{ "_id": "6ac6c850de46216d5edcd3fb", "Package": "phutil", "Title": "Persistence Homology Utilities", "Version": "0.0.3.9000", "Authors@R": "c(\nperson(\"Aymeric\", \"Stamm\", , \"aymeric.stamm@cnrs.fr\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8725-3654\")),\nperson(\"Jason Cory\", \"Brunson\", , \"cornelioid@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-3126-9494\")),\nperson(\"Michael\", \"Kerber\", role = \"ctb\", comment = \"HERA C++ code\"),\nperson(\"Dmitriy\", \"Morozov\", role = \"ctb\", comment = \"HERA C++ code\"),\nperson(\"Arnur\", \"Nigmetov\", role = \"ctb\", comment = \"HERA C++ code\")\n)", "Description": "A low-level package for hosting persistence data. It is\npart of the 'TDAverse' suite of packages, which is designed to\nprovide a collection of packages for enabling machine learning\nand data science tasks using persistent homology. Implements a\nclass for hosting persistence data, a number of coercers from\nand to already existing and used data structures from other\npackages and functions to compute distances between persistence\ndiagrams. A formal definition and study of bottleneck and\nWasserstein distances can be found in Bubenik, Scott and\nStanley (2023) . Their\nimplementation in 'phutil' relies on the 'C++' Hera library\ndeveloped by Kerber, Morozov and Nigmetov (2017)\n.", "License": "MIT + file LICENSE", "URL": "https://github.com/tdaverse/phutil,\nhttps://tdaverse.github.io/phutil/", "BugReports": "https://github.com/tdaverse/phutil/issues", "VignetteBuilder": "quarto", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "Config/roxygen2/version": "8.1.0", "Repository": "https://tdaverse.r-universe.dev", "Date/Publication": "2026-10-07 20:25:44 UTC", "RemoteUrl": "https://github.com/tdaverse/phutil", "RemoteRef": "HEAD", "RemoteSha": "39d259f99a99d5559babf6463314e23bbe8b8b54", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-07 22:21:11 UTC", "User": "root" }, "Author": "Aymeric Stamm [aut, cre] (ORCID:\n),\nJason Cory Brunson [aut] (ORCID:\n),\nMichael Kerber [ctb] (HERA C++ code),\nDmitriy Morozov [ctb] (HERA C++ code),\nArnur Nigmetov [ctb] (HERA C++ code)", "Maintainer": "Aymeric Stamm ", "_user": "tdaverse", "_type": "src", "_file": "phutil_0.0.3.9000.tar.gz", "_fileid": "https://r2.ropensci.org/54920a358ca0975c65a89b03662236fdeeb753890bdaf208e49563de0163cb76", "_filesize": 627220, "_sha256": "54920a358ca0975c65a89b03662236fdeeb753890bdaf208e49563de0163cb76", "_expires": "2027-01-15T22:31:42.000Z", "_created": "2026-10-07T22:21:11.000Z", "_published": "2026-10-07T22:31:44.486Z", "_buildurl": "https://github.com/r-universe/tdaverse/actions/runs/37695248921", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 113046691667, "time": 152, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11515377096" }, { "job": 113046691738, "time": 151, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11515556477" }, { "job": 113046691568, "time": 115, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11514968233" }, { "job": 113046691542, "time": 178, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11515412041" }, { "job": 113046691626, "time": 180, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11514868519" }, { "job": 113046691656, "time": 248, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11515019458" }, { "job": 113046691634, "time": 192, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11515746831" }, { "job": 113046691696, "time": 244, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11515058689" }, { "job": 113045362172, "time": 218, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11514837926" }, { "job": 113046691419, "time": 116, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11516030414" }, { "job": 113046691830, "time": 389, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11514733964" }, { "job": 113046691605, "time": 287, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11515123111" }, { "job": 113046691749, "time": 157, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11514623877" }, { "job": 113046691772, "time": 364, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11514978958" }, { "job": 113046691674, "time": 145, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11514753715" } ], "_upstream": "https://github.com/tdaverse/phutil", "_commit": { "id": "39d259f99a99d5559babf6463314e23bbe8b8b54", "author": "Aymeric Stamm ", "committer": "Aymeric Stamm ", "message": "Increment version number to 0.0.3.9000\n", "time": 1791404744 }, "_maintainer": { "name": "Aymeric Stamm", "email": "aymeric.stamm@cnrs.fr", "login": "astamm", "mastodon": "@aymeric_stamm@mastodon.social", "bluesky": "@aymeric-stamm.bsky.social", "orcid": "0000-0002-8725-3654", "description": "", "uuid": 6044838 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "BH", "role": "LinkingTo" }, { "package": "cpp11", "role": "LinkingTo" }, { "package": "cli", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "microbenchmark", "role": "Suggests" }, { "package": "quarto", "role": "Suggests" }, { "package": "TDA", "role": "Suggests" }, { "package": "tdaunif", "role": "Suggests" }, { "package": "tinysnapshot", "role": "Suggests" }, { "package": "tinytest", "role": "Suggests" } ], "_owner": "tdaverse", "_selfowned": true, "_usedby": 2, "_updates": [ { "week": "2026-16", "n": 7 }, { "week": "2026-28", "n": 2 }, { "week": "2026-41", "n": 8 } ], "_tags": [ { "name": "v0.0.2", "date": "2026-04-14" }, { "name": "v0.0.3", "date": "2026-10-06" } ], "_stars": 0, "_contributors": [ { "user": "astamm", "count": 202, "uuid": 6044838 }, { "user": "corybrunson", "count": 54, "uuid": 7768027 }, { "user": "a1danbryant", "count": 11, "uuid": 124316415 } ], "_userbio": { "uuid": 74478337, "type": "organization", "name": "tdaverse", "followers": 14, "description": "an inceptive R package collection for computational topology and topological data analysis" }, "_downloads": { "count": 398, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/phutil" }, "_devurl": "https://github.com/tdaverse/phutil", "_pkgdown": "https://tdaverse.github.io/phutil/", "_searchresults": 32, "_quarto": true, "_topics": [ "quarto", "cpp", "openmp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/phutil.html", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/tdaverse/phutil", "_realowner": "tdaverse", "_cranurl": true, "_releases": [ { "version": "0.0.1", "date": "2025-05-15" }, { "version": "0.0.2", "date": "2026-04-17" }, { "version": "0.0.3", "date": "2026-10-06" } ], "_exports": [ "as_diagram", "as_persistence", "as_persistence_set", "bottleneck_distance", "bottleneck_pairwise_distances", "get_pairs", "kantorovich_distance", "kantorovich_pairwise_distances", "wasserstein_distance", "wasserstein_pairwise_distances" ], "_datasets": [ { "name": "arch_spirals", "title": "A sample of persistence diagrams from the arch spiral", "object": "arch_spirals", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "noisy_circle_points", "title": "Toy Data: Noisy circle", "object": "noisy_circle_points", "class": [ "matrix", "array" ], "fields": [ "x", "y" ], "rows": 100, "table": true, "tojson": true }, { "name": "noisy_circle_ripserr", "title": "Toy Data: Noisy circle", "object": "noisy_circle_ripserr", "class": [ "PHom", "data.frame" ], "fields": [ "dimension", "birth", "death" ], "rows": 101, "table": true, "tojson": true }, { "name": "noisy_circle_tda_rips", "title": "Toy Data: Noisy circle", "object": "noisy_circle_tda_rips", "class": [ "list" ], "fields": [], "table": true, "tojson": false }, { "name": "persistence_sample", "title": "Toy Data: A sample of persistence diagrams", "object": "persistence_sample", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "trefoils", "title": "A sample of persistence diagrams