{ "_id": "6ae20c783d0f299392dcfbfe", "Package": "NAM", "Type": "Package", "Title": "Nested Association Mapping", "Version": "1.8.0", "Date": "2026-01-23", "Maintainer": "Alencar Xavier ", "Authors@R": "c(person(\"Alencar\", \"Xavier\", role=c(\"aut\", \"cre\"), email = \"alenxav@gmail.com\"), person(\"William\", \"Muir\", role=c(\"aut\")),person(\"Katy\", \"Rainey\", role=c(\"aut\")),person(\"Shizhong\", \"Xu\", role=c(\"aut\")))", "Description": "Designed for association studies in nested association\nmapping (NAM) panels, experimental and random panels. The\nmethod is described by Xavier et al. (2015)\n. It includes tools for\ngenome-wide associations of multiple populations, marker\nquality control, population genetics analysis, genome-wide\nprediction, solving mixed models and finding variance\ncomponents through likelihood and Bayesian methods.", "License": "GPL-3", "NeedsCompilation": "yes", "VignetteBuilder": "knitr", "Packaged": { "Date": "2026-10-28 11:07:26 UTC", "User": "root" }, "Author": "Alencar Xavier [aut, cre], William Muir [aut], Katy Rainey\n[aut], Shizhong Xu [aut]", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-01-24 06:49:49 UTC", "RemoteUrl": "https://github.com/cran/NAM", "RemoteRef": "HEAD", "RemoteSha": "e2980d8fc7be457e0a5e65abead7b96a1ce01111", "_user": "cran", "_type": "src", "_file": "NAM_1.8.0.tar.gz", "_fileid": "https://r2.ropensci.org/a7cd71f7f756f9195e16b6ae11d47006a6daa52da31fa7e1c870994a65beb85b", "_filesize": 1369940, "_sha256": "a7cd71f7f756f9195e16b6ae11d47006a6daa52da31fa7e1c870994a65beb85b", "_expires": "2027-02-05T11:18:29.000Z", "_created": "2026-10-28T11:07:26.000Z", "_published": "2026-10-28T14:53:44.568Z", "_upstream": "https://github.com/cran/NAM", "_status": "success", "_maintainer": { "name": "Alencar Xavier", "email": "alenxav@gmail.com", "login": "alenxav", "description": "BS in agronomy and PhD in plant breeding & statistical genetics\n", "uuid": 33139566 }, "_jobs": [ { "job": 122891405143, "time": 109, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12811093450" }, { "job": 122891404166, "time": 567, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12810709461" }, { "job": 122891405591, "time": 612, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12810984942" }, { "job": 122891404912, "time": 133, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12810943063" }, { "job": 122891402716, "time": 193, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12811605852" }, { "job": 122891404351, "time": 103, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12811153261" }, { "job": 122891401918, "time": 248, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12826216323" }, { "job": 122891405261, "time": 135, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12811072860" }, { "job": 122891404883, "time": 241, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12810379030" }, { "job": 122891404667, "time": 471, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12811761009" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/40677089389", "_commit": { "id": "e2980d8fc7be457e0a5e65abead7b96a1ce01111", "author": "Alencar Xavier ", "committer": "cran-robot ", "message": "version 1.8.0\n", "time": 1769237389 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.2.