{ "_id": "6a2a64fb7b7a29ca6004046a", "Package": "diaQTL", "Title": "QTL Analysis in Diallel Populations", "Version": "1.13", "Author": "Jeffrey B. Endelman and Rodrigo R. Amadeu", "Maintainer": "Jeffrey Endelman ", "Description": "QTL analysis of diploid and autotetraploid diallel\npopulations. Phenotypes are regressed on genotype\nprobabilities, and the regression coefficients are random\neffects.", "License": "GPL-3 + file LICENSE", "LazyData": "true", "RoxygenNote": "7.3.2", "Roxygen": "list(markdown = TRUE)", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libgmp3-dev libicu-dev libjpeg-dev libpng-dev\nlibxml2-dev libssl-dev", "Repository": "https://polyploids.r-universe.dev", "Date/Publication": "2026-03-13 15:10:01 UTC", "RemoteUrl": "https://github.com/jendelman/diaQTL", "RemoteRef": "HEAD", "RemoteSha": "9526a6d991074822b638f6673a16c100c8cdf242", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-11 07:30:21 UTC", "User": "root" }, "MD5sum": "a0e39f1b6d0971aa3109110eef4e0c9a", "_user": "polyploids", "_type": "src", "_file": "diaQTL_1.13.tar.gz", "_fileid": "8895e75ac44409805fc679895c587032d3bc3f8729c68b2a09d3b0cf3cae9cad", "_filesize": 5872571, "_sha256": "8895e75ac44409805fc679895c587032d3bc3f8729c68b2a09d3b0cf3cae9cad", "_created": "2026-06-11T07:30:21.000Z", "_published": "2026-06-11T07:34:19.662Z", "_distro": "noble", "_jobs": [ { "job": 80743764957, "time": 185, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7557624139" }, { "job": 80743764946, "time": 180, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7557622610" }, { "job": 80743764915, "time": 130, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7557606726" }, { "job": 80743764932, "time": 132, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7557607355" }, { "job": 80741952170, "time": 684, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7557563723" }, { "job": 80743764899, "time": 143, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7557610425" }, { "job": 80743764941, "time": 148, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7557612356" }, { "job": 80743764916, "time": 126, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7557605599" }, { "job": 80743764950, "time": 118, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7557602944" } ], "_buildurl": "https://github.com/r-universe/polyploids/actions/runs/27330623922", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/jendelman/diaQTL", "_commit": { "id": "9526a6d991074822b638f6673a16c100c8cdf242", "author": "jendelman ", "committer": "jendelman ", "message": "v1.13\n", "time": 1773414601 }, "_maintainer": { "name": "Jeffrey Endelman", "email": "endelman@wisc.edu", "login": "jendelman", "description": "", "uuid": 51009800 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "BGLR", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "coda", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "scam", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "arrangements", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "ggfittext", "role": "Imports" }, { "package": "ggdendro", "role": "Imports" }, { "package": "labeling", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "jendelman", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-49", "n": 1 }, { "week": "2026-10", "n": 1 }, { "week": "2026-11", "n": 1 } ], "_tags": [], "_stars": 12, "_contributors": [ { "user": "jendelman", "count": 90, "uuid": 51009800 }, { "user": "rramadeu", "count": 70, "uuid": 10066681 }, { "user": "cristianetaniguti", "count": 1, "uuid": 7572527 } ], "_userbio": { "uuid": 85083275, "type": "organization", "name": "Tools for Polyploids", "description": "Software for molecular breeding of polyploid crops" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/diaQTL" }, "_devurl": "https://github.com/jendelman/diaqtl", "_searchresults": 5, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/diaQTL.