from the trefoil", "object": "trefoils", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "arch_spirals", "title": "A sample of persistence diagrams from the arch spiral", "topics": [ "arch_spirals" ] }, { "page": "distances", "title": "Distances between two persistence diagrams", "topics": [ "bottleneck_distance", "distances", "kantorovich_distance", "wasserstein_distance" ] }, { "page": "noisy_circle", "title": "Toy Data: Noisy circle", "topics": [ "noisy_circle", "noisy_circle_points", "noisy_circle_ripserr", "noisy_circle_tda_rips" ] }, { "page": "pairwise-distances", "title": "Pairwise distances within a set of persistence diagrams", "topics": [ "bottleneck_pairwise_distances", "kantorovich_pairwise_distances", "pairwise-distances", "wasserstein_pairwise_distances" ] }, { "page": "persistence", "title": "An 'S3' class for storing persistence data", "topics": [ "as.data.frame.persistence", "as.matrix.persistence", "as_diagram", "as_diagram.persistence", "as_diagram.PHom", "as_persistence", "as_persistence.data.frame", "as_persistence.diagram", "as_persistence.hclust", "as_persistence.list", "as_persistence.matrix", "as_persistence.persistence", "as_persistence.PHom", "format.persistence", "get_pairs", "persistence", "print.persistence" ] }, { "page": "persistence_sample", "title": "Toy Data: A sample of persistence diagrams", "topics": [ "persistence_sample" ] }, { "page": "persistence-set", "title": "An 'S3' class object for storing sets of persistence diagrams", "topics": [ "as_persistence_set", "format.persistence_set", "persistence-set", "print.persistence_set" ] }, { "page": "trefoils", "title": "A sample of persistence diagrams from the trefoil", "topics": [ "trefoils" ] } ], "_readme": "https://github.com/tdaverse/phutil/raw/HEAD/README.md", "_rundeps": [ "BH", "cli", "cpp11", "rlang" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "persistence-class.qmd", "filename": "persistence-class.html", "title": "The persistence class", "engine": "quarto::html", "headings": [ "Structure of the class", "Supported inputs" ], "created": "2025-05-02 12:02:41", "modified": "2025-05-02 12:02:41", "commits": 1 }, { "source": "validation-benchmark.qmd", "filename": "validation-benchmark.html", "title": "Validation and Benchmark of Wasserstein Distances", "engine": "quarto::html", "headings": [ "Definitions", "Validation", "Distances between nontrivial diagrams", "Distances from the trivial diagram", "Benchmarks", "References" ], "created": "2025-04-27 10:27:03", "modified": "2025-09-01 10:10:35", "commits": 6 } ], "_score": 6.061452479087193, "_indexed": true, "_nocasepkg": "phutil", "_universes": [ "tdaverse", "astamm" ], "_previous": "0.0.3", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.3.9000", "date": "2026-10-07T22:23:49.000Z", "distro": "resolute", "arch": "aarch64", "commit": "39d259f99a99d5559babf6463314e23bbe8b8b54", "fileid": "https://r2.ropensci.org/31a9004304dd758085dbc16d0126945e946e662e90383f061c1ed9220512b753", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tdaverse/actions/runs/37695248921" }, { "r": "4.7.0", "os": "linux", "version": "0.0.3.9000", "date": "2026-10-07T22:23:37.000Z", "distro": "resolute", "arch": "x86_64", "commit": "39d259f99a99d5559babf6463314e23bbe8b8b54", "fileid": "https://r2.ropensci.org/3ff8574c95bd76f086ec89dddfc5eaaf1d6eb73ddbc9ca661047bbe3ea0e14ad", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tdaverse/actions/runs/37695248921" }, { "r": "4.6.1", "os": "linux", "version": "0.0.3.9000", "date": "2026-10-07T22:23:14.000Z", "distro": "resolute", "arch": "aarch64", "commit": "39d259f99a99d5559babf6463314e23bbe8b8b54", "fileid": "https://r2.ropensci.org/3aaed05ebeb6541ea68c1f9c7a99946d339dfe60977b127280529ce14a207e52", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tdaverse/actions/runs/37695248921" }, { "r": "4.6.1", "os": "linux", "version": "0.0.3.9