{ "_id": "6a156386acfb0bcc41d614fa", "Package": "ashapesampler", "Title": "Generating Alpha Shapes", "Version": "1.0.0", "Authors@R": "c(person(\"Emily\", \"Winn-Nunez\", email=\"emily_winn-nunez@brown.edu\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-6759-5406\")), person(\"Lorin\", \"Crawford\",\nemail=\"lorin_crawford@brown.edu\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-0178-8242\")))", "Description": "Understanding morphological variation is an important task\nin many applications. Recent studies in computational biology\nhave focused on developing computational tools for the task of\nsub-image selection which aims at identifying structural\nfeatures that best describe the variation between classes of\nshapes. A major part in assessing the utility of these\napproaches is to demonstrate their performance on both\nsimulated and real datasets. However, when creating a model for\nshape statistics, real data can be difficult to access and the\nsample sizes for these data are often small due to them being\nexpensive to collect. Meanwhile, the landscape of current shape\nsimulation methods has been mostly limited to approaches that\nuse black-box inference---making it difficult to systematically\nassess the power and calibration of sub-image models. In this R\npackage, we introduce the alpha-shape sampler: a probabilistic\nframework for simulating realistic 2D and 3D shapes based on\nprobability distributions which can be learned from real data\nor explicitly stated by the user. The 'ashapesampler' package\nsupports two mechanisms for sampling shapes in two and three\ndimensions. The first, empirically sampling based on an\nexisting data set, was highlighted in the original main text of\nthe paper. The second, probabilistic sampling from a known\ndistribution, is the computational implementation of the theory\nderived in that paper. Work based on Winn-Nunez et al. (2024)\n.", "License": "GPL (>= 3)", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-26 09:05:56 UTC", "User": "root" }, "Author": "Emily Winn-Nunez [aut, cre]\n(), Lorin Crawford [aut]\n()", "Maintainer": "Emily Winn-Nunez ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2024-01-31 02:30:57 UTC", "RemoteUrl": "https://github.com/cran/ashapesampler", "RemoteRef": "HEAD", "RemoteSha": "1c423b30ed10a78b08f40fa3ca37b4016523e3f1", "MD5sum": "351504d689f41c129168d9a6d37f8c2b", "_user": "cran", "_type": "src", "_file": "ashapesampler_1.0.0.tar.gz", "_fileid": "f23b7d3e319bd7dead8a273f30eb4c5951bf7e4e27fc83d5a97feb9d2c1f004c", "_filesize": 1912985, "_sha256": "f23b7d3e319bd7dead8a273f30eb4c5951bf7e4e27fc83d5a97feb9d2c1f004c", "_created": "2026-05-26T09:05:56.000Z", "_published": "2026-05-26T09:10:30.798Z", "_distro": "noble", "_jobs": [ { "job": 77842101100, "time": 241, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7213122350" }, { "job": 77842101158, "time": 229, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7213117759" }, { "job": 77841168047, "time": 338, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7213041332" }, { "job": 77842101200, "time": 175, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7213099998" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26442587296", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/ashapesampler", "_commit": { "id": "1c423b30ed10a78b08f40fa3ca37b4016523e3f1", "author": "Emily Winn-Nunez ", "committer": "cran-robot ", "message": "version 1.0.0\n", "time": 1706668257 }, "_maintainer": { "name": "Emily Winn-Nunez", "email": "emily_winn-nunez@brown.edu", "orcid": "0000-0001-6759-5406" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.1.0", "role": "Depends" }, { "package": "pracma", "role": "Imports" }, { "package": "alphahull", "role": "Imports" }, { "package": "alphashape3d", "role": "Imports" }, { "package": "truncnorm", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "Rvcg", "role": "Imports" }, { "package": "TDA", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "rgl", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 198, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ashapesampler" }, "_searchresults": 8, "_rbuild": "4.6.0", "_assets": [ "extra/ashapesampler.