{ "_id": "6ab39fac3d719c1f84091fa6", "Package": "AlphaPart", "Title": "Partition/Decomposition of Breeding Values by Paths of\nInformation", "Description": "A software that implements a method for partitioning\ngenetic trends to quantify the sources of genetic gain in\nbreeding programmes. The partitioning method is described in\nGarcia-Cortes et al. (2008) .\nThe package includes the main function AlphaPart for\npartitioning breeding values and auxiliary functions for\nmanipulating data and summarizing, visualizing, and saving\nresults.", "Authors@R": "c(\nperson(\"Gregor\", \"Gorjanc\", role=c(\"aut\", \"cre\"),\nemail = \"highlander.research.lab@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8008-2787\")),\nperson(\"Jana\",\"Obsteter\", role=\"aut\",\nemail = \"jana.obsteter@kis.si\",\ncomment = c(ORCID = \"0000-0003-1511-3916\")),\nperson(\"Thiago\", \"de Paula Oliveira\", role=c(\"aut\"),\nemail = \"thiago.oliveira@ed.ac.uk\",\ncomment = c(ORCID = \"0000-0002-4555-2584\"))\n)", "Maintainer": "Gregor Gorjanc ", "License": "GPL (>= 2)", "LazyLoad": "yes", "Version": "0.9.8", "Date": "2022-11-13", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-09-23 09:40:00 UTC", "User": "root" }, "VignetteBuilder": "knitr", "RoxygenNote": "7.1.2.9000", "Encoding": "UTF-8", "LazyData": "true", "Config/testthat/edition": "3", "Author": "Gregor Gorjanc [aut, cre]\n(), Jana Obsteter [aut]\n(), Thiago de Paula\nOliveira [aut] ()", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2022-11-15 20:40:05 UTC", "RemoteUrl": "https://github.com/cran/AlphaPart", "RemoteRef": "HEAD", "RemoteSha": "fc954079177b9c84d7b361cca111660ed7e2ae35", "_user": "cran", "_type": "src", "_file": "AlphaPart_0.9.8.tar.gz", "_fileid": "https://r2.ropensci.org/f97bf0dd2de6722361b1853635869260a80260b205e41555b85952194bae375c", "_filesize": 2559716, "_sha256": "f97bf0dd2de6722361b1853635869260a80260b205e41555b85952194bae375c", "_expires": "2027-01-01T09:45:14.000Z", "_created": "2026-09-23T09:40:00.000Z", "_published": "2026-09-23T09:45:16.713Z", "_jobs": [ { "job": 107126672550, "time": 164, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "10743145326" }, { "job": 107126672483, "time": 183, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10743245034" }, { "job": 107126672576, "time": 139, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10742717278" }, { "job": 107126672500, "time": 198, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10742328520" }, { "job": 107125539945, "time": 210, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10742328004" }, { "job": 107126672394, "time": 135, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10742930787" }, { "job": 107126672553, "time": 271, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "10742388364" }, { "job": 107126672468, "time": 193, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10741889974" }, { "job": 107126672625, "time": 227, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10742857074" }, { "job": 107126672574, "time": 135, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10742518686" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/cran/actions/runs/35843934762", "_status": "success", "_upstream": "https://github.com/cran/AlphaPart", "_commit": { "id": "fc954079177b9c84d7b361cca111660ed7e2ae35", "author": "Gregor Gorjanc ", "committer": "cran-robot ", "message": "version 0.9.8\n", "time": 1668544805 }, "_maintainer": { "name": "Gregor Gorjanc", "email": "highlander.research.lab@gmail.com", "orcid": "0000-0001-8008-2787" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "directlabels", "version": ">= 1.1", "role": "Imports" }, { "package": "ggplot2", "version": ">= 0.8.9", "role": "Imports" }, { "package": "pedigree", "version": ">= 1.3.1", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.9.4", "role": "Imports" }, { "package": "methods", "version": ">= 3.6.2", "role": "Imports" }, { "package": "reshape", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "tibble", "version": ">= 3.1.7", "role": "Imports" }, { "package": "RColorBrewer", "version": ">= 1.0-2", "role": "Suggests" }, { "package": "truncnorm", "version": ">= 1.0-5", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "ggridges", "version": ">= 0.5.3", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "gregorgorjanc", "count": 5, "uuid": 725834 }, { "user": "janaobsteter", "count": 1, "uuid": 18226551 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 630, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 451, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/AlphaPart" }, "_mentions": 1, "_searchresults": 28, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/AlphaPart.