000", "date": "2026-10-07T22:24:09.000Z", "distro": "resolute", "arch": "x86_64", "commit": "39d259f99a99d5559babf6463314e23bbe8b8b54", "fileid": "https://r2.ropensci.org/950fc38012974019702eb844d947e6eeeed4c7f5348595ee200c0fc354d7d093", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tdaverse/actions/runs/37695248921" }, { "r": "4.5.3", "os": "mac", "version": "0.0.3.9000", "date": "2026-10-07T22:26:17.000Z", "arch": "aarch64", "commit": "39d259f99a99d5559babf6463314e23bbe8b8b54", "fileid": "https://r2.ropensci.org/ba24ae1b6e573c27b74d2c868ad2a5306eb462d4e595da60ff2d54db89fca97e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tdaverse/actions/runs/37695248921" }, { "r": "4.5.3", "os": "mac", "version": "0.0.3.9000", "date": "2026-10-07T22:29:21.000Z", "arch": "x86_64", "commit": "39d259f99a99d5559babf6463314e23bbe8b8b54", "fileid": "https://r2.ropensci.org/fe748e350c8b9dbb9c15a5898ad96de7b4046ce72e3c5907ff35f7bde1596e08", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tdaverse/actions/runs/37695248921" }, { "r": "4.6.1", "os": "mac", "version": "0.0.3.9000", "date": "2026-10-07T22:28:11.000Z", "arch": "aarch64", "commit": "39d259f99a99d5559babf6463314e23bbe8b8b54", "fileid": "https://r2.ropensci.org/a6de087c4daa4a60e08d39d5eb0997f5b6bd86669f745d1e681b88fdda9bca61", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tdaverse/actions/runs/37695248921" }, { "r": "4.6.1", "os": "mac", "version": "0.0.3.9000", "date": "2026-10-07T22:28:28.000Z", "arch": "x86_64", "commit": "39d259f99a99d5559babf6463314e23bbe8b8b54", "fileid": "https://r2.ropensci.org/6daf8125c5b60ba3c75646138f6cb6a0aa5ab84e6208bd34c2b3b6f7659bdce1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tdaverse/actions/runs/37695248921" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.3.9000", "date": "2026-10-07T22:23:25.000Z", "arch": "emscripten", "commit": "39d259f99a99d5559babf6463314e23bbe8b8b54", "fileid": "https://r2.ropensci.org/4917e9bc2389af12a572bfabf0b54dc4f5ff54d2b89514471f4c5a5a1c05965a", "status": "success", "buildurl": "https://github.com/r-universe/tdaverse/actions/runs/37695248921" }, { "r": "4.7.0", "os": "win", "version": "0.0.3.9000", "date": "2026-10-07T22:27:23.000Z", "arch": "aarch64", "commit": "39d259f99a99d5559babf6463314e23bbe8b8b54", "fileid": "https://r2.ropensci.org/9e4da5e68ed45c2bd8a6bf9a3da6fcdcefde876d5b8ebef49236de0dcfa79089", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tdaverse/actions/runs/37695248921" }, { "r": "4.7.0", "os": "win", "version": "0.0.3.9000", "date": "2026-10-07T22:24:58.000Z", "arch": "x86_64", "commit": "39d259f99a99d5559babf6463314e23bbe8b8b54", "fileid": "https://r2.ropensci.org/839e2aef8d5222f0480b314bed417a4f9bdd1149dd15bf7e1d0ffd83baf6f829", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tdaverse/actions/runs/37695248921" }, { "r": "4.5.3", "os": "win", "version": "0.0.3.9000", "date": "2026-10-07T22:23:27.000Z", "arch": "x86_64", "commit": "39d259f99a99d5559babf6463314e23bbe8b8b54", "fileid": "https://r2.ropensci.org/d18cd3e00fd452657e233fdee30d123fc96adf33b48b0f3bc6ec3f1b2d6b6f1d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tdaverse/actions/runs/37695248921" }, { "r": "4.6.1", "os": "win", "version": "0.0.3.9000", "date": "2026-10-07T22:27:18.000Z", "arch": "aarch64", "commit": "39d259f99a99d5559babf6463314e23bbe8b8b54", "fileid": "https://r2.ropensci.org/13049d8c3124f3d73655ab9d4d6da88a2f268c67d574b3fa35e7cd8d0306c559", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tdaverse/actions/runs/37695248921" }, { "r": "4.6.1", "os": "win", "version": "0.0.3.9000", "date": "2026-10-07T22:23:14.000Z", "arch": "x86_64", "commit": "39d259f99a99d5559babf6463314e23bbe8b8b54", "fileid": "https://r2.ropensci.org/13ef58221cd4dfc81d99968e0e2cfdf80f1647065d7010a09226b8d50b68cd65", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tdaverse/actions/runs/37695248921" } ] }