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "bWGR", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2026-04", "n": 1 } ], "_tags": [ { "name": "1.8.0", "date": "2026-01-24" } ], "_stars": 0, "_contributors": [ { "user": "alenxav", "count": 21, "uuid": 33139566 }, { "user": "alencarx", "count": 17, "uuid": 6987882 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 634, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 689, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/NAM" }, "_mentions": 18, "_searchresults": 44, "_topics": [ "openblas", "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NAM.html" ], "_homeurl": "https://github.com/alenxav/nam", "_realowner": "alenxav", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2015-01-03" }, { "version": "1.0.1", "date": "2015-01-05" }, { "version": "1.0.2", "date": "2015-01-15" }, { "version": "1.0.2.1", "date": "2015-01-24" }, { "version": "1.0.2.2", "date": "2015-02-03" }, { "version": "1.1", "date": "2015-03-11" }, { "version": "1.1.2", "date": "2015-04-01" }, { "version": "1.2", "date": "2015-04-07" }, { "version": "1.3", "date": "2015-04-22" }, { "version": "1.3.2", "date": "2015-05-03" }, { "version": "1.3.3", "date": "2015-07-16" }, { "version": "1.3.4", "date": "2015-08-09" }, { "version": "1.4", "date": "2015-09-02" }, { "version": "1.4.1", "date": "2015-10-16" }, { "version": "1.4.2", "date": "2015-11-20" }, { "version": "1.4.3", "date": "2016-01-28" }, { "version": "1.4.4", "date": "2016-03-19" }, { "version": "1.4.5", "date": "2016-06-17" }, { "version": "1.4.6", "date": "2016-08-08" }, { "version": "1.4.7", "date": "2016-09-14" }, { "version": "1.4.8", "date": "2016-09-21" }, { "version": "1.4.9", "date": "2016-10-20" }, { "version": "1.5.0", "date": "2016-10-20" }, { "version": "1.5.1", "date": "2017-04-11" }, { "version": "1.5.3", "date": "2017-08-15" }, { "version": "1.5.4", "date": "2017-10-17" }, { "version": "1.5.5", "date": "2018-02-11" }, { "version": "1.6", "date": "2018-05-11" }, { "version": "1.6.1", "date": "2018-06-28" }, { "version": "1.6.2", "date": "2018-08-24" }, { "version": "1.6.3", "date": "2018-09-12" }, { "version": "1.6.4", "date": "2018-09-29" }, { "version": "1.6.5", "date": "2019-02-11" }, { "version": "1.7", "date": "2019-02-13" }, { "version": "1.7.1", "date": "2019-03-11" }, { "version": "1.7.2", "date": "2019-04-12" }, { "version": "1.7.3", "date": "2019-09-23" }, { "version": "1.8.0", "date": "2026-01-24" } ], "_exports": [ "BCpi", "ben", "BRR2", "calcSize", "cleanREP", "CNT", "covar", "eigX", "emBA", "emBB", "emBC", "emBD", "emBL", "emCV", "emDE", "emEN", "emGWA", "emML", "emML2", "emMX", "emRR", "Fst", "funI", "funX", "G2A_Kernels", "GAU", "Gdist", "gibbs", "gibbs2", "gmm", "GRM", "gs", "gwas", "gwas2", "gwas3", "gwasGE", "IMP", "Import_data", "inputRow", "KMUP", "KMUP2", "LD", "markov", "MCreml", "meta3", "mkr", "mkr2X", "ml", "mrr", "mrr2X", "mrrFast", "mrrV2", "MSX", "NNcov", "NNsrc", "NOR", "PedMat", "PedMat2", "pegs", "PEGS_lapack", "plot.fst", "plot.gibbs", "plot.H2", "plot.NAM", "press", "reference", "reml", "SAMP", "SAMP2", "snpH2", "snpQC", "SPC", "SPM", "timesMatrix", "timesVec", "wgr" ], "_datasets": [ { "name": "chr", "title": "Tetra-seed Pods", "object": "tpod", "file": "tpod.RData", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "fam", "title": "Tetra-seed Pods", "object": "tpod", "file": "tpod.RData", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "gen", "title": "Tetra-seed Pods", "object": "tpod", "file": "tpod.RData", "class": [ "matrix", "array" ], "fields": [], "rows": 196, "table": true, "tojson": true }, { "name": "Gen", "title": "Multi-environmental trial", "object": "met", "file": "met.RData", "class": [ "data.frame" ], "fields": [], "rows": 5555, "table": true, "tojson": true }, { "name": "Obs", "title": "Multi-environmental trial", "object": "met", "file": "met.RData", "class": [ "data.frame" ], "fields": [ "ID", "Year", "Block", "Row", "Col", "YLD", "DTM", "ACC" ], "rows": 12762, "table": true, "tojson": true }, { "name": "simu", "title": "Pseudo-Expectation Gauss-Seidel for Multivariate Models", "object": "test", "file": "test.