{ "_id": "6a27eca724555f66ed549e77", "Package": "cause", "Type": "Package", "Title": "CAUSE: Causal Analysis Using Summary Effect Estimates", "Version": "1.2.0.0335", "Author": "Jean Morrison", "Maintainer": "Jean Morrison ", "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": "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": "2026-06-09 10:29:30 UTC", "User": "root" }, "MD5sum": "bf45372f90cf8cd064a8ea87c346de57", "_user": "mrcieu", "_type": "src", "_file": "cause_1.2.0.0335.tar.gz", "_fileid": "7f8e307752216e19928b099ba0f9cd7809bdef674dccf40d072ef8d00c92f314", "_filesize": 184651, "_sha256": "7f8e307752216e19928b099ba0f9cd7809bdef674dccf40d072ef8d00c92f314", "_created": "2026-06-09T10:29:30.000Z", "_published": "2026-06-09T10:36:23.639Z", "_distro": "noble", "_jobs": [ { "job": 80301666704, "time": 168, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7505130896" }, { "job": 80301666724, "time": 179, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7505133226" }, { "job": 80301666703, "time": 180, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7505134277" }, { "job": 80301666715, "time": 187, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7505136146" }, { "job": 80301666725, "time": 131, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7505116363" }, { "job": 80301666743, "time": 365, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7505198887" }, { "job": 80301666740, "time": 133, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7505119321" }, { "job": 80301666716, "time": 274, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7505166820" }, { "job": 80301123574, "time": 193, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7505071035" }, { "job": 80301666659, "time": 126, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 80301666718, "time": 167, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7505128643" }, { "job": 80301666747, "time": 189, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7505136758" }, { "job": 80301666734, "time": 205, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7505142154" } ], "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27199927739", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/jean997/cause", "_commit": { "id": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5", "author": "Jean Morrison ", "committer": "Jean Morrison ", "message": "saveRDS -> write_lines\n", "time": 1638298846 }, "_maintainer": { "name": "Jean Morrison", "email": "jvmorr@umich.edu", "login": "jean997", "twitter": "@jeanv_morrison", "description": "", "uuid": 11408688 }, "_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" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/cause" }, "_devurl": "https://github.com/jean997/cause", "_searchresults": 118, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/cause.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_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": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 4.5417040232842885, "_indexed": false, "_nocasepkg": "cause", "_universes": [ "mrcieu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.0.0335", "date": "2026-06-09T10:32:08.000Z", "distro": "noble", "arch": "aarch64", "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5", "fileid": "287a11101e7f98424155d002eb2d5b81299db0c259601ce0327ff6a156f98237", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27199927739" }, { "r": "4.7.0", "os": "linux", "version": "1.2.0.0335", "date": "2026-06-09T10:32:08.000Z", "distro": "noble", "arch": "x86_64", "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5", "fileid": "bcc58b239e82bf6419f1c0f8256cbaab50d5891e58afa41f9fc6efc4a2c058b6", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27199927739" }, { "r": "4.6.0", "os": "linux", "version": "1.2.0.0335", "date": "2026-06-09T10:32:16.000Z", "distro": "noble", "arch": "aarch64", "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5", "fileid": "0a4210ee620219ffe43ede9cae2c90112f9ad2edbbf3772c23cc7ece1c3b7ffa", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27199927739" }, { "r": "4.6.0", "os": "linux", "version": "1.2.0.0335", "date": "2026-06-09T10:32:15.000Z", "distro": "noble", "arch": "x86_64", "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5", "fileid": "24408c88d75810c15958a6e556fe1982190bbe529d551c267317aaa51f28c252", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27199927739" }, { "r": "4.5.3", "os": "mac", "version": "1.2.0.0335", "date": "2026-06-09T10:31:28.000Z", "arch": "aarch64", "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5", "fileid": "e62344d59d020fcd569657868c9838535a01d42a1f4f3b02a12d4571eaed1dde", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27199927739" }, { "r": "4.5.3", "os": "mac", "version": "1.2.0.0335", "date": "2026-06-09T10:32:40.000Z", "arch": "x86_64", "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5", "fileid": "f87d6bcb2fbb918161722f170ca7b88d878cbf6cff79ebf4af3273c323d0ec5e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27199927739" }, { "r": "4.6.0", "os": "mac", "version": "1.2.0.0335", "date": "2026-06-09T10:31:33.000Z", "arch": "aarch64", "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5", "fileid": "2a9ac964e8198bc5d6685a7211f578222e52eb31119c6ae5d80b203f7bfc40a9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27199927739" }, { "r": "4.6.0", "os": "mac", "version": "1.2.0.0335", "date": "2026-06-09T10:33:05.000Z", "arch": "x86_64", "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5", "fileid": "9bf027bcfc02c872491fe6d277f5a370c837af19bb7741fbb698a596cf427dc8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27199927739" }, { "r": "4.7.0", "os": "win", "version": "1.2.0.0335", "date": "2026-06-09T10:31:11.000Z", "arch": "x86_64", "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5", "fileid": "38f504575443ad96f7cecb302d2763c7c2ae61696c0d7f66603e55419b4f5280", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27199927739" }, { "r": "4.5.3", "os": "win", "version": "1.2.0.0335", "date": "2026-06-09T10:31:32.000Z", "arch": "x86_64", "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5", "fileid": "0c8616913aa316608f42c3868e11f92f5a2711aa1400326c6b081f702bd73a34", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27199927739" }, { "r": "4.6.0", "os": "win", "version": "1.2.0.0335", "date": "2026-06-09T10:31:46.000Z", "arch": "x86_64", "commit": "6257e6c66e6c1518c8750d1e4d2b4d6e42644fa5", "fileid": "a53429736cf3a1f84e1f2d010becc067142125e2d5d6c78f0795bfe045736955", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27199927739" } ] }