{ "_id": "6a19eb4b1d7bb097a09c71cc", "Type": "Package", "Package": "QBMS", "Title": "Query the Breeding Management System(s)", "Version": "2.0.0", "Date": "2025-08-02", "Authors@R": "c(\nperson(\"Khaled\", \"Al-Shamaa\", , \"k.el-shamaa@cgiar.org\", role = c(\"aut\", \"cre\")),\nperson(\"Mariano Omar\", \"Crimi\", , \"m.crimi@cgiar.org\", role = \"ctb\"),\nperson(\"Zakaria\", \"Kehel\", , \"z.kehel@cgiar.org\", role = \"ctb\"),\nperson(\"Johan\", \"Aparicio\", , \"j.aparicio@cgiar.org\", role = \"ctb\"),\nperson(\"ICARDA\", role = \"cph\")\n)", "Author": "Khaled Al-Shamaa [aut, cre], Mariano Omar Crimi [ctb], Zakaria\nKehel [ctb], Johan Aparicio [ctb], ICARDA [cph]", "Maintainer": "Khaled Al-Shamaa ", "Description": "This R package assists breeders in linking data systems\nwith their analytic pipelines, a crucial step in digitizing\nbreeding processes. It supports querying and retrieving\nphenotypic and genotypic data from systems like 'EBS'\n, 'BMS'\n, 'BreedBase' ,\n'GIGWA' (using\n'BrAPI' calls), and 'Germinate'\n. Extra\nhelper functions support environmental data sources, including\n'TerraClimate'\n and 'FAO'\n'HWSDv2' soil database.", "License": "GPL (>= 3)", "URL": "https://icarda.github.io/QBMS/", "BugReports": "https://github.com/icarda/QBMS/issues", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "NeedsCompilation": "no", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libgdal-dev gdal-bin libgeos-dev libnetcdf-dev\nlibssl-dev libproj-dev libsqlite3-dev libudunits2-dev", "Repository": "https://icarda.r-universe.dev", "Date/Publication": "2026-05-10 12:41:45 UTC", "RemoteUrl": "https://github.com/icarda/qbms", "RemoteRef": "HEAD", "RemoteSha": "f4b0ce37ddd8d6410849cffd56c2f0e9ceb12a75", "Packaged": { "Date": "2026-05-29 19:34:39 UTC", "User": "root" }, "MD5sum": "ca399c623ad8c326be85dd52f8480452", "_user": "icarda", "_type": "src", "_file": "QBMS_2.0.0.tar.gz", "_fileid": "f46541a9ebf1c0a77488026f6b5f7bad62acc9cccc1d450ae623dd3487bf6232", "_filesize": 322685, "_sha256": 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"extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/QBMS.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/icarda/qbms", "_realowner": "icarda", "_cranurl": true, "_releases": [ { "version": "0.6", "date": "2021-10-19" }, { "version": "0.7.0", "date": "2022-03-02" }, { "version": "0.8.0", "date": "2022-05-19" }, { "version": "0.9.0", "date": "2023-03-28" }, { "version": "0.9.1", "date": "2023-03-28" }, { "version": "1.0.0", "date": "2024-03-07" }, { "version": "1.5.0", "date": "2024-09-18" }, { "version": "2.0.0", "date": "2025-08-01" } ], "_exports": [ "calc_biovars", "debug_qbms", "get_germplasm_attributes", "get_germplasm_data", "get_germplasm_list", "get_hwsd2", "get_marker_map", "get_pedigree_table", "get_program_studies", "get_qbms_connection", "get_study_data", "get_study_info", "get_terraclimate", "get_trial_data", "get_trial_obs_ontology", "get_trial_pedigree", "get_variants", "get_variantset", "gigwa_get_allelematrix", "gigwa_get_markers", "gigwa_get_metadata", "gigwa_get_samples", "gigwa_get_sequences", "gigwa_get_variants", "gigwa_list_dbs", "gigwa_list_projects", "gigwa_list_runs", "gigwa_set_db", "gigwa_set_project", "gigwa_set_run", "ini_hwsd2", "ini_terraclimate", "list_crops", "list_programs", "list_studies", "list_trials", "list_variantsets", "login", "login_bms", "login_breedbase", "login_germinate", "login_gigwa", "login_oauth2", "scan_brapi_endpoints", "set_crop", "set_program", "set_qbms_config", "set_qbms_connection", "set_study", "set_token", "set_trial", "set_variantset" ], "_help": [ { "page": "brapi_get_call", "title": "Internal Function for Core BrAPI GET Calls", "topics": [ "brapi_get_call" ] }, { "page": "brapi_map", "title": "BrAPI Mapping Table", "topics": [ "brapi_map" ] }, { "page": "brapi_post_search_allelematrix", "title": "Internal Function Used for Core BrAPI POST Calls (Allele Matrix Search)", "topics": [ "brapi_post_search_allelematrix" ] }, { "page": "brapi_post_search_call", "title": "Internal Function Used for Core BrAPI POST Calls", "topics": [ "brapi_post_search_call" ] }, { "page": "build_pedigree_table", "title": "Building Pedigree Table Recursively", "topics": [ "build_pedigree_table" ] }, { "page": "calc_biovars", "title": "Calculate the Bioclimatic Variables", "topics": [ "calc_biovars" ] }, { "page": "debug_qbms", "title": "Debug Internal QBMS Status Object", "topics": [ "debug_qbms" ] }, { "page": "get_async_page", "title": "Asynchronously Fetch a Single API Page", "topics": [ "get_async_page" ] }, { "page": "get_async_pages", "title": "Asynchronously Fetch Multiple API Pages", "topics": [ "get_async_pages" ] }, { "page": "get_brapi_url", "title": "Get the BrAPI Endpoint URL for a given QBMS function", "topics": [ "get_brapi_url" ] }, { "page": "get_germplasm_attributes", "title": "Retrieve Attributes for a Specified Germplasm", "topics": [ "get_germplasm_attributes" ] }, { "page": "get_germplasm_data", "title": "Retrieve Observations Data for a Specified Germplasm.", "topics": [ "get_germplasm_data" ] }, { "page": "get_germplasm_id", "title": "Get Germplasm ID for a Specified Germplasm Name", "topics": [ "get_germplasm_id" ] }, { "page": "get_germplasm_list", "title": "Get the Germplasm List of the Current Active Study", "topics": [ "get_germplasm_list" ] }, { "page": "get_hwsd2", "title": "Get HWSD v2 Soil Data for a Given Location(s)", "topics": [ "get_hwsd2" ] }, { "page": "get_login_details", "title": "Login Pop-Up Window", "topics": [ "get_login_details" ] }, { "page": "get_marker_map", "title": "Get marker position information", "topics": [ "get_marker_map" ] }, { "page": "get_parents", "title": "Get Direct Parents", "topics": [ "get_parents" ] }, { "page": "get_pedigree_table", "title": "Get the Pedigree Table", "topics": [ "get_pedigree_table" ] }, { "page": "get_program_studies", "title": "Get the List of Trials, Studies, and Locations Information for the Current Selected Program", "topics": [ "get_program_studies" ] }, { "page": "get_program_trials", "title": "Retrieve the List of Trials for the Active Breeding Program", "topics": [ "get_program_trials" ] }, { "page": "get_qbms_connection", "title": "Get the QBMS Connection", "topics": [ "get_qbms_connection" ] }, { "page": "get_study_data", "title": "Get the Observations Data of the Current Active Study", "topics": