{ "_id": "6a0f75eeacfb0bcc41c61adb", "Package": "gpyramid", "Type": "Package", "Title": "Identify Efficient Crossing Schemes for Gene Pyramiding", "Version": "0.0.1", "Authors@R": "c(\nperson(\"Shoji\", \"Taniguchi\", email = \"taniguchi.shoji938@naro.go.jp\", role = c(\"aut\", \"cre\")),\nperson(\"The National Agriculture and Food Research Organization (NARO)\", role = \"cph\")\n)", "Maintainer": "Shoji Taniguchi ", "Description": "Calculates the cost of crossing in terms of the number of\nindividuals and generations, which is theoretically formulated\nby Servin et al. (2004) . This\npackage has been designed for selecting appropriate parental\ngenotypes and find the most efficient crossing scheme for gene\npyramiding, especially for plant breeding.", "License": "GPL-2 | GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-21 06:30:00 UTC", "User": "root" }, "Author": "Shoji Taniguchi [aut, cre], The National Agriculture and Food\nResearch Organization (NARO) [cph]", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2025-12-12 21:10:02 UTC", "RemoteUrl": "https://github.com/cran/gpyramid", "RemoteRef": "HEAD", "RemoteSha": "2e20ecc0016fdd8038f44997f81de1c5ec97a72a", "MD5sum": "919e2419eb53944ee6f6c66a118d7a2c", "_user": "cran", "_type": "src", "_file": "gpyramid_0.0.1.tar.gz", "_fileid": "51aef020f9f7b9d0e530df08f424455237baf5cec3cf0f24dfa6af8224f91a2a", "_filesize": 207710, "_sha256": "51aef020f9f7b9d0e530df08f424455237baf5cec3cf0f24dfa6af8224f91a2a", "_created": "2026-05-21T06:30:00.000Z", "_published": "2026-05-21T21:15:26.379Z", "_distro": "noble", "_jobs": [ { "job": 77270181340, "time": 132, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7128785782" }, { "job": 77270181186, "time": 128, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7128784564" }, { "job": 77270180597, "time": 162, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7128749390" }, { "job": 77270180586, "time": 113, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7147379697" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26209295266", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/gpyramid", "_commit": { "id": "2e20ecc0016fdd8038f44997f81de1c5ec97a72a", "author": "Shoji Taniguchi ", "committer": "cran-robot ", "message": "version 0.0.1\n", "time": 1765573802 }, "_maintainer": { "name": "Shoji Taniguchi", "email": "taniguchi.shoji938@naro.go.jp" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "utils", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-50", "n": 1 } ], "_tags": [ { "name": "0.0.1", "date": "2025-12-12" } ], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 153, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/gpyramid" }, "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/gpyramid.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "0.0.1", "date": "2025-12-12" } ], "_exports": [ "allCrosses", "calcCost", "calcCostAll", "findPset", "getFromAll", "util_haplo", "util_recom_mat" ], "_help": [ { "page": "allCrosses", "title": "Generate all crosses from given parent set.", "topics": [ "allCrosses" ] }, { "page": "calcCost", "title": "Function to calculate N_total by the algorithm proposed by Sevin et al. (2004)", "topics": [ "calcCost" ] }, { "page": "calcCostAll", "title": "Function to calculate the number of necessary individuals and generations as the crossing cost for all the crossing schemes. This is the wrapper function of calCost.", "topics": [ "calcCostAll" ] }, { "page": "findPset", "title": "Find parent sets from the candidate cultivars", "topics": [ "findPset" ] }, { "page": "getFromAll", "title": "Function to get one crossing scheme from all the crossing schemes.", "topics": [ "getFromAll" ] }, { "page": "util_haplo", "title": "Util fuunction to generate haplotype dataframe from raw data.", "topics": [ "util_haplo" ] }, { "page": "util_recom_mat", "title": "Util function to generate recom_mat from raw data. It returens the recombination probability based on Halden's map function", "topics": [ "util_recom_mat" ] } ], "_readme": "https://github.com/cran/gpyramid/raw/HEAD/README.md", "_rundeps": [ "ape", "cli", "digest", "dplyr", "generics", "glue", "lattice", "lifecycle", "magrittr", "nlme", "pillar", "pkgconfig", "R6", "Rcpp", "rlang", "tibble", "tidyselect", "utf8", "vctrs", "withr" ], "_vignettes": [ { "source": "Introduction.Rmd", "filename": "Introduction.html", "title": "Introduction", "author": "Shoji Taniguchi", "engine": "knitr::rmarkdown", "headings": [ "0. Introduction to gpyramid package", "1. Set up", "2. Prepare data", "2.1 Gene data", "2.2 Position data", "2.3 Preprosessing", "Generate haplotype dataframe from row data", "Generate recombination probability matrix from raw data", "3. Find parent sets from candidate lines (cultivars)", "4. Calculate the number of necessary individuals and generations", "4.1 Fig 4a (Servin et al., 2004)", "4.2 Fig 4b (Servin et al., 2004)", "4.3 Fig 4c (Servin et al., 2004)" ], "created": "2025-12-12 21:10:02", "modified": "2025-12-12 21:10:02", "commits": 1 }, { "source": "Tutorial.Rmd", "filename": "Tutorial.html", "title": "Tutorial of R package gpyramid", "author": "Shoji Taniguchi", "engine": "knitr::rmarkdown", "headings": [ "1. Set up", "2. Prepare data", "2.1 Gene data", "2.2 Position data", "2.3 Preprosessing", "Generate haplotype dataframe from row data", "Generate recombination probability matrix from raw data", "3. Find parent sets from candidate lines (cultivars)", "4. Calculate the number of necessary individuals and generations", "4.1 Calculate cost of all the crossing schemes", "4.2 Plot cost of each crossing scheme", "4.3 Select the most cost-effective crossing strategy", "4.4 Another example" ], "created": "2025-12-12 21:10:02", "modified": "2025-12-12 21:10:02", "commits": 1 } ], "_score": 3, "_indexed": true, "_nocasepkg": "gpyramid", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.1", "date": "2026-05-21T06:32:08.000Z", "distro": "noble", "commit": "2e20ecc0016fdd8038f44997f81de1c5ec97a72a", "fileid": "accba3766d2486c88746491037948188e2083d6d714a24e7917c3def8970ff51", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26209295266" }, { "r": "4.6.0", "os": "linux", "version": "0.0.1", "date": "2026-05-21T06:32:01.000Z", "distro": "noble", "commit": "2e20ecc0016fdd8038f44997f81de1c5ec97a72a", "fileid": "f1c239014371ec4dd73008d03f83a742312b29955abb5bf54505af296896a692", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26209295266" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.1", "date": "2026-05-21T21:15:09.000Z", "commit": "2e20ecc0016fdd8038f44997f81de1c5ec97a72a", "fileid": "6bb4f2e2e93fe0c361acf5680e4d375e49326a9cca14ad3da625c41fb8a39a17", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26209295266" } ] }