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "BayesCI", "convert_mappoly", "convert_onemap", "convert_polyorigin", "convert_rabbit", "diallel_geno", "diallel_geno_pheno", "DIC_thresh", "diplo_freq", "diplo_get", "fine_map", "fitQTL", "get_map", "haplo_cluster", "haplo_freq", "haplo_get", "haplo_match", "haplo_plot", "IBDmat", "phased_parents", "read_data", "scan1", "scan1_permute", "scan1_summary", "set_params" ], "_datasets": [ { "name": "F1codes", "title": "Genotype codes for F1 populations", "object": "F1codes", "class": [ "data.frame" ], "fields": [ "Code", "State" ], "rows": 100, "table": true, "tojson": true }, { "name": "S1codes", "title": "Genotype codes for S1 populations", "object": "S1codes", "class": [ "data.frame" ], "fields": [ "Code", "State" ], "rows": 35, "table": true, "tojson": true } ], "_help": [ { "page": "BayesCI", "title": "Bayesian Credible Interval for QTL position", "topics": [ "BayesCI" ] }, { "page": "convert_mappoly", "title": "Generate diaQTL input files from MAPpoly", "topics": [ "convert_mappoly" ] }, { "page": "convert_onemap", "title": "Generate diaQTL input files from OneMap", "topics": [ "convert_onemap" ] }, { "page": "convert_polyorigin", "title": "Create diaQTL input files from PolyOrigin output", "topics": [ "convert_polyorigin" ] }, { "page": "convert_rabbit", "title": "Generate diaQTL input files from RABBIT MagicReconstruct", "topics": [ "convert_rabbit" ] }, { "page": "diallel_geno_pheno-class", "title": "S4 class with genotype and phenotype data", "topics": [ "diallel_geno_pheno", "diallel_geno_pheno-class" ] }, { "page": "diallel_geno-class", "title": "S4 class with genotype data", "topics": [ "diallel_geno", "diallel_geno-class" ] }, { "page": "DIC_thresh", "title": "delta DIC thresholds for scan1", "topics": [ "DIC_thresh" ] }, { "page": "diplo_freq", "title": "Diplotype frequencies", "topics": [ "diplo_freq" ] }, { "page": "diplo_get", "title": "Dosage of parental diplotypes", "topics": [ "diplo_get" ] }, { "page": "F1codes", "title": "Genotype codes for F1 populations", "topics": [ "F1codes" ] }, { "page": "fine_map", "title": "Visualize haplotype switches for fine mapping", "topics": [ "fine_map" ] }, { "page": "fitQTL", "title": "Fit multiple QTL model", "topics": [ "fitQTL" ] }, { "page": "get_map", "title": "Get map summary from diallel_geno object", "topics": [ "get_map" ] }, { "page": "haplo_cluster", "title": "Cluster parental haplotypes", "topics": [ "haplo_cluster" ] }, { "page": "haplo_freq", "title": "Haplotype frequencies", "topics": [ "haplo_freq" ] }, { "page": "haplo_get", "title": "Dosage of parental haplotypes", "topics": [ "haplo_get" ] }, { "page": "haplo_match", "title": "Match up parental haplotypes", "topics": [ "haplo_match" ] }, { "page": "haplo_plot", "title": "Plot parental haplotype dosage", "topics": [ "haplo_plot" ] }, { "page": "IBDmat", "title": "Realized IBD relationship", "topics": [ "IBDmat" ] }, { "page": "phased_parents", "title": "Visualize phased SNPs of parents", "topics": [ "phased_parents" ] }, { "page": "read_data", "title": "Read data files", "topics": [ "read_data" ] }, { "page": "S1codes", "title": "Genotype codes for S1 populations", "topics": [ "S1codes" ] }, { "page": "scan1", "title": "Single QTL scan", "topics": [ "scan1" ] }, { "page": "scan1_permute", "title": "Permutation test for scan1", "topics": [ "scan1_permute" ] }, { "page": "scan1_summary", "title": "Summary of scan1 result", "topics": [ "scan1_summary" ] }, { "page": "set_params", "title": "Determine number of iterations for MCMC", "topics": [ "set_params" ] } ], "_readme": "https://github.com/jendelman/diaQTL/raw/HEAD/README.md", "_rundeps": [ "arrangements", "BGLR", "cli", "coda", "commonmark", "cpp11", "curl", "dplyr", "farver", "generics", "ggdendro", "ggfittext", "ggplot2", "glue", "gmp", "gridtext", "gtable", "isoband", "jpeg", "labeling", "lattice", "lifecycle", "litedown", "magrittr", "markdown", "MASS", "Matrix", "mgcv", "nlme", "pillar", "pkgconfig", "plyr", "png", "purrr", "R6", "RColorBrewer", "Rcpp", "reshape2", "rlang", "S7", "scales", "scam", "shades", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "truncnorm", "utf8", "vctrs", "viridisLite", "withr", "xfun", "xml2" ], "_vignettes": [ { "source": "diaQTL_vignette.Rmd", "filename": "diaQTL_vignette.html", "title": "diaQTL Vignette", "engine": "knitr::rmarkdown", "headings": [ "Structure of the input files", "1) Pedigree file", "2) Genotype file", "3) Phenotype file", "Read the data", "Setting parameters", "QTL Discovery", "Dominance", "QTL Modeling", "Haplotype-based Selection" ], "created": "2021-04-27 00:46:03", "modified": "2021-06-01 22:28:19", "commits": 3 } ], "_score": 4.556302500767288, "_indexed": false, "_nocasepkg": "diaqtl", "_universes": [ "polyploids" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.13", "date": "2026-06-11T07:33:04.000Z", "distro": "noble", "commit": "9526a6d991074822b638f6673a16c100c8cdf242", "fileid": "de8ab6c3c3c12fb0451dc05659fb9be1bf41b0418b29dc66bd244e1245ba50f7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/polyploids/actions/runs/27330623922" }, { "r": "4.6.0", "os": "linux", "version": "1.13", "date": "2026-06-11T07:33:00.000Z", "distro": "noble", "commit": "9526a6d991074822b638f6673a16c100c8cdf242", "fileid": "f1bfb3cc033424c3cc9764b1f690af9a528e73dace7af5cd5df36bcfb1a86d54", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/polyploids/actions/runs/27330623922" }, { "r": "4.5.3", "os": "mac", "version": "1.13", "date": "2026-06-11T07:32:26.000Z", "commit": "9526a6d991074822b638f6673a16c100c8cdf242", "fileid": "c457253f473e54cec000fbbb7c8ab4dff330b0075d53239fc2803512b2cef731", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/polyploids/actions/runs/27330623922" }, { "r": "4.6.0", "os": "mac", "version": "1.13", "date": "2026-06-11T07:32:25.000Z", "commit": "9526a6d991074822b638f6673a16c100c8cdf242", "fileid": "278481f8eaaf7afd4fd4153875eac7002032d540ac3310964b21fe94414da017", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/polyploids/actions/runs/27330623922" }, { "r": "4.6.0", "os": "wasm", "version": "1.13", "date": "2026-06-11T07:33:03.000Z", "commit": "9526a6d991074822b638f6673a16c100c8cdf242", "fileid": "a811a1ba625f8e4c94bafc01ed559eae002649ac2bbac5c14cce0511312fc9f8", "status": "success", "buildurl": "https://github.com/r-universe/polyploids/actions/runs/27330623922" }, { "r": "4.7.0", "os": "win", "version": "1.13", "date": "2026-06-11T07:32:01.000Z", "commit": "9526a6d991074822b638f6673a16c100c8cdf242", "fileid": "6da8f8bce1b11b84be7cde9dfb6d5678d54cd52541d66efdeadc9954ab456bd6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/polyploids/actions/runs/27330623922" }, { "r": "4.5.3", "os": "win", "version": "1.13", "date": "2026-06-11T07:32:01.000Z", "commit": "9526a6d991074822b638f6673a16c100c8cdf242", "fileid": "9344d5d45c9abe122715fab2024c5d923fe050402c193ffcdbc819c9363da729", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/polyploids/actions/runs/27330623922" }, { "r": "4.6.0", "os": "win", "version": "1.13", "date": "2026-06-11T07:31:53.000Z", "commit": "9526a6d991074822b638f6673a16c100c8cdf242", "fileid": "60f3f39713ab3e3b9dafd6b2dc6831ab213e7ac3fd646e9825386c4099efa582", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/polyploids/actions/runs/27330623922" } ] }