{ "_id": "6a1ef9a4b401979e7341805c", "Package": "GWASBrewer", "Type": "Package", "Title": "Simulate Realistic GWAS Summary Statistics", "Version": "0.3.0.0238", "Author": "Jean Morrison", "Maintainer": "Jean Morrison ", "Description": "Simulate GWAS summary statistics from specified DAG or\nfactor structure.", "License": "GPL (>= 3)", "URL": "https://github.com/jean997/GWASBrewer", "BugReports": "https://github.com/jean997/GWASBrewer/issues", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "Config/testthat/edition": "3", "LazyDataCompression": "xz", "Remotes": [ "cran/hapsim" ], "Config/pak/sysreqs": "libicu-dev", "Repository": "https://mrcieu.r-universe.dev", "Date/Publication": "2026-05-18 17:53:59 UTC", "RemoteUrl": "https://github.com/jean997/GWASBrewer", "RemoteRef": "HEAD", "RemoteSha": "8ab3b99ce5303911b9a5bcdc9aa0f76295d43612", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-18 23:05:55 UTC", "User": "root" }, "MD5sum": "71d572017f9bcc37802de9a9ce1f33d5", "_user": "mrcieu", "_type": "src", "_file": "GWASBrewer_0.3.0.0238.tar.gz", "_fileid": "07b78c34317fa8bd7d24058f57718cba6c9a766e9221e38dde1cf326ad4d46db", "_filesize": 41593175, "_sha256": "07b78c34317fa8bd7d24058f57718cba6c9a766e9221e38dde1cf326ad4d46db", "_created": "2026-05-18T23:05:55.000Z", "_published": "2026-06-02T15:41:24.545Z", "_distro": "noble", "_jobs": [ { "job": 79110733864, "time": 191, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7071153739" }, { "job": 79110732809, "time": 215, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7071159454" }, { "job": 79110733381, "time": 227, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7071162148" }, { "job": 79110732922, "time": 203, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7071156488" }, { "job": 79110733556, "time": 191, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7071153831" }, { "job": 79110733133, "time": 396, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7071201837" }, { "job": 79110732897, "time": 188, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7071153224" }, { "job": 79110732828, "time": 425, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7071209278" }, { "job": 79110731685, "time": 348, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7071108729" }, { "job": 79110732099, "time": 153, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7362592792" }, { "job": 79110732510, "time": 198, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7071155499" }, { "job": 79110733195, "time": 197, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7071155852" }, { "job": 79110732783, "time": 216, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7071159796" } ], "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26065413563", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/jean997/GWASBrewer", "_commit": { "id": "8ab3b99ce5303911b9a5bcdc9aa0f76295d43612", "author": "Jean Morrison ", "committer": "GitHub ", "message": "Merge pull request #18 from remlapmot/suggestions-3\n\nSome additional fixes", "time": 1779126839 }, "_maintainer": { "name": "Jean Morrison", "email": "jvmorr@umich.edu", "login": "jean997", "twitter": "@jeanv_morrison", "description": "", "uuid": 11408688 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "dplyr", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "Rcpp", "version": ">= 1.0.5", "role": "Imports" }, { "package": "DiagrammeR", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "hapsim", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "jean997", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-20", "n": 1 }, { "week": "2025-26", "n": 2 }, { "week": "2025-44", "n": 3 }, { "week": "2026-21", "n": 1 } ], "_tags": [], "_stars": 11, "_contributors": [ { "user": "jean997", "count": 146, "uuid": 11408688 }, { "user": "remlapmot", "count": 58, "uuid": 3777473 } ], "_userbio": { "uuid": 15654827, "type": "organization", "name": "MRC Integrative Epidemiology Unit" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/GWASBrewer" }, "_devurl": "https://github.com/jean997/gwasbrewer", "_searchresults": 24, "_topics": [ "openblas", "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GWASBrewer.