{ "_id": "6acd783da14063b82c3ac11b", "Package": "Familia", "Title": "'shiny' Application for Population Structure and Ancestry\nAssessments", "Version": "2.0.0", "Authors@R": "c(\nperson(\"Josue\", \"Chinchilla-Vargas\",\nrole = c(\"aut\",\"cre\"),\nemail = \"josue.chinchilla@ufl.edu\"),\nperson(c(\"Alexander\", \"M.\"), \"Sandercock\",\nrole = \"aut\"),\nperson(\"Breeding Insight Team\",\nrole = \"aut\"))", "Description": "Provides a 'shiny' web application developed by the\nBreeding Insight team to support pedigree validation and\nancestry assessment of plant and animal populations. The app\nintegrates Mendelian error analysis, parentage assignment and\ngenetic composition/ancestry methods to help researchers\nevaluate genomic relationships through an accessible, web-based\ninterface without requiring command-line tools. Pedigree\nvalidation, Mendelian error analysis and parentage assignment\nbuild on the 'BIGpopA' package\n() and support\ndiploid and polyploid data. Ancestry estimation uses the sparse\nnon-negative matrix factorization method of Frichot et al.\n(2014) as implemented in the\n'LEA' package by Frichot and Francois (2015)\n. Line and breed composition are\nestimated using the breed composition regression method of\nFunkhouser et al. (2017) , extended\nto polyploid species by Sandercock et al. (2025)\n.", "License": "Apache License (>= 2)", "URL": "https://github.com/Breeding-Insight/Familia", "BugReports": "https://github.com/Breeding-Insight/Familia/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "biocViews": "", "Language": "en-US", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nzlib1g-dev", "Repository": "https://breeding-insight.r-universe.dev", "Date/Publication": "2026-08-24 13:30:47 UTC", "RemoteUrl": "https://github.com/breeding-insight/familia", "RemoteRef": "HEAD", "RemoteSha": "03a5beded1e2f96f118cac87bc5ad94737d5ef88", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-13 00:12:09 UTC", "User": "root" }, "Author": "Josue Chinchilla-Vargas [aut, cre],\nAlexander M. Sandercock [aut],\nBreeding Insight Team [aut]", "Maintainer": "Josue Chinchilla-Vargas ", "_user": "breeding-insight", "_type": "src", "_file": "Familia_2.0.0.tar.gz", "_fileid": "https://r2.ropensci.org/e9b829b9e6a38b89ad75f1d6ea6c3b6408db706d440f1a318b45f6365ac2f2e4", "_filesize": 719460, "_sha256": "e9b829b9e6a38b89ad75f1d6ea6c3b6408db706d440f1a318b45f6365ac2f2e4", "_expires": "2027-01-21T00:15:55.000Z", "_created": "2026-10-13T00:12:09.000Z", "_published": "2026-10-13T00:15:57.706Z", "_buildurl": "https://github.com/r-universe/breeding-insight/actions/runs/38325770958", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 115064989802, "time": 169, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11779974406" }, { "job": 115064989813, "time": 186, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11780328942" }, { "job": 115064989801, "time": 81, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11780278866" }, { "job": 115064989872, "time": 146, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11780573671" }, { "job": 115064032075, "time": 212, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11780358602" }, { "job": 115064989749, "time": 148, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11781167018" }, { "job": 115064989709, "time": 112, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11780633576" }, { "job": 115064989775, "time": 106, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11780588534" }, { "job": 115064989769, "time": 116, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11780094197" } ], "_upstream": "https://github.com/breeding-insight/familia", "_commit": { "id": "03a5beded1e2f96f118cac87bc5ad94737d5ef88", "author": "josue.chinchilla ", "committer": "josue.chinchilla ", "message": "2.0.0 submission to CRAN\n", "time": 1787578247 }, "_maintainer": { "name": "Josue Chinchilla-Vargas", "email": "josue.chinchilla@ufl.edu", "login": "josuechinchilla", "description": "Interested in using animal breeding and genomics to improve food security and adaptation to changing environmental conditions", "uuid": 50248642 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "BIGpopA", "version": ">= 2.0.0", "role": "Imports" }, { "package": "bs4Dash", "role": "Imports" }, { "package": "config", "role": "Imports" }, { "package": "curl", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "DT", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "golem", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "openxlsx", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "shiny", "role": "Imports" }, { "package": "shinydisconnect", "role": "Imports" }, { "package": "shinyjs", "role": "Imports" }, { "package": "shinyWidgets", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "vcfR", "version": ">= 1.15.0", "role": "Imports" }, { "package": "withr", "role": "Imports" }, { "package": "zip", "role": "Imports" }, { "package": "LEA", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "breeding-insight", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-03", "n": 3 }, { "week": "2026-09", "n": 1 }, { "week": "2026-10", "n": 2 }, { "week": "2026-21", "n": 1 }, { "week": "2026-23", "n": 4 }, { "week": "2026-25", "n": 1 }, { "week": "2026-28", "n": 3 }, { "week": "2026-30", "n": 2 }, { "week": "2026-33", "n": 2 }, { "week": "2026-34", "n": 1 }, { "week": "2026-35", "n": 1 } ], "_tags": [ { "name": "v0.1.0", "date": "2026-06-02" }, { "name": "v1.0.0", "date": "2026-06-02" }, { "name": "v1.0.1", "date": "2026-06-15" }, { "name": "v1.0.2", "date": "2026-07-09" }, { "name": "v1.0.4", "date": "2026-08-13" }, { "name": "v2.0.0", "date": "2026-08-22" } ], "_stars": 0, "_contributors": [ { "user": "josuechinchilla", "count": 40, "uuid": 50248642 }, { "user": "alex-sandercock", "count": 11, "uuid": 39815775 }, { "user": "amsande", "count": 11, "uuid": 222830770 } ], "_userbio": { "uuid": 57234414, "type": "organization", "name": "Breeding Insight", "followers": 65, "description": "Combining genomics and informatics to accelerate genetic gains." }, "_downloads": { "count": 245, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Familia" }, "_devurl": "https://github.com/breeding-insight/familia", "_searchresults": 1, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/Familia.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/breeding-insight/familia", "_realowner": "breeding-insight", "_cranurl": true, "_releases": [ { "version": "1.0.3", "date": "2026-07-29" }, { "version": "2.0.0", "date": "2026-08-24" } ], "_exports": [ "run_app" ], "_help": [ { "page": "run_app", "title": "Run the Shiny Application", "topics": [ "run_app" ] } ], "_readme": "https://github.com/breeding-insight/familia/raw/HEAD/README.md", "_rundeps": [ "ape", "askpass", "attempt", "backports", "base64enc", "BIGpopA", "bs4Dash", "bslib", "cachem", "checkmate", "cli", "cluster", "codetools", "commonmark", "config", "cpp11", "crosstalk", "curl", "data.table", "digest", "dplyr", "DT", "evaluate", "farver", "fastmap", "fontawesome", "fresh", "fs", "generics", "ggplot2", "glue", "golem", "gtable", "highr", "hms", "htmltools", "htmlwidgets", "httpuv", "httr", "isoband", "janitor", "jquerylib", "jsonlite", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "lubridate", "magrittr", "MASS", "Matrix", "memoise", "memuse", "mgcv", "mime", "nlme", "openssl", "openxlsx", "otel", "permute", "pillar", "pinfsc50", "pkgconfig", "promises", "purrr", "quadprog", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rlang", "rmarkdown", "rstudioapi", "S7", "sass", "scales", "shiny", "shinydisconnect", "shinyjs", "shinyWidgets", "snakecase", "sourcetools", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "timechange", "tinytex", "utf8", "vcfR", "vctrs", "vegan", "viridisLite", "waiter", "withr", "xfun", "xtable", "yaml", "zip" ], "_score": 4.041392685158225, "_indexed": true, "_nocasepkg": "familia", "_universes": [ "breeding-insight", "josuechinchilla" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.0.0", "date": "2026-10-13T00:14:49.000Z", "distro": "resolute", "commit": "03a5beded1e2f96f118cac87bc5ad94737d5ef88", "fileid": "https://r2.ropensci.org/3cd523d85a9d06fcac9914cd50ffddd527d59a07942a74e7f6f971d6175869a9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/breeding-insight/actions/runs/38325770958" }, { "r": "4.6.1", "os": "linux", "version": "2.0.0", "date": "2026-10-13T00:14:57.000Z", "distro": "resolute", "commit": "03a5beded1e2f96f118cac87bc5ad94737d5ef88", "fileid": "https://r2.ropensci.org/f864aa894957a65a9cd21fda5363cdcbb4c068f40e7c42e5563df467488ebec8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/breeding-insight/actions/runs/38325770958" }, { "r": "4.5.3", "os": "mac", "version": "2.0.0", "date": "2026-10-13T00:13:41.000Z", "commit": "03a5beded1e2f96f118cac87bc5ad94737d5ef88", "fileid": "https://r2.ropensci.org/7f6f66b47d0856ad2abb93c01f006fd1c897138c0a570438824af11f419657b2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/breeding-insight/actions/runs/38325770958" }, { "r": "4.6.1", "os": "mac", "version": "2.0.0", "date": "2026-10-13T00:14:29.000Z", "commit": "03a5beded1e2f96f118cac87bc5ad94737d5ef88", "fileid": "https://r2.ropensci.org/ad3d718ef3248b9d865fcb4ba019d8e710320de88f72df0e4d404b0726066e62", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/breeding-insight/actions/runs/38325770958" }, { "r": "4.6.0", "os": "wasm", "version": "2.0.0", "date": "2026-10-13T00:14:55.000Z", "commit": "03a5beded1e2f96f118cac87bc5ad94737d5ef88", "fileid": "https://r2.ropensci.org/b8994b2ee4a257569b81bcd8afd0c970e527b0150e4604749477dd24747ad132", "status": "success", "buildurl": "https://github.com/r-universe/breeding-insight/actions/runs/38325770958" }, { "r": "4.7.0", "os": "win", "version": "2.0.0", "date": "2026-10-13T00:13:35.000Z", "commit": "03a5beded1e2f96f118cac87bc5ad94737d5ef88", "fileid": "https://r2.ropensci.org/074f1a393b4b3ae5c63668e3802ff0c9f10b98546289eb1f5545dd59cc52a5e1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/breeding-insight/actions/runs/38325770958" }, { "r": "4.5.3", "os": "win", "version": "2.0.0", "date": "2026-10-13T00:13:32.000Z", "commit": "03a5beded1e2f96f118cac87bc5ad94737d5ef88", "fileid": "https://r2.ropensci.org/bf6847623cbe3cdddc830968ea6e64dfc0044abdac3143e57070c4f966dd5782", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/breeding-insight/actions/runs/38325770958" }, { "r": "4.6.1", "os": "win", "version": "2.0.0", "date": "2026-10-13T00:13:34.000Z", "commit": "03a5beded1e2f96f118cac87bc5ad94737d5ef88", "fileid": "https://r2.ropensci.org/50b30231f059a675af7e283a5aafb6a98a6ad3feb0c4fa898135b7f975c20645", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/breeding-insight/actions/runs/38325770958" } ] }