{ "_id": "6ab9637599f7aa8c6aa3a4fb", "Package": "ISPAT3D", "Type": "Package", "Title": "Spatial Conditional Association Networks in Registered Tumor\nVolumes", "Version": "0.3.1", "Authors@R": "person(\"Sagnik\", \"Bhadury\", email = \"bhadury@umich.edu\",\nrole = c(\"aut\", \"cre\"))", "Description": "Fits tumor-zone-specific conditional cell-density networks\nfrom registered three-dimensional multiplex imaging. An\nanisotropic Matern-3/2 Gaussian process is estimated per\nvariable and zone using a Vecchia likelihood on spatially\nbalanced anchors; predictions at all selected cells yield\nresidual covariance sufficient statistics. Gaussian maximum\nlikelihood then fits a shared-plus-zone factor covariance\nmodel. A matched section-wise planar fit uses the same selected\ncells and covariance estimator. This extends the spatially\ninformed cell-density analysis of Bhadury et al. (2026)\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "URL": "https://github.com/sagnikbhadury/ISPAT-3D", "BugReports": "https://github.com/sagnikbhadury/ISPAT-3D/issues", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-27 18:39:09 UTC", "User": "root" }, "Author": "Sagnik Bhadury [aut, cre]", "Maintainer": "Sagnik Bhadury ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-09-27 16:40:37 UTC", "RemoteUrl": "https://github.com/cran/ISPAT3D", "RemoteRef": "HEAD", "RemoteSha": "4bdee8cad8611848f11492d616c59438234e7dd5", "_user": "cran", "_type": "src", "_file": "ISPAT3D_0.3.1.tar.gz", "_fileid": "https://r2.ropensci.org/5c2c57fead8c04b03d1b147c6667e7d6387ba680918500779203b8fa0d021eae", "_filesize": 325119, "_sha256": "5c2c57fead8c04b03d1b147c6667e7d6387ba680918500779203b8fa0d021eae", "_expires": "2027-01-05T18:41:54.000Z", "_created": "2026-09-27T18:39:09.000Z", "_published": "2026-09-27T18:41:57.056Z", "_jobs": [ { "job": 108682238475, "time": 116, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10938589642" }, { "job": 108682238492, "time": 125, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10939565527" }, { "job": 108681670043, "time": 196, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10939630091" }, { "job": 108682238677, "time": 116, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10939052414" }, { "job": 108682238478, "time": 66, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10938997711" }, { "job": 108682238460, "time": 62, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10938564665" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/cran/actions/runs/36341235538", "_status": "success", "_upstream": "https://github.com/cran/ISPAT3D", "_commit": { "id": "4bdee8cad8611848f11492d616c59438234e7dd5", "author": "Sagnik Bhadury ", "committer": "cran-robot ", "message": "version 0.3.1\n", "time": 1790527237 }, "_maintainer": { "name": "Sagnik Bhadury", "email": "bhadury@umich.edu", "login": "rijubhadury", "description": "", "uuid": 146100465 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "gpboost", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "data.table", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-39", "n": 1 } ], "_tags": [ { "name": "0.3.1", "date": "2026-09-27" } ], "_stars": 0, "_contributors": [ { "user": "rijubhadury", "count": 1, "uuid": 146100465 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 630, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ISPAT3D" }, "_devurl": "https://github.com/sagnikbhadury/ispat-3d", "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ISPAT3D.html", "extra/manual.pdf", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_cranurl": false, "_releases": [ { "version": "0.3.1", "date": "2026-09-27" } ], "_exports": [ "ispat3d_edge_table", "ispat3d_example_image", "ispat3d_fit", "ispat3d_fit_2d", "ispat3d_fit_covariance", "ispat3d_partial_correlation", "ispat3d_plot_network", "ispat3d_plot_zones", "ispat3d_sample" ], "_help": [ { "page": "ispat3d_edge_table", "title": "Extract signed conditional-association edges", "topics": [ "ispat3d_edge_table" ] }, { "page": "ispat3d_example_image", "title": "Simulate a small registered