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "compute_h2", "fast_eigen", "fast_eigen_vals", "fast_lm", "fixed_to_scale_fam", "gen_genos_mvn", "generate_F_simple", "generate_F2", "generate_random_F", "hapsim_simple", "mixnorm_to_scale_fam", "resample_inddata", "resample_sumstats", "rescale_sumstats", "rnormalmix", "sim_extract_ld", "sim_ld_proxy", "sim_ld_prune", "sim_lf", "sim_mv", "sim_mv_determined", "xyz_to_G" ], "_datasets": [ { "name": "AF", "title": "Example allele frequencies", "object": "AF", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "ld_mat_list", "title": "Example LD block matrices", "object": "ld_mat_list", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "snpdata", "title": "Example SNP data", "object": "snpdata", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "AF", "SNP", "allele", "chr", "ld_snp_id", "map", "pos", "region_id", "snp_id", "in_hapmap", "ldscore_1kg", "ldscore_hm3", "keep_ld_prune_0.1", "keep_ld_prune_0.01" ], "rows": 19490, "table": true, "tojson": true } ], "_help": [ { "page": "AF", "title": "Example allele frequencies", "topics": [ "AF" ] }, { "page": "compute_h2", "title": "Compute heritability from standardized or non-standardized effects", "topics": [ "compute_h2" ] }, { "page": "fast_eigen", "title": "Fast Eigen Decomposition using RcppArmadillo", "topics": [ "fast_eigen" ] }, { "page": "fast_eigen_vals", "title": "Fast Eigenvalues using RcppArmadillo", "topics": [ "fast_eigen_vals" ] }, { "page": "gen_bhat_from_b", "title": "Generate beta hats from standardized or non-standardized direct SNP effects and LD", "topics": [ "gen_bhat_from_b" ] }, { "page": "generate_random_F", "title": "Generate random F", "topics": [ "generate_random_F" ] }, { "page": "GWASBrewer", "title": "GWASBrewer", "topics": [ "GWASBrewer" ] }, { "page": "hapsim_simple", "title": "Generate haplotype data from a haplotype object", "topics": [ "hapsim_simple" ] }, { "page": "ld_mat_list", "title": "Example LD block matrices", "topics": [ "ld_mat_list" ] }, { "page": "R_LD_to_haplodat", "title": "Convert LD matrices to haplotype data", "topics": [ "R_LD_to_haplodat" ] }, { "page": "resample_inddata", "title": "Sample individual level data with joint effects matching a sim_mv object", "topics": [ "resample_inddata" ] }, { "page": "resample_sumstats", "title": "Resample Summary Statistics for Existing Simulation Object", "topics": [ "resample_sumstats" ] }, { "page": "rescale_sumstats", "title": "Re-Scale Effects of a Simulation Object", "topics": [ "rescale_sumstats" ] }, { "page": "rnormalmix", "title": "Simulate from a normal mixture distribution", "topics": [ "rnormalmix" ] }, { "page": "sim_extract_ld", "title": "Extract LD matrix from simulated data", "topics": [ "sim_extract_ld" ] }, { "page": "sim_ld_proxy", "title": "Retrieve LD proxies", "topics": [ "sim_ld_proxy" ] }, { "page": "sim_ld_prune", "title": "LD prune simulated data", "topics": [ "sim_ld_prune" ] }, { "page": "sim_lf", "title": "Simulate summary statistics", "topics": [ "sim_lf" ] }, { "page": "sim_mv", "title": "Simulate multivariate GWAS data", "topics": [ "sim_mv" ] }, { "page": "sim_mv_determined", "title": "Simulate multivariate GWAS Data with Specified Direct Effects", "topics": [ "sim_mv_determined" ] }, { "page": "snpdata", "title": "Example SNP data", "topics": [ "snpdata" ] }, { "page": "xyz_to_G", "title": "Generate G from XYZ Specification", "topics": [ "xyz_to_G" ] } ], "_readme": "https://github.com/jean997/GWASBrewer/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "dplyr", "generics", "glue", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "pillar", "pkgconfig", "plyr", "purrr", "R6", "Rcpp", "RcppArmadillo", "reshape2", "rlang", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "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" } ], "_vignettes": [ { "source": "effect_distribution.Rmd", "filename": "effect_distribution.html", "title": "Controlling Effect Size Distributions", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Default Behavior", "Controlling which Variants are Effect Variants", "Controlling Effect Size Distribution", "Drawing Effects from a Mixture of Normals", "Providing a fixed list of relative effect sizes", "Providing an Exact Set of Direct Effects", "Different effect distributions for different traits", "Example Using Pre-Specified Effects", "Custom Effect Size Distributions" ], "created": "2023-04-17 16:20:39", "modified": "2024-03-27 21:32:26", "commits": 11 }, { "source": "resampling.Rmd", "filename": "resampling.html", "title": "Resampling and Re-Scaling Summary and Individual Level Data", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Resampling Summary Statistics or Individual Level Data from the Same Population", "Resampling Summary Statistics from the Same Population", "Resampling Individual Level Data from the Same Population", "Generating genotypes only", "Generating Genotypes and Phenotypes", "Generating Phenotypes Only", "Resampling Data from a Different Population", "Understanding Effect Size Units", "Changing LD and Allele Frequencies", "Changing Environmental Variance or Covariance", "Rescaling Effect Size