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "X", "title": "Pseudo-Expectation Gauss-Seidel for Multivariate Models", "object": "test", "file": "test.RData", "class": [ "matrix", "array" ], "fields": [], "rows": 500, "table": true, "tojson": true }, { "name": "y", "title": "Tetra-seed Pods", "object": "tpod", "file": "tpod.RData", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "Y", "title": "Pseudo-Expectation Gauss-Seidel for Multivariate Models", "object": "test", "file": "test.RData", "class": [ "matrix", "array" ], "fields": [ "y1", "y2", "y3", "y4", "y5", "y6", "y7", "y8", "y9", "y10" ], "rows": 500, "table": true, "tojson": true } ], "_help": [ { "page": "NAM-package", "title": "Nested Association Mapping", "topics": [ "NAM-package", "NAM" ] }, { "page": "tpod", "title": "Tetra-seed Pods", "topics": [ "chr", "fam", "gen", "tpod", "y" ] }, { "page": "met", "title": "Multi-environmental trial", "topics": [ "Gen", "met", "Obs" ] }, { "page": "Fst", "title": "Fixation Index", "topics": [ "Fst", "plot.fst" ] }, { "page": "gwas", "title": "Empirical Bayes Genome Wide Association Mapping", "topics": [ "gwas", "gwas2", "gwas3", "gwasGE", "meta3" ] }, { "page": "wgr", "title": "Genome-wide prediction", "topics": [ "ben", "wgr" ] }, { "page": "Manhattan", "title": "Manhattan plot for Association Studies", "topics": [ "plot.NAM" ] }, { "page": "gibbs", "title": "Bayesian Mixed Model", "topics": [ "gibbs", "gibbs2", "ml", "plot.gibbs" ] }, { "page": "pegs", "title": "Pseudo-Expectation Gauss-Seidel for Multivariate Models", "topics": [ "pegs", "PEGS_lapack", "simu", "X", "Y" ] }, { "page": "reml", "title": "Restricted Maximum Likelihood", "topics": [ "MCreml", "reml" ] }, { "page": "gmm", "title": "Genomic mixed model", "topics": [ "gmm" ] }, { "page": "Internals", "title": "Internal functions", "topics": [ "BCpi", "BRR2", "calcSize", "CNT", "covar", "eigX", "emBA", "emBB", "emBC", "emBD", "emBL", "emCV", "emDE", "emEN", "emGWA", "emML", "emML2", "emMX", "emRR", "funI", "funX", "G2A_Kernels", "GAU", "Gdist", "GRM", "gs", "IMP", "Import_data", "inputRow", "KMUP", "KMUP2", "LD", "markov", "mkr", "mkr2X", "mrr", "mrr2X", "mrrFast", "mrrV2", "MSX", "NNcov", "NNsrc", "NOR", "PedMat", "PedMat2", "press", "RcppExports", "SAMP", "SAMP2", "SPC", "SPM", "timesMatrix", "timesVec" ] }, { "page": "snpH2", "title": "SNP heritability", "topics": [ "plot.H2", "snpH2" ] }, { "page": "snpQC", "title": "SNP Quality Control", "topics": [ "cleanREP", "reference", "snpQC" ] } ], "_rundeps": [ "Rcpp" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "vignette2.Rmd", "filename": "vignette2.html", "title": "Meta-analysis", "author": "Alencar Xavier and Shizhong Xu", "engine": "knitr::rmarkdown", "headings": [ "Meta-analysis of multiple populations along with GxE", "Genome-wide association", "Meta-analysis", "AMMI term", "Hypothesis testing", "Woodbury's matrix identities" ], "created": "2016-01-29 00:10:31", "modified": "2026-01-24 06:49:49", "commits": 9 }, { "source": "vignette1.Rmd", "filename": "vignette1.html", "title": "Introduction to NAM", "author": "Alencar Xavier (alenxav@gmail.com)", "engine": "knitr::rmarkdown", "headings": [ "1. Installing