{
  "_id": "6ac64f8ff511ae58c09a9ed6",
  "Package": "cause",
  "Type": "Package",
  "Title": "CAUSE: Causal Analysis Using Summary Effect Estimates",
  "Version": "1.2.0.0335",
  "Author": "Jean Morrison",
  "Maintainer": "Jean Morrison <jvmorr@umich.edu>",
  "Description": "Identify causal patterns using pairs of GWAS summary\nstatistics.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "URL": "http://github.com/jean997/cause",
  "BugReports": "http://github.com/jean997/cause/issues",
  "RoxygenNote": "7.1.1",
  "SystemRequirements": "GNU make",
  "Config/pak/sysreqs": "cmake make libicu-dev libx11-dev",
  "Repository": "https://mrcieu.r-universe.dev",
  "Date/Publication": "2021-11-30 19:00:46 UTC",
  "RemoteUrl": "https://github.com/jean997/cause",
  "RemoteRef": "HEAD",
  "RemoteSha": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-07 11:23:17 UTC",
    "User": "root"
  },
  "_user": "mrcieu",
  "_type": "src",
  "_file": "cause_1.2.0.0335.tar.gz",
  "_fileid": "https://r2.ropensci.org/ef1c19e55245e878f6bc893793c7bfae92dd618e44ae39c44bbf14bc77b8d446",
  "_filesize": 186672,
  "_sha256": "ef1c19e55245e878f6bc893793c7bfae92dd618e44ae39c44bbf14bc77b8d446",
  "_expires": "2027-01-15T13:56:28.000Z",
  "_created": "2026-10-07T11:23:17.000Z",
  "_published": "2026-10-07T13:56:30.779Z",
  "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37613309556",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 112767173046,
      "time": 132,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11478866802"
    },
    {
      "job": 112767173076,
      "time": 163,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11479242028"
    },
    {
      "job": 112767173103,
      "time": 120,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11479361994"
    },
    {
      "job": 112767172988,
      "time": 161,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11479262047"
    },
    {
      "job": 112767173051,
      "time": 120,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11487346478"
    },
    {
      "job": 112767172911,
      "time": 247,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11485379680"
    },
    {
      "job": 112767172921,
      "time": 132,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11487456294"
    },
    {
      "job": 112767172982,
      "time": 243,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11485819972"
    },
    {
      "job": 112765716657,
      "time": 227,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11479501350"
    },
    {
      "job": 112767172820,
      "time": 112,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 112767172924,
      "time": 239,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11478557365"
    },
    {
      "job": 112767172931,
      "time": 181,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11478866925"
    },
    {
      "job": 112767172957,
      "time": 129,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11479566776"
    },
    {
      "job": 112767172962,
      "time": 244,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11479717126"
    },
    {
      "job": 112767172955,
      "time": 127,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11478926665"
    }
  ],
  "_upstream": "https://github.com/jean997/cause",
  "_commit": {
    "id": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5",
    "author": "Jean Morrison <jeanm@uchicago.edu>",
    "committer": "Jean Morrison <jeanm@uchicago.edu>",
    "message": "saveRDS -> write_lines\n",
    "time": 1638298846
  },
  "_maintainer": {
    "name": "Jean Morrison",
    "email": "jvmorr@umich.edu",
    "login": "jean997",
    "twitter": "@jeanv_morrison",
    "description": "",
    "uuid": 11408688
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppParallel",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "RcppParallel",
      "role": "Imports"
    },
    {
      "package": "mixsqp",
      "version": ">= 0.3-43",
      "role": "Imports"
    },
    {
      "package": "numDeriv",
      "role": "Imports"
    },
    {
      "package": "ashr",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "loo",
      "version": ">= 2.3.0",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "intervals",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "jean997",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 59,