Units" ], "created": "2023-08-23 22:42:32", "modified": "2024-03-27 21:32:26", "commits": 4 }, { "source": "simulating_data.Rmd", "filename": "simulating_data.html", "title": "Simulating Data", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Introduction to sim_mv", "Basic Usage", "Input", "Output", "Simplest Usage", "Specifying Causal Relationships Between Traits", "Specifying Allele Frequencies", "Simulating Data with LD", "LD-Pruning, LD-Proxies, and LD Matrix Extraction", "Specifying Sample Size, Sample Overlap, and Environmental Correlation", "Specifying Sample Size and Sample Overlap", "Using Sample Size 0 to Omit Traits", "Understanding Genetic and Environmental Covariance" ], "created": "2022-08-24 22:12:06", "modified": "2024-04-07 17:26:13", "commits": 15 } ], "_score": 5.199755177253475, "_indexed": false, "_nocasepkg": "gwasbrewer", "_universes": [ "mrcieu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.0.0238", "date": "2026-05-18T23:08:59.000Z", "distro": "noble", "arch": "aarch64", "commit": "8ab3b99ce5303911b9a5bcdc9aa0f76295d43612", "fileid": "35290eb456dd7b8358d7e6dcc283ea135de11ef316c8389be5f97bef04f04782", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26065413563" }, { "r": "4.7.0", "os": "linux", "version": "0.3.0.0238", "date": "2026-05-18T23:09:09.000Z", "distro": "noble", "arch": "x86_64", "commit": "8ab3b99ce5303911b9a5bcdc9aa0f76295d43612", "fileid": "780298f5ed38f6270ebf7c1f8a2eb4af988893a5b1e02fefcb2dd035e119f745", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26065413563" }, { "r": "4.6.0", "os": "linux", "version": "0.3.0.0238", "date": "2026-05-18T23:09:30.000Z", "distro": "noble", "arch": "aarch64", "commit": "8ab3b99ce5303911b9a5bcdc9aa0f76295d43612", "fileid": "b9ca14bdb6deb4c818ea0ff1716e2163994ebc23fe8087793c2dcba7ac015d7c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26065413563" }, { "r": "4.6.0", "os": "linux", "version": "0.3.0.0238", "date": "2026-05-18T23:09:02.000Z", "distro": "noble", "arch": "x86_64", "commit": "8ab3b99ce5303911b9a5bcdc9aa0f76295d43612", "fileid": "3dbdbf79e51efda310f2a07d9f24499762c31ca2dd5f1f89c6c7f479f231fda4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26065413563" }, { "r": "4.5.3", "os": "mac", "version": "0.3.0.0238", "date": "2026-05-18T23:08:35.000Z", "arch": "aarch64", "commit": "8ab3b99ce5303911b9a5bcdc9aa0f76295d43612", "fileid": "d6d891f6b73195427aad461ea4d702211f65de26725e2e30e5c398e18d01129f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26065413563" }, { "r": "4.5.3", "os": "mac", "version": "0.3.0.0238", "date": "2026-05-18T23:10:29.000Z", "arch": "x86_64", "commit": "8ab3b99ce5303911b9a5bcdc9aa0f76295d43612", "fileid": "5522c43a51a19fd3b01c332a09275f32804524b690028278d74f3b9b51480d76", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26065413563" }, { "r": "4.6.0", "os": "mac", "version": "0.3.0.0238", "date": "2026-05-18T23:08:37.000Z", "arch": "aarch64", "commit": "8ab3b99ce5303911b9a5bcdc9aa0f76295d43612", "fileid": "15817cbf22a1aa5fc88541f946e3bb8dce66d71ce653e66c44063db435db86c9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26065413563" }, { "r": "4.6.0", "os": "mac", "version": "0.3.0.0238", "date": "2026-05-18T23:10:48.000Z", "arch": "x86_64", "commit": "8ab3b99ce5303911b9a5bcdc9aa0f76295d43612", "fileid": "397357482e510ae01e807a5c58331f0c33dd2974c4c95cfc528924404f6eb84e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26065413563" }, { "r": "4.7.0", "os": "win", "version": "0.3.0.0238", "date": "2026-05-18T23:08:14.000Z", "arch": "x86_64", "commit": "8ab3b99ce5303911b9a5bcdc9aa0f76295d43612", "fileid": "5c3c51e88c5185d42e4932469a9f40dae6a577e49ad8ba3e3d573a73227b96dc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26065413563" }, { "r": "4.5.3", "os": "win", "version": "0.3.0.0238", "date": "2026-05-18T23:08:21.000Z", "arch": "x86_64", "commit": "8ab3b99ce5303911b9a5bcdc9aa0f76295d43612", "fileid": "1a84b6454f2f747b56df68a45b29aa30038a2c8e3c57879bc182037c863f67cf", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26065413563" }, { "r": "4.6.0", "os": "win", "version": "0.3.0.0238", "date": "2026-05-18T23:08:14.000Z", "arch": "x86_64", "commit": "8ab3b99ce5303911b9a5bcdc9aa0f76295d43612", "fileid": "6a8a784e584ef0b79bf5a5c62a1dbefa3d7404d50d667140df2c17ed681c875a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26065413563" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.0.0238", "date": "2026-06-02T15:40:21.000Z", "arch": "emscripten", "commit": "8ab3b99ce5303911b9a5bcdc9aa0f76295d43612", "fileid": "539c5e2b04371891312ea4069877b75cf31083d83aaf7fe0f76d4945b37d9877", "status": "success", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26065413563" } ] }