{ "_id": "6a1042e6acfb0bcc41c9dd40", "Encoding": "UTF-8", "Package": "MRPC", "Type": "Package", "Version": "3.2.0", "Date": "2025-09-04", "Title": "PC Algorithm with the Principle of Mendelian Randomization", "Authors@R": "c(person(given = c(\"Md\", \"Bahadur\"),\nfamily = \"Badsha\",\nrole = \"aut\"),\nperson(given = c(\"Evan\", \"A\"),\nfamily = \"Martin\",\nrole = \"ctb\"),\nperson(given = \"Audrey\",\nfamily = \"Fu\",\nrole = c(\"aut\", \"cre\"),\nemail = \"audreyqyfu@gmail.com\"))", "Description": "A PC Algorithm with the Principle of Mendelian\nRandomization. This package implements the MRPC (PC with the\nprinciple of Mendelian randomization) algorithm to infer causal\ngraphs. It also contains functions to simulate data under a\ncertain topology, to visualize a graph in different ways, and\nto compare graphs and quantify the differences. See Badsha and\nFu (2019) , Badsha, Martin and Fu\n(2021) , Kvamme and Badsha, et\nal. (2025) .", "License": "GPL (>= 2)", "LazyData": "TRUE", "NeedsCompilation": "no", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libssl-dev libx11-dev zlib1g-dev", "Repository": "https://audreyfulab.r-universe.dev", "Date/Publication": "2025-09-13 03:24:32 UTC", "RemoteUrl": "https://github.com/audreyfulab/mrpc", "RemoteRef": "HEAD", "RemoteSha": "c4968a4c67ced1c291d263244168f954a931c56e", "Packaged": { "Date": "2026-05-11 07:19:25 UTC", "User": "root" }, "Author": "Md Bahadur Badsha [aut],\nEvan A Martin [ctb],\nAudrey Fu [aut, cre]", "Maintainer": "Audrey Fu ", "MD5sum": "59a5daa74532e5a903e71b7ae1cd59fc", "_user": "audreyfulab", "_type": "src", "_file": "MRPC_3.2.0.tar.gz", "_fileid": "fbbad6d146cf47151a67d9197ec0c55dfe374efdbaba897cd71175fac893f5fe", "_filesize": 1712475, "_sha256": "fbbad6d146cf47151a67d9197ec0c55dfe374efdbaba897cd71175fac893f5fe", "_created": "2026-05-11T07:19:25.000Z", "_published": "2026-05-22T11:49:58.369Z", "_distro": "noble", "_jobs": [ { "job": 77373306892, "time": 244, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6912520848" }, { "job": 77373307118, "time": 312, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6912540057" }, { "job": 77373306750, "time": 238, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6912522868" }, { "job": 77373307048, "time": 236, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6912530240" }, { "job": 77373306368, "time": 319, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6912448984" }, { "job": 77373306448, "time": 238, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7159773795" }, { "job": 77373306743, "time": 203, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6912508489" }, { "job": 77373307246, "time": 181, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6912502399" }, { "job": 77373306894, "time": 172, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6912499397" } ], "_buildurl": "https://github.com/r-universe/audreyfulab/actions/runs/25655820707", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/audreyfulab/mrpc", "_commit": { "id": "c4968a4c67ced1c291d263244168f954a931c56e", "author": "Audrey Fu ", "committer": "Audrey Fu ", "message": "Update to 3.2.0\n\nMRPC: modernize build with roxygen2, fix docs/links, and clean NAMESPACE\n\nPackaging / infrastructure\n- Switch to roxygen2-managed NAMESPACE (remove manual NAMESPACE).\n- Add `Encoding: UTF-8` to DESCRIPTION.\n- Add/clean `Authors@R` (replace legacy Author/Maintainer where applicable).\n- Ensure DESCRIPTION Imports are accurate for runtime (methods, stats, utils, pcalg, graph, Rgraphviz, …); removed 'sna'.\n\nNamespace / imports\n- Create `R/imports.R` and declare explicit imports.\n - graphics: plot (for S4 plot generic)\n - Rgraphviz: agopen (keep `Rgraphviz::plot()` called explicitly to avoid masking `graphics::plot`)\n- Resolve NOTES about unused Imports (add import for Rgraphviz).