{ "_id": "6a4b5171a6574ff277f997cd", "Package": "GraphMRcML", "Type": "Package", "Title": "Causal Network Inference via Mendelian Randomization with cML\nand Network Deconvolution", "Version": "0.1.0", "Authors@R": "c(\nperson(\"Zhaotong\", \"Lin\", role = c(\"aut\", \"cre\"),\nemail = \"lin00374@umn.edu\"),\nperson(\"Haoran\", \"Xue\", role = \"aut\"),\nperson(\"Wei\", \"Pan\", role = \"aut\"))", "Description": "Combines Mendelian randomization (constrained maximum\nlikelihood, cML) and network deconvolution for inference of\ncausal networks from GWAS summary data, as described in Lin,\nXue, and Pan (2023) .", "License": "GPL (>= 3)", "URL": "https://github.com/ZhaotongL/GraphMRcML,\nhttps://mrcieu.r-universe.dev/GraphMRcML", "Encoding": "UTF-8", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://mrcieu.r-universe.dev", "Date/Publication": "2026-05-07 18:57:42 UTC", "RemoteUrl": "https://github.com/ZhaotongL/GraphMRcML", "RemoteRef": "refs/pull/2/head", "RemoteSha": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-06 06:53:13 UTC", "User": "root" }, "Author": "Zhaotong Lin [aut, cre],\nHaoran Xue [aut],\nWei Pan [aut]", "Maintainer": "Zhaotong Lin ", "_user": "mrcieu", "_type": "src", "_file": "GraphMRcML_0.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/b32ad20d63526718e4d05f54e1b419e205463d64d5ebe1dd2d57849788f657e9", "_filesize": 123491, "_sha256": "b32ad20d63526718e4d05f54e1b419e205463d64d5ebe1dd2d57849788f657e9", "_expires": "2026-10-14T06:55:42.000Z", "_created": "2026-07-06T06:53:13.000Z", "_published": "2026-07-06T06:55:45.179Z", "_jobs": [ { "job": 85312029807, "time": 113, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8101708898" }, { "job": 85312029792, "time": 107, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8101707037" }, { "job": 85312029804, "time": 99, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8101704896" }, { "job": 85312029867, "time": 64, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8101698702" }, { "job": 85311715157, "time": 140, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8101678554" }, { "job": 85312029776, "time": 106, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8101706630" }, { "job": 85312029818, "time": 72, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8101698505" }, { "job": 85312029854, "time": 59, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8101694369" }, { "job": 85312029820, "time": 58, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8101694281" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/28773336908", "_status": "success", "_upstream": "https://github.com/ZhaotongL/GraphMRcML", "_commit": { "id": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "author": "Tom Palmer ", "committer": "Tom Palmer ", "message": "Document\n", "time": 1778180262 }, "_maintainer": { "name": "Zhaotong Lin", "email": "lin00374@umn.edu", "login": "zhaotongl", "description": "", "uuid": 45536679 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "dplyr", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "pbmcapply", "role": "Imports" }, { "package": "stats", "role": "Imports" } ], "_owner": "zhaotongl", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 1 }, { "week": "2025-45", "n": 1 }, { "week": "2026-19", "n": 14 } ], "_tags": [], "_stars": 9, "_contributors": [ { "user": "zhaotongl", "count": 15, "uuid": 45536679 } ], "_userbio": { "uuid": 15654827, "type": "organization", "name": "MRC Integrative Epidemiology Unit", "followers": 250 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/GraphMRcML" }, "_devurl": "https://github.com/zhaotongl/graphmrcml", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GraphMRcML.html", "manual.pdf" ], "_cranurl": false, "_exports": [ "cML_estimate_O", "cML_estimate_random_O", "cML_SdTheta_O", "Generate_Perturb", "Graph_Estimate", "Graph_Perturb", "Graph_Screen", "loglik", "mr_cML_DP_O", "mr_cML_O", "plot_graph", "subset_Graph_d1" ], "_help": [ { "page": "cML_estimate_O", "title": "Constrained maximum likelihood estimate (single start)", "topics": [ "cML_estimate_O" ] }, { "page": "cML_estimate_random_O", "title": "Constrained