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "0.6.0", "date": "2019-06-18" }, { "version": "0.7.0", "date": "2019-06-27" }, { "version": "0.8.0", "date": "2020-03-17" }, { "version": "0.8.1", "date": "2020-03-25" }, { "version": "0.8.2", "date": "2021-09-21" }, { "version": "0.8.3", "date": "2021-09-28" }, { "version": "0.8.4", "date": "2021-10-22" }, { "version": "0.9.0", "date": "2022-01-10" }, { "version": "0.9.1", "date": "2022-02-14" }, { "version": "0.9.2", "date": "2022-03-09" }, { "version": "0.9.3", "date": "2022-03-10" }, { "version": "0.9.5", "date": "2022-07-07" }, { "version": "0.9.7", "date": "2022-09-23" }, { "version": "0.9.8", "date": "2022-11-15" } ], "_exports": [ ".checkLevelsMap", ".checkListLevelsMap", ".isCharacterMap", ".unknownList", ".unlistLevelsMap", "AlphaPart", "AlphaPartSubset", "AlphaPartSum", "as.levelsMap", "as.listLevelsMap", "as.object_sizes", "centerPop", "getScale", "is.levelsMap", "is.listLevelsMap", "is.object_sizes", "isUnknown", "mapLevels", "mapLevels<-", "NAToUnknown", "object.size", "pedFixBirthYear", "pedSetBase", "savePlot", "sEBV", "unknownToNA", "write.csv" ], "_datasets": [ { "name": "AlphaPart.ped", "title": "Sample pedigree for partition.", "object": "AlphaPart.ped", "class": [ "data.frame" ], "fields": [ "IId", "FId", "MId", "gen", "country", "gender", "bv1", "bv2" ], "rows": 8, "table": true, "tojson": true } ], "_help": [ { "page": "AlphaPart", "title": "AlphaPart.R", "topics": [ "AlphaPart" ] }, { "page": "AlphaPart.ped", "title": "Sample pedigree for partition.", "topics": [ "AlphaPart.ped" ] }, { "page": "AlphaPartSubset", "title": "AlphaPartSubset.R", "topics": [ "AlphaPartSubset" ] }, { "page": "AlphaPartSum", "title": "AlphaPartSum.R", "topics": [ "AlphaPartSum" ] }, { "page": "pedFixBirthYear", "title": "pedFixBirthYear.R", "topics": [ "pedFixBirthYear" ] }, { "page": "pedSetBase", "title": "pedSetBase.R", "topics": [ "pedSetBase" ] }, { "page": "plot.summaryAlphaPart", "title": "A function to plot summary of partitioned breeding values.", "topics": [ "plot.summaryAlphaPart" ] }, { "page": "print.AlphaPart", "title": "Print method for the output of AlphaPart function.", "topics": [ "print.AlphaPart" ] }, { "page": "print.plotSummaryAlphaPart", "title": "Print a plot generate by the function 'plotSummaryAlphaPart'", "topics": [ "print.plotSummaryAlphaPart" ] }, { "page": "print.summaryAlphaPart", "title": "Print method for objects of the class summaryAlphaPart.", "topics": [ "print.summaryAlphaPart" ] }, { "page": "savePlot", "title": "Save plot method for 'AlphaPart'", "topics": [ "savePlot" ] }, { "page": "savePlot.plotSummaryAlphaPart", "title": "Save plot objects on the disk for permanent storage. Function 'savePlot' from the 'grDevices' package works for current page on graphical device. This is an attempt to make this function generic so that one can define 'savePlot' methods for particular needs.", "topics": [ "savePlot.default", "savePlot.plotSummaryAlphaPart" ] }, { "page": "summary.AlphaPart", "title": "A function to summarize AlphaPart object.", "topics": [ "summary.AlphaPart" ] }, { "page": "write.csv", "title": "write.csv.R", "topics": [ "write.csv", "write.csv.AlphaPart", "write.csv.default", "write.csv.summaryAlphaPart" ] } ], "_pkglogo": "https://github.com/cran/AlphaPart/raw/HEAD/man/figures/logo.svg", "_rundeps": [ "cli", "cpp11", "data.table", "directlabels", "dplyr", "farver", "generics", "ggplot2", "glue", "gtable", "HaploSim", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "pedigree", "pillar", "pkgconfig", "plyr", "R6", "RColorBrewer", "Rcpp", "reshape", "rlang", "S7", "scales", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "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": "alphapart-vignette.Rmd", "filename": "alphapart-vignette.html", "title": "AlphaPart - R implementation of the method for partitioning genetic trends", "author": "Gregor Gorjanc, Jana Obsteter, Thiago de Paula Oliveira", "engine": "knitr::rmarkdown", "headings": [ "AlphaPart" ], "created": "2021-09-21 05:50:05", "modified": "2022-09-23 06:10:06", "commits": 2 }, { "source": "alphapart-variance.Rmd", "filename": "alphapart-variance.html", "title": "Partitioning genetic trends in mean and variance", "author": "Gregor Gorjanc, Jana Obsteter, Thiago de Paula Oliveira", "engine": "knitr::rmarkdown", "headings": [ "Loading packages", "Loading datafile", "Partitioning trends in genetic mean and variance", "Example of plots to analyse the results" ], "created": "2022-09-23 06:10:06", "modified": "2022-09-23 06:10:06", "commits": 1 } ], "_score": 2.7481880270062007, "_indexed": true, "_nocasepkg": "alphapart", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.9.8", "date": "2026-09-23T09:42:29.000Z", "distro": "resolute", "arch": "aarch64", "commit": "fc954079177b9c84d7b361cca111660ed7e2ae35", "fileid": "https://r2.ropensci.org/9f783b4b0d0425a301f1169dc2789026b815d0ee9f5e7fb3d8e1efa1e4c18235", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/35843934762" }, { "r": "4.7.0", "os": "linux", "version": "0.9.8", "date": "2026-09-23T09:42:50.000Z", "distro": "resolute", "arch": "x86_64", "commit": "fc954079177b9c84d7b361cca111660ed7e2ae35", "fileid": "https://r2.ropensci.org/99aac7371d46c31ce0d8c690d130d8586f43418a441f04343f6d158c01edce9a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/35843934762" }, { "r": "4.6.1", "os": "linux", "version": "0.9.8", "date": "2026-09-23T09:42:08.000Z", "distro": "resolute", "arch": "aarch64", "commit": "fc954079177b9c84d7b361cca111660ed7e2ae35", "fileid": "https://r2.ropensci.org/6569b6d972e463e05cf78be2089a03e269ceb80471d1a54fa3b2b152479bc3a9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/35843934762" }, { "r": "4.6.1", "os": "linux", "version": "0.9.8", "date": "2026-09-23T09:42:52.000Z", "distro": "resolute", "arch": "x86_64", "commit": "fc954079177b9c84d7b361cca111660ed7e2ae35", "fileid": "https://r2.ropensci.org/e38b0029b52a422e6739e1348d864bb794dbac8409e676deb43bc3b0cdb3d6c9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/35843934762" }, { "r": "4.6.0", "os": "wasm", "version": "0.9.8", "date": "2026-09-23T09:42:28.000Z", "arch": "emscripten", "commit": "fc954079177b9c84d7b361cca111660ed7e2ae35", "fileid": "https://r2.ropensci.org/512cb04d656ff6728cdff61074744ca6dbe2c0edad84a4c2836f8f027e6380ef", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/35843934762" }, { "r": "4.7.0", "os": "win", "version": "0.9.8", "date": "2026-09-23T09:43:50.000Z", "arch": "aarch64", "commit": "fc954079177b9c84d7b361cca111660ed7e2ae35", "fileid": "https://r2.ropensci.org/898990768b1f5da164582d071a670c85c3357358930f889f608335fd157401b9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/35843934762" }, { "r": "4.7.0", "os": "win", "version": "0.9.8", "date": "2026-09-23T09:41:33.000Z", "arch": "x86_64", "commit": "fc954079177b9c84d7b361cca111660ed7e2ae35", "fileid": "https://r2.ropensci.org/642fd7413a55ff11b82f45e27a34634b1715c0eab2216c1ceaa4c61174cbb97d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/35843934762" }, { "r": "4.6.1", "os": "win", "version": "0.9.8", "date": "2026-09-23T09:43:11.000Z", "arch": "aarch64", "commit": "fc954079177b9c84d7b361cca111660ed7e2ae35", "fileid": "https://r2.ropensci.org/9db8b910c9db80da892907c07f6896af22cb492dbe337cb9056d4605613427e5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/35843934762" }, { "r": "4.6.1", "os": "win", "version": "0.9.8", "date": "2026-09-23T09:41:18.000Z", "arch": "x86_64", "commit": "fc954079177b9c84d7b361cca111660ed7e2ae35", "fileid": "https://r2.ropensci.org/7c59fda643bafee3ed5edee479c7c023450e80937344ece46dc65e318ae13f62", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/35843934762" } ] }