the NAM package", "2. Loading and formatting data", "3. Genome-wide association studies", "4. Marker quality control", "5. Signatures of selection", "6. BLUPs and GEBVs", "7. Finding substructures", "8. Other structured populations", "9. Further background" ], "created": "2016-08-09 01:10:41", "modified": "2026-01-24 06:49:49", "commits": 14 } ], "_score": 4.421603926869831, "_indexed": false, "_nocasepkg": "nam", "_universes": [ "cran" ], "_indexurl": "https://alenxav.r-universe.dev/NAM", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.8.0", "date": "2026-10-28T11:09:13.000Z", "distro": "resolute", "arch": "aarch64", "commit": "e2980d8fc7be457e0a5e65abead7b96a1ce01111", "fileid": "https://r2.ropensci.org/a1d0c4e3749ef2c9eea410387ee76d54d4cf94f698db3182cb7af5d0fe8e483a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40677089389" }, { "r": "4.7.0", "os": "linux", "version": "1.8.0", "date": "2026-10-28T11:14:03.000Z", "distro": "resolute", "arch": "x86_64", "commit": "e2980d8fc7be457e0a5e65abead7b96a1ce01111", "fileid": "https://r2.ropensci.org/90b05b32cfe9add6ba99253a16cc297be85456382d05d69a7406714b8082602e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40677089389" }, { "r": "4.6.1", "os": "linux", "version": "1.8.0", "date": "2026-10-28T11:16:53.000Z", "distro": "resolute", "arch": "aarch64", "commit": "e2980d8fc7be457e0a5e65abead7b96a1ce01111", "fileid": "https://r2.ropensci.org/e9d199d55d9b508312aa5d75b66e41b66983ef7419f9f96091331c62dfd83c8a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40677089389" }, { "r": "4.6.1", "os": "linux", "version": "1.8.0", "date": "2026-10-28T11:09:29.000Z", "distro": "resolute", "arch": "x86_64", "commit": "e2980d8fc7be457e0a5e65abead7b96a1ce01111", "fileid": "https://r2.ropensci.org/4e95dfa7f75f0e2b4f187a0958e03122b176ad37ef64ca8f5c6409e40b3e5eff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40677089389" }, { "r": "4.6.0", "os": "wasm", "version": "1.8.0", "date": "2026-10-28T11:09:33.000Z", "arch": "emscripten", "commit": "e2980d8fc7be457e0a5e65abead7b96a1ce01111", "fileid": "https://r2.ropensci.org/aac52a150c0de8f45f11aa4bafdcea4044bcf6f540cfa0780ab474a468e7b159", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/40677089389" }, { "r": "4.7.0", "os": "win", "version": "1.8.0", "date": "2026-10-28T14:52:28.000Z", "arch": "aarch64", "commit": "e2980d8fc7be457e0a5e65abead7b96a1ce01111", "fileid": "https://r2.ropensci.org/a1af04930383fde96dec4a8a45c59c2d8ce85735b10ddc731e8165fa42033acf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40677089389" }, { "r": "4.7.0", "os": "win", "version": "1.8.0", "date": "2026-10-28T11:08:49.000Z", "arch": "x86_64", "commit": "e2980d8fc7be457e0a5e65abead7b96a1ce01111", "fileid": "https://r2.ropensci.org/d8a52b619fe907e8ace9f889771d22741fae5f3cbfde8c103c17c5745bee3ef5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40677089389" }, { "r": "4.6.1", "os": "win", "version": "1.8.0", "date": "2026-10-28T11:11:06.000Z", "arch": "aarch64", "commit": "e2980d8fc7be457e0a5e65abead7b96a1ce01111", "fileid": "https://r2.ropensci.org/4af29dd4388f715941027e0592ab78299d3ee7499c0e298b6fe545357c3df535", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40677089389" }, { "r": "4.6.1", "os": "win", "version": "1.8.0", "date": "2026-10-28T11:14:35.000Z", "arch": "x86_64", "commit": "e2980d8fc7be457e0a5e65abead7b96a1ce01111", "fileid": "https://r2.ropensci.org/249320359c4c565e4eee3d1c8e2cf83935b450e45f7da541c26a62187240f1c5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40677089389" } ] }