cell map with section-wise KDE inputs", "topics": [ "ispat3d_example_image" ] }, { "page": "ispat3d_fit", "title": "Fit current ISPAT-3D on selected cells", "topics": [ "ispat3d_fit" ] }, { "page": "ispat3d_fit_2d", "title": "Fit the matched section-wise ISPAT-2D comparator", "topics": [ "ispat3d_fit_2d" ] }, { "page": "ispat3d_fit_covariance", "title": "Fit shared and zone-specific factor covariance from sufficient statistics", "topics": [ "ispat3d_fit_covariance" ] }, { "page": "ispat3d_partial_correlation", "title": "Convert a full covariance matrix to partial correlations", "topics": [ "ispat3d_partial_correlation" ] }, { "page": "ispat3d_plot_network", "title": "Plot a circular partial-correlation network using base graphics", "topics": [ "ispat3d_plot_network" ] }, { "page": "ispat3d_plot_zones", "title": "Facet all fitted zone networks in one base-R figure", "topics": [ "ispat3d_plot_zones" ] }, { "page": "ispat3d_sample", "title": "Select spatially balanced cells by zone and section", "topics": [ "ispat3d_sample" ] } ], "_readme": "https://github.com/cran/ISPAT3D/raw/HEAD/README.md", "_rundeps": [ "data.table", "gpboost", "lattice", "Matrix", "R6", "RJSONIO" ], "_vignettes": [ { "source": "volumetric-network.Rmd", "filename": "volumetric-network.html", "title": "A volumetric cell-density network from a small registered image", "engine": "knitr::rmarkdown", "headings": [ "1. Simulate a registered cell map and inspect the image", "2. Select a reproducible roster", "3. Fit the volumetric GP and factor covariance", "4. Obtain and display zone networks", "5. Apply the same path to a processed image", "References" ], "created": "2026-09-27 16:40:37", "modified": "2026-09-27 16:40:37", "commits": 1 }, { "source": "matched-planar-network.Rmd", "filename": "matched-planar-network.html", "title": "Matched section-wise 2D networks and a 3D comparison", "engine": "knitr::rmarkdown", "headings": [ "1. Prepare a small serial-section image", "2. Fix the cell roster before either fit", "3. Fit the section-wise planar model", "4. Compute and plot conditional networks", "5. Compare with the volumetric fit on identical cells", "6. Use processed serial-section data", "References" ], "created": "2026-09-27 16:40:37", "modified": "2026-09-27 16:40:37", "commits": 1 } ], "_score": 3, "_indexed": false, "_nocasepkg": "ispat3d", "_universes": [ "cran", "rijubhadury", "sagnikbhadury" ], "_indexurl": "https://sagnikbhadury.r-universe.dev/ISPAT3D", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.1", "date": "2026-09-27T18:41:10.000Z", "distro": "resolute", "commit": "4bdee8cad8611848f11492d616c59438234e7dd5", "fileid": "https://r2.ropensci.org/94ab879c23ccda541c1d95dd5d59a3713c96a0ace9ace5ced900fde0e45f45a3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/36341235538" }, { "r": "4.6.1", "os": "linux", "version": "0.3.1", "date": "2026-09-27T18:41:16.000Z", "distro": "resolute", "commit": "4bdee8cad8611848f11492d616c59438234e7dd5", "fileid": "https://r2.ropensci.org/390f6d9ff120346d954784e432394bc959da32983cd7633d5bf472a71cfe0b21", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/36341235538" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.1", "date": "2026-09-27T18:41:21.000Z", "commit": "4bdee8cad8611848f11492d616c59438234e7dd5", "fileid": "https://r2.ropensci.org/453a9fef089a663aec5dbbea72ef06356019834c1ce2eeee85dfd1a6bd62160b", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/36341235538" }, { "r": "4.7.0", "os": "win", "version": "0.3.1", "date": "2026-09-27T18:40:11.000Z", "commit": "4bdee8cad8611848f11492d616c59438234e7dd5", "fileid": "https://r2.ropensci.org/66d51db4017a3c545d786a5decc91dd8db94d92a117ad641242e4747ba0ebe71", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/36341235538" }, { "r": "4.6.1", "os": "win", "version": "0.3.1", "date": "2026-09-27T18:40:13.000Z", "commit": "4bdee8cad8611848f11492d616c59438234e7dd5", "fileid": "https://r2.ropensci.org/49ac6802c6e32076f6f3998afae464810d7a65581bed0ad84054298384f55c21", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/36341235538" } ] }