\n- Qualify a few external calls with `pkg::fun` where preferable.\n\nPublic API / methods\n- Export user-facing functions (e.g., `MRPC`) via `@export`.\n- Define `MRPCclass` S4 class and export with `@exportClass MRPCclass`.\n- Convert printing to S4 with setMethod and export it.\n- `plot(MRPCclass)`: ensure `main` is a string of length 1 to avoid logical-length error in `Rgraphviz::plot()`.\n- Keep/adjust S4 methods for `plot`, `summary`, `show` (export where user-facing).\n- Internal helper `show.MRPC.amat`: mark as internal and remove standalone Rd to silence Rd-usage WARNING.\n\nDocumentation\n- Add 2025 publication.\n- Fix Rd cross-references:\n - Use explicit anchors for external S4 classes:\n - `\\link[graph:graph-class]{graph}`\n - `\\link[pcalg:pcAlgo-class]{pcAlgo}`\n- Update `MRPCclass.Rd` usage/aliases to document S4 methods:\n - `\\S4method{print}{MRPCclass}(...)` (replace old `\\S3method{print}{MRPCclass}`)\n - Keep aliases like `print,MRPCclass-method`, `plot,MRPCclass,ANY-method`, etc.\n- Clean up argument docs where needed; remove obsolete Rd for internal helpers.\n", "time": 1757733872 }, "_maintainer": { "name": "Audrey Fu", "email": "audreyqyfu@gmail.com", "login": "audreyqyfu", "uuid": 12000393 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "bnlearn", "role": "Imports" }, { "package": "compositions", "role": "Imports" }, { "package": "dynamicTreeCut", "role": "Imports" }, { "package": "GGally", "role": "Imports" }, { "package": "fastcluster", "role": "Imports" }, { "package": "gtools", "role": "Imports" }, { "package": "graph", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "Hmisc", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "mice", "role": "Imports" }, { "package": "network", "role": "Imports" }, { "package": "pcalg", "role": "Imports" }, { "package": "psych", "role": "Imports" }, { "package": "Rgraphviz", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "WGCNA", "role": "Imports" }, { "package": "plyr", "role": "Imports" } ], "_owner": "audreyfulab", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-36", "n": 4 }, { "week": "2025-37", "n": 1 } ], "_tags": [ { "name": "v3.2.0", "date": "2025-09-13" } ], "_stars": 8, "_contributors": [ { "user": "audreyqyfu", "count": 73, "uuid": 12000393 }, { "user": "evanamartin", "count": 12, "uuid": 14840192 }, { "user": "mdbahadur", "count": 10, "uuid": 25463913 }, { "user": "molotfy", "count": 2, "uuid": 37003715 } ], "_userbio": { "uuid": 228121504, "type": "organization", "name": "Audrey Fu Lab", "description": "Statistics; 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data but with different node orderings.", "topics": [ "CompareMethodsNodeOrdering" ] }, { "page": "CompareMethodsVStructure", "title": "Comparison of inference accuracy of different methods on data with and without a v-structure", "topics": [ "CompareMethodsVStructure" ] }, { "page": "CutModules", "title": "Cut a numeric variable into intervals", "topics": [ "CutModules" ] }, { "page": "data_examples", "title": "Example data under simple and complex models", "topics": [ "data_examples" ] }, { "page": "Data_GEUVADIS", "title": "GEUVADIS data with 62 eQTL-gene sets", "topics": [ "data_GEUVADIS" ] }, { "page": "data_GEUVADIS_combined", "title": "Combined genotype and gene expression data from 62 eQTL-gene sets in 373 Europeans from GEUVADIS", "topics": [ "data_GEUVADIS_combined" ] }, { "page": "data_with_outliers", "title": "Example data with outliers", "topics": [ "data_with_outliers" ] }, { "page": "data_without_outliers", "title": "Example data without outliers", "topics": [ 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