MLE with random restarts", "topics": [ "cML_estimate_random_O" ] }, { "page": "cML_SdTheta_O", "title": "Standard error of the cML causal-effect estimate", "topics": [ "cML_SdTheta_O" ] }, { "page": "Generate_Perturb", "title": "Generate one LD-aware perturbed copy of the GWAS estimates", "topics": [ "Generate_Perturb" ] }, { "page": "Graph_Estimate", "title": "Estimate the pairwise causal-effect graph", "topics": [ "Graph_Estimate" ] }, { "page": "Graph_Perturb", "title": "GraphMRcML with data perturbation", "topics": [ "Graph_Perturb" ] }, { "page": "Graph_Screen", "title": "Screen instruments and prepare LD-aware perturbation matrices", "topics": [ "Graph_Screen" ] }, { "page": "loglik", "title": "Profile log-likelihood for the cML model", "topics": [ "loglik" ] }, { "page": "mr_cML_DP_O", "title": "MR-cML with data perturbation", "topics": [ "mr_cML_DP_O" ] }, { "page": "mr_cML_O", "title": "Mendelian randomization via cML with BIC selection", "topics": [ "mr_cML_O" ] }, { "page": "plot_graph", "title": "Build an igraph object for a GraphMRcML summary graph", "topics": [ "plot_graph" ] }, { "page": "subset_Graph_d1", "title": "Summarise GraphMRcML perturbation results for a subset of traits", "topics": [ "subset_Graph_d1" ] } ], "_rundeps": [ "cli", "cpp11", "dplyr", "generics", "glue", "igraph", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "pbmcapply", "pillar", "pkgconfig", "R6", "rlang", "tibble", "tidyselect", "utf8", "vctrs", "withr" ], "_score": 2.4313637641589874, "_indexed": true, "_nocasepkg": "graphmrcml", "_universes": [ "mrcieu", "zhaotongl" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-07-06T06:55:11.000Z", "distro": "resolute", "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "fileid": "https://r2.ropensci.org/486e36cf67f76024a1e015baa10dd5e9f3a3a95165b3a92d0549fce9564f1622", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/28773336908" }, { "r": "4.6.1", "os": "linux", "version": "0.1.0", "date": "2026-07-06T06:55:03.000Z", "distro": "resolute", "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "fileid": "https://r2.ropensci.org/de46c5fc3b04e1eb1e9c8845cfe0155ca4981f68390caa9ca2cceff75ce19b01", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/28773336908" }, { "r": "4.5.3", "os": "mac", "version": "0.1.0", "date": "2026-07-06T06:54:51.000Z", "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "fileid": "https://r2.ropensci.org/6d152ab04c351bf0f35aec8d20fac39f12202cfa9d750fc930e0ed86298b7364", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/28773336908" }, { "r": "4.6.1", "os": "mac", "version": "0.1.0", "date": "2026-07-06T06:54:36.000Z", "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "fileid": "https://r2.ropensci.org/66e4d7e00fe885df67d5a4d393118f8c1f7e49adad5f1f175dc26ec877343d18", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/28773336908" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.0", "date": "2026-07-06T06:55:10.000Z", "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "fileid": "https://r2.ropensci.org/bcfdfb93f2b515dcbd09714a36b4a51567c7c8758b412903aee0d4d75bec93f0", "status": "success", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/28773336908" }, { "r": "4.7.0", "os": "win", "version": "0.1.0", "date": "2026-07-06T06:54:28.000Z", "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "fileid": "https://r2.ropensci.org/81019ef40410aa799d5ed345d0df4ab70f394bd4e171f2b6c5ef87217ef55548", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/28773336908" }, { "r": "4.5.3", "os": "win", "version": "0.1.0", "date": "2026-07-06T06:54:12.000Z", "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "fileid": "https://r2.ropensci.org/129041ea443cdbed94096b2acefff2c8b69dd93f494f1645de69e35cd734a5d1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/28773336908" }, { "r": "4.6.1", "os": "win", "version": "0.1.0", "date": "2026-07-06T06:54:12.000Z", "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "fileid": "https://r2.ropensci.org/b9625c3b6f114146eadf943e3d3a69b3f42532bef7ef7902dfa397a9f1c16fa6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/28773336908" } ] }