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2024-01-30" } ], "_exports": [ "calc_overlap_2D", "calc_overlap_3D", "count_neighbors", "euclid_dists_point_cloud_2D", "euclid_dists_point_cloud_3D", "extract_complex_edges", "extract_complex_faces", "extract_complex_tet", "extreme_pts", "generate_ashape2d", "generate_ashape3d", "get_alpha_complex", "n_bound_connect_2D", "n_bound_connect_3D", "n_bound_homology_2D", "n_bound_homology_3D", "read_alpha_txt", "readOFF", "runif_annulus", "runif_ball_3D", "runif_cube", "runif_disk", "runif_shell_3D", "runif_square", "sampling2Dashape", "sampling3Dashape", "tau_bound", "write_alpha_txt" ], "_help": [ { "page": "calc_overlap_2D", "title": "Calculate Overlap 2D", "topics": [ "calc_overlap_2D" ] }, { "page": "calc_overlap_3D", "title": "calculate overlap in three dimensions (calc_overlap_3D)", "topics": [ "calc_overlap_3D" ] }, { "page": "cap_intersect_vol", "title": "Intersection of spheres", "topics": [ "cap_intersect_vol" ] }, { "page": "circ_face_2D", "title": "Circumcenter face - three points in 2D Given 3 sets of coordinates, calculates the circumcenter", "topics": [ "circ_face_2D" ] }, { "page": "circ_face_3D", "title": "Circumcenter face - three points in 3D Given 3 sets of coordinates, calculates the circumcenter", "topics": [ "circ_face_3D" ] }, { "page": "circ_tet_3D", "title": "Circumcenter tetrahedron - 4 points in 3D Given 3D coordinates of 4 points, calculates circumcenter", "topics": [ "circ_tet_3D" ] }, { "page": "circle_overlap_cc", "title": "Circle Overlap Centered on Circumference", "topics": [ "circle_overlap_cc" ] }, { "page": "circle_overlap_ia", "title": "Circle Overlap Inner Annulus", "topics": [ "circle_overlap_ia" ] }, { "page": "circumcenter_face", "title": "circumcenter Face", "topics": [ "circumcenter_face" ] }, { "page": "circumcenter_tet", "title": "circumcenter Tetrahedra", "topics": [ "circumcenter_tet" ] }, { "page": "count_neighbors", "title": "Neighbors function - finds number of neighbors for each point in point cloud.", "topics": [ "count_neighbors" ] }, { "page": "euclid_dists_point_cloud_2D", "title": "Euclidean Distance Point Cloud 2D", "topics": [ "euclid_dists_point_cloud_2D" ] }, { "page": "euclid_dists_point_cloud_3D", "title": "Euclidean Distance Point Cloud 3D", "topics": [ "euclid_dists_point_cloud_3D" ] }, { "page": "extract_complex_edges", "title": "Returns the edges of complex.", "topics": [ "extract_complex_edges" ] }, { "page": "extract_complex_faces", "title": "Returns faces of complex.", "topics": [ "extract_complex_faces" ] }, { "page": "extract_complex_tet", "title": "Returns tetrahedra of complex (3 dimensions)", "topics": [ "extract_complex_tet" ] }, { "page": "extreme_pts", "title": "Extreme points Finds the boundary points of a simplicial complex", "topics": [ "extreme_pts" ] }, { "page": "generate_ashape2d", "title": "Generate 2D alpha shape", "topics": [ "generate_ashape2d" ] }, { "page": "generate_ashape3d", "title": "Generate 3D alpha shape", "topics": [ "generate_ashape3d" ] }, { "page": "get_alpha_complex", "title": "Get alpha complex", "topics": [ "get_alpha_complex" ] }, { "page": "get_area", "title": "Get area", "topics": [ "get_area" ] }, { "page": "get_volume", "title": "Get volume", "topics": [ "get_volume" ] }, { "page": "n_bound_connect_2D", "title": "n Bound Connect 2D", "topics": [ "n_bound_connect_2D" ] }, { "page": "n_bound_connect_3D", "title": "N Bound Connect 3D", "topics": [ "n_bound_connect_3D" ] }, { "page": "n_bound_homology_2D", "title": "n Bound Homology 2D", "topics": [ "n_bound_homology_2D" ] }, { "page": "n_bound_homology_3D", "title": "n Bound Homology 3D", "topics": [ "n_bound_homology_3D" ] }, { "page": "read_alpha_txt", "title": "Read alpha text file", "topics": [ "read_alpha_txt" ] }, { "page": "readOFF", "title": "Read OFF File", "topics": [ "readOFF" ] }, { "page": "runif_annulus", "title": "Uniform Sampling from Annulus", "topics": [ "runif_annulus" ] }, { "page": "runif_ball_3D", "title": "Uniform Ball 3D", "topics": [ "runif_ball_3D" ] }, { "page": "runif_cube", "title": "r Uniform Cube", "topics": [ "runif_cube" ] }, { "page": "runif_disk", "title": "Uniform sampling from disk", "topics": [ "runif_disk" ] }, { "page": "runif_shell_3D", "title": "Uniform Shell 3D", "topics": [ "runif_shell_3D" ] }, { "page": "runif_square", "title": "Uniform Sampling from Square", "topics": [ "runif_square" ] }, { "page": "sampling2Dashape", "title": "Sampling 2D alpha shapes", "topics": [ "sampling2Dashape" ] }, { "page": "sampling3Dashape", "title": "Sample 3D alpha shapes", "topics": [ "sampling3Dashape" ] }, { "page": "sphere_overlap_cs", "title": "sphere overlap when one is centered on circumference of the other", "topics": [ "sphere_overlap_cs" ] }, { "page": "sphere_overlap_is", "title": "sphere overlap inner shell", "topics": [ "sphere_overlap_is" ] }, { "page": "spherical_cap", "title": "Spherical cap", "topics": [ "spherical_cap" ] }, { "page": "tau_bound", "title": "tau_bound", "topics": [ "tau_bound" ] }, { "page": "write_alpha_txt", "title": "Write Alpha Text file", "topics": [ "write_alpha_txt" ] } ], "_readme": "https://github.com/cran/ashapesampler/raw/HEAD/README.md", "_rundeps": [ "abind", "alphahull", "alphashape3d", "base64enc", "BH", "bslib", "cachem", "cli", "codetools", "cpp11", "deldir", "digest", "doParallel", "dplyr", "evaluate", "farver", "fastmap", "FNN", "fontawesome", "foreach", "fs", "generics", "geometry", "ggplot2", "glue", "gtable", "highr", "htmltools", "htmlwidgets", "igraph", "interp", "isoband", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lifecycle", "linprog", "lpSolve", "magic", "magrittr", "Matrix", "memoise", "mime", "pillar", "pkgconfig", "polyclip", "pracma", "R.methodsS3", "R.oo", "R.utils", "R6", "RANN", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppProgress", "rgl", "rlang", "rmarkdown", "Rvcg", "S7", "sass", "scales", "sgeostat", "sp", "spatstat.data", "spatstat.geom", "spatstat.random", "spatstat.sparse", "spatstat.univar", "spatstat.utils", "splancs", "TDA", "tensor", "tibble", "tidyselect", "tinytex", "truncnorm", "utf8", "vctrs", "viridisLite", "withr", "xfun", "yaml" ], "_vignettes": [ { "source": "annulus_demo.Rmd", "filename": "annulus_demo.html", "title": "annulus_demo", "engine": "knitr::rmarkdown", "headings": [], "created": "2024-01-31 02:30:57", "modified": "2024-01-31 02:30:57", "commits": 1 }, { "source": "probability_demo_2D.Rmd", "filename": "probability_demo_2D.html", "title": "probability_demo_2D", "engine": "knitr::rmarkdown", "headings": [], "created": "2024-01-31 02:30:57", "modified": "2024-01-31 02:30:57", "commits": 1 }, { "source": "probability_demo_3D.Rmd", "filename": "probability_demo_3D.html", "title": "probability_demo_3D", "engine": "knitr::rmarkdown", "headings": [], "created": "2024-01-31 02:30:57", "modified": "2024-01-31 02:30:57", "commits": 1 }, { "source": "torus_demo.Rmd", "filename": "torus_demo.html", "title": "torus_demo", "engine": "knitr::rmarkdown", "headings": [], "created": "2024-01-31 02:30:57", "modified": "2024-01-31 02:30:57", "commits": 1 } ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "ashapesampler", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-05-26T09:08:55.000Z", "distro": "noble", "commit": "1c423b30ed10a78b08f40fa3ca37b4016523e3f1", "fileid": "d9aba059820c1ab9ab3a62c7f414928437a4f956bbc517c652473237a6e250c8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26442587296" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-05-26T09:08:36.000Z", "distro": "noble", "commit": "1c423b30ed10a78b08f40fa3ca37b4016523e3f1", "fileid": "e5743a6ec72fe8c3377f2622fad99c745a81270c32c26c23fe0921dd6373bcf3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26442587296" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-05-26T09:09:07.000Z", "commit": "1c423b30ed10a78b08f40fa3ca37b4016523e3f1", "fileid": "de408c605c3858ce30d4c48f096c85cf0a21151ba57151241d4e81a352ebc6c1", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26442587296" } ] }