  "_contributors": [
    {
      "user": "jean997",
      "count": 10,
      "uuid": 11408688
    },
    {
      "user": "crerecombinase",
      "count": 8,
      "uuid": 3493159
    }
  ],
  "_userbio": {
    "uuid": 15654827,
    "type": "organization",
    "name": "MRC Integrative Epidemiology Unit",
    "followers": 257
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/cause"
  },
  "_devurl": "https://github.com/jean997/cause",
  "_searchresults": 196,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/cause.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_cranurl": false,
  "_exports": [
    "cause",
    "cause_download_example_gwas_data",
    "cause_grid_adapt",
    "est_cause_params",
    "gwas_format",
    "gwas_merge",
    "in_sample_elpd_loo",
    "ld_prune",
    "loglik",
    "loglik_ij",
    "loglik_ij_Z0",
    "loglik_ij_Z1",
    "loglik_loo",
    "loglik_mat",
    "loglik_samps_Z0",
    "loglik_samps_Z1",
    "map_pi_rho",
    "map_pi_rho_nonnull_eqg",
    "map_pi_rho_nonnull_fixed",
    "map_pi_rho_nonnull_geq",
    "map_pi_rho_nonnull_qge",
    "new_cause_data",
    "new_cause_data_fit",
    "read_standard_format",
    "recompute_elpd_table",
    "samp_from_grid",
    "setup_cause_pipeline",
    "setup_gwas_pairs",
    "step_quantile",
    "variance_pair_candidates"
  ],
  "_help": [
    {
      "page": "adapt2_grid",
      "title": "Adaptive grid estimation of posteriors",
      "topics": [
        "adapt2_grid"
      ]
    },
    {
      "page": "cause",
      "title": "CAUSE",
      "topics": [
        "cause"
      ]
    },
    {
      "page": "cause_download_example_gwas_data",
      "title": "Download GWAS data to use in examples",
      "topics": [
        "cause_download_example_gwas_data"
      ]
    },
    {
      "page": "cause_grid_adapt",
      "title": "CAUSE posterior density estimation",
      "topics": [
        "cause_grid_adapt"
      ]
    },
    {
      "page": "est_cause_params",
      "title": "Estimate CAUSE Nuisance Parameters",
      "topics": [
        "est_cause_params"
      ]
    },
    {
      "page": "est_cause_params_future",
      "title": "Estimate CAUSE Nuisance Parameters",
      "topics": [
        "est_cause_params_future"
      ]
    },
    {
      "page": "eta_gamma_prior",
      "title": "Prior variance for gamma and eta",
      "topics": [
        "eta_gamma_prior"
      ]
    },
    {
      "page": "gwas_format",
      "title": "Convert GWAS summary statistics to a standard format",
      "topics": [
        "gwas_format"
      ]
    },
    {
      "page": "gwas_merge",
      "title": "Format data for CAUSE",
      "topics": [
        "gwas_merge"
      ]
    },
    {
      "page": "in_sample_elpd_loo",
      "title": "Estimate delta elpd for pairs of models",
      "topics": [
        "in_sample_elpd_loo"
      ]
    },
    {
      "page": "ld_prune",
      "title": "Prune variants for LD",
      "topics": [
        "ld_prune"
      ]
    },
    {
      "page": "loglik",
      "title": "Calculate likelihood - version 7",
      "topics": [
        "loglik"
      ]
    },
    {
      "page": "loglik_ij",
      "title": "Calculate likelihood of (beta_hat_1[j], beta_hat_2[j])) given rho, b, sigma_1j, sigma_2j, s_1j, s_2j where alpha_kj ~ N(0, sigma_kj)",
      "topics": [
        "loglik_ij"
      ]
    },
    {
      "page": "loglik_loo",
      "title": "Calculate likelihood matrix for LOO (SNPs by posterior samples)",
      "topics": [
        "loglik_loo"
      ]
    },
    {
      "page": "loglik_mat",
      "title": "Calculate likelihood matrix - version 7",
      "topics": [
        "loglik_mat"
      ]
    },
    {
      "page": "loglik_samps_Z0",
      "title": "Calculate likelihood matrix for LOO (SNPs by posterior samples)",
      "topics": [
        "loglik_samps_Z0"
      ]
    },
    {
      "page": "loglik_samps_Z1",
      "title": "Calculate likelihood matrix for LOO (SNPs by posterior samples)",
      "topics": [
        "loglik_samps_Z1"
      ]
    },
    {
      "page": "map_pi_rho",
      "title": "Estimate pi and mixture proportions under null model",
      "topics": [
        "map_pi_rho"
      ]
    },
    {
      "page": "map_pi_rho_nonnull",
      "title": "Estimate pi and mixture proportions under a specified model",
      "topics": [
        "map_pi_rho_nonnull"
      ]
    },
    {
      "page": "map_pi_rho_nonnull_eqg",
      "title": "Estimate pi and mixture proportions under a specified model",
      "topics": [
        "map_pi_rho_nonnull_eqg"
      ]
    },
    {
      "page": "map_pi_rho_nonnull_fixed",
      "title": "Estimate pi and mixture proportions under a specified model",
      "topics": [
        "map_pi_rho_nonnull_fixed"
      ]
    },
    {
      "page": "map_pi_rho_nonnull_geq",
      "title": "Estimate pi and mixture proportions under a specified model",
      "topics": [
        "map_pi_rho_nonnull_geq"
      ]
    },
    {
      "page": "map_pi_rho_nonnull_qge",
      "title": "Estimate pi and mixture proportions under a specified model",
      "topics": [
        "map_pi_rho_nonnull_qge"
      ]
    },
    {
      "page": "new_cause_data",
      "title": "Create a new cause_data object",
      "topics": [
        "new_cause_data"
      ]
    },
    {
      "page": "new_cause_data_fit",
      "title": "Create a new cause_data_fit object",
      "topics": [
        "new_cause_data_fit"
      ]
    },
    {
      "page": "plot.cause",
      "title": "Plot CAUSE",
      "topics": [
        "plot.cause"
      ]
    },
    {
      "page": "plot.cause_post",
      "title": "Plot posteriors for one CAUSE fit",
      "topics": [
        "plot.cause_post"
      ]
    },
    {
      "page": "print.cause_summary",
      "title": "Print CAUSE Summary",
      "topics": [
        "print.cause_summary"
      ]
    },
    {
      "page": "print.summary_cause_post",
      "title": "Print CAUSE fit Summary",
      "topics": [
        "print.summary_cause_post"
      ]
    },
    {
      "page": "recompute_elpd_table",
      "title": "Recompute elpd table for a CAUSE fit that is already computed",
      "topics": [
        "recompute_elpd_table"
      ]
    },
    {
      "page": "samp_from_grid",
      "title": "Sample from grid approximation of posterior distribuitions",
      "topics": [
        "samp_from_grid"
      ]
    },
    {
      "page": "setup_cause_pipeline",
      "title": "Set up analysis directory for pairs of GWAS summary statistics",
      "topics": [
        "setup_cause_pipeline"
      ]
    },
    {
      "page": "setup_gwas_pairs",
      "title": "Set up analysis directory for pairs of GWAS summary statistics",
      "topics": [
        "setup_gwas_pairs"
      ]
    },
    {
      "page": "step_quantile",
      "title": "Quantile of a step pdf",
      "topics": [
        "step_quantile"
      ]
    },
    {
      "page": "summary.cause",
      "title": "Summarize CAUSE Results",
      "topics": [
        "summary.cause"
      ]
    },
    {
      "page": "summary.cause_post",
      "title": "Summarize CAUSE Results for a single fit",
      "topics": [
        "summary.cause_post"
      ]
    },
    {
      "page": "Z_post",
      "title": "Posterior probability of acting through U",
      "topics": [
        "Z_post"
      ]
    }
  ],
  "_readme": "https://github.com/jean997/cause/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "ashr",
    "backports",
    "bit",
    "bit64",
    "checkmate",
    "cli",
    "clipr",
    "cpp11",
    "crayon",
    "distributional",
    "dplyr",
    "etrunct",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "hms",
    "intervals",
    "invgamma",
    "irlba",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "loo",
    "magrittr",
    "Matrix",
    "matrixStats",
    "mixsqp",
    "numDeriv",
    "pillar",
    "pkgconfig",
    "posterior",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppParallel",
    "readr",
    "rlang",
    "S7",
    "scales",
    "SQUAREM",
    "stringi",
    "stringr",
    "tensorA",
    "tibble",
    "tidyr",
    "tidyselect",
    "truncnorm",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr"
  ],
  "_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"
    }
  ],
  "_score": 4.762078087334639,
  "_indexed": false,
  "_nocasepkg": "cause",
  "_universes": [
    "mrcieu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.0.0335",
      "date": "2026-10-07T11:25:25.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5",
      "fileid": "https://r2.ropensci.org/ddc722435adca5462bd10bb946cab4489c8133d205b7aeefcc5907f4c6345d33",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37613309556"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.0.0335",
      "date": "2026-10-07T11:25:42.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5",
      "fileid": "https://r2.ropensci.org/4a2e881dc5b53d3093fc633758b63beb43d947234881a7e24402811f226d2b7b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37613309556"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.2.0.0335",
      "date": "2026-10-07T11:25:18.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5",
      "fileid": "https://r2.ropensci.org/7b313b071722d49aa067a9bf625a31670c85d6b0b3336a22f27c5253bb1f7e79",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37613309556"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.2.0.0335",
      "date": "2026-10-07T11:25:46.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5",
      "fileid": "https://r2.ropensci.org/a8d41adee65ec590c7ffe7191a16c0813f42bffb9db5f4b06e9655906904ed19",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37613309556"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.0.0335",
      "date": "2026-10-07T13:55:07.000Z",
      "arch": "aarch64",
      "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5",
      "fileid": "https://r2.ropensci.org/216b2ad059e59ddce154cc2ec433eb353db6ee36d9c3ed24918ba103d37a95b6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37613309556"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.0.0335",
      "date": "2026-10-07T13:40:50.000Z",
      "arch": "x86_64",
      "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5",
      "fileid": "https://r2.ropensci.org/cce4ee9be15f53e0ba5797cd0498d75311c4c78fcf61475b6d376b22594f3386",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37613309556"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.2.0.0335",
      "date": "2026-10-07T13:55:00.000Z",
      "arch": "aarch64",
      "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5",
      "fileid": "https://r2.ropensci.org/7c7096dc8e7f290c90d88722c463672cbed4703931a10bc7ef2c8a23d45e4326",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37613309556"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.2.0.0335",
      "date": "2026-10-07T13:47:37.000Z",
      "arch": "x86_64",
      "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5",
      "fileid": "https://r2.ropensci.org/1e11c2f376ccc3d9e81a1a0319a12f8560fa4ef988245fecfa4b71e63177f78a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37613309556"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2.0.0335",
      "date": "2026-10-07T11:26:51.000Z",
      "arch": "aarch64",
      "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5",
      "fileid": "https://r2.ropensci.org/ad74045308b68d9245ac381c6b028a4400a58b34b079f284027a036a93eb100e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37613309556"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2.0.0335",
      "date": "2026-10-07T11:25:00.000Z",
      "arch": "x86_64",
      "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5",
      "fileid": "https://r2.ropensci.org/48afe43f84e5e50169cb1a54f1a0e0838570cfa91f6d9eb4a10f476287e1da94",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37613309556"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.2.0.0335",
      "date": "2026-10-07T11:24:44.000Z",
      "arch": "x86_64",
      "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5",
      "fileid": "https://r2.ropensci.org/c08e8c023126200d42c6812c23d409ad3f8486fd1bb871624551e4c6eaff49f2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37613309556"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.2.0.0335",
      "date": "2026-10-07T11:26:59.000Z",
      "arch": "aarch64",
      "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5",
      "fileid": "https://r2.ropensci.org/d0693b66a51f4fc04fda85d2e9219d0fe25f9f899c705e49a8727c0ec0802a3e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37613309556"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.2.0.0335",
      "date": "2026-10-07T11:25:04.000Z",
      "arch": "x86_64",
      "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5",
      "fileid": "https://r2.ropensci.org/5cb3c3db74861b63c444b76fe69a5f6ca85fac45bfb17b92ec1aa352ec817358",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37613309556"
    }
  ]
}