2 The discrete multivariate phase-type", "6. Full simulation from a phase-type distribution", "Get one simulation from a phase-type", "References" ], "created": "2021-06-21 10:31:31", "modified": "2022-07-17 17:16:15", "commits": 14 }, { "source": "a2_pop_gen_iker.Rmd", "filename": "a2_pop_gen_iker.html", "title": "Using PhaseTypeR for population genetics", "author": "Iker Rivas-González", "engine": "knitr::rmarkdown", "headings": [ "1. Introduction to the package", "2. The Univariate Continuous Phase-Type Distribution: $T_{MRCA}$ and $T_{Total}$", "2.1. Theoretical background", "2.2. Time until the most recent common ancestor ($T_{MRCA}$)", "$$\\boldsymbol", "2.3. Total tree length ($T_{Total}$) and the reward-transformation", "2.4. Density, distribution and quantile functions", "3. The Univariate Discrete Phase-Type Distribution: $S_{total}$, $\\xi_i$ and $\\xi_{k+}$", "3.1. Theoretical background", "3.2. Total number of segregating sites ($S_{total}$)", "3.3. i-tons ($\\xi_i$)", "3.4. Density, distribution and quantile functions", "4. The Multivariate Continuous Phase-Type Distribution: $Y_i$", "References" ], "created": "2021-10-06 09:43:28", "modified": "2021-11-22 09:37:45", "commits": 3 }, { "source": "a3_phasetypeR_SFS.Rmd", "filename": "a3_phasetypeR_SFS.html", "title": "Using PhaseTypeR for the site frequency spectrum", "engine": "knitr::rmarkdown", "headings": [ "Figure 1", "Figure 2", "Figure 5", "Figure 7", "Figure 8", "Auxiliary functions" ], "created": "2021-10-06 09:43:28", "modified": "2023-02-22 09:11:45", "commits": 9 } ], "_score": 5.3692158574101425, "_indexed": true, "_nocasepkg": "phasetyper", "_universes": [ "rivasiker" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.5.9000", "date": "2026-06-03T08:34:58.000Z", "distro": "noble", "commit": "a370d2070057985b69cf17483cd24888ca39b1e9", "fileid": "7d2a16a8254b057b072f0611de436859bcdb54226db98004c042aff086a623ba", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rivasiker/actions/runs/26873038770" }, { "r": "4.6.0", "os": "linux", "version": "1.0.5.9000", "date": "2026-06-03T08:34:48.000Z", "distro": "noble", "commit": "a370d2070057985b69cf17483cd24888ca39b1e9", "fileid": "999826e772d5cb7d84ff13a4632455c02576ef4beabc68d27be6c2176facb5a7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rivasiker/actions/runs/26873038770" }, { "r": "4.5.3", "os": "mac", "version": "1.0.5.9000", "date": "2026-06-03T08:35:37.000Z", "commit": "a370d2070057985b69cf17483cd24888ca39b1e9", "fileid": "1a7258c757aefd44a58bd186ec9eb81171e0cf5067137b0f9e93d27adb24a6ef", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rivasiker/actions/runs/26873038770" }, { "r": "4.6.0", "os": "mac", "version": "1.0.5.9000", "date": "2026-06-03T08:36:04.000Z", "commit": "a370d2070057985b69cf17483cd24888ca39b1e9", "fileid": "ad07734f330f686c33fd15e2b5d40b01c3dde1c311c8b03b97858c9104d291b3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rivasiker/actions/runs/26873038770" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.5.9000", "date": "2026-06-03T08:35:01.000Z", "commit": "a370d2070057985b69cf17483cd24888ca39b1e9", "fileid": "f5f46d0afb89b10f455fa3388e8dc6dfe57cb449de3805e73995913e72fa0d95", "status": "success", "buildurl": "https://github.com/r-universe/rivasiker/actions/runs/26873038770" }, { "r": "4.7.0", "os": "win", "version": "1.0.5.9000", "date": "2026-06-03T08:34:05.000Z", "commit": "a370d2070057985b69cf17483cd24888ca39b1e9", "fileid": "e61a048163d4461dc62094f52978c528bf7f8787910f309315c8768b49ee50bb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rivasiker/actions/runs/26873038770" }, { "r": "4.5.3", "os": "win", "version": "1.0.5.9000", "date": "2026-06-03T08:34:22.000Z", "commit": "a370d2070057985b69cf17483cd24888ca39b1e9", "fileid": "14d6145d4417ac95e3f11196f487d9a1fa97030c0c874ab1795cc0f012224d8b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rivasiker/actions/runs/26873038770" }, { "r": "4.6.0", "os": "win", "version": "1.0.5.9000", "date": "2026-06-03T08:34:40.000Z", "commit": "a370d2070057985b69cf17483cd24888ca39b1e9", "fileid": "03db7bb9b8ae94db00b8f7abe9fa0f8dd54bc53e26efc383c4a62272f08336a8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rivasiker/actions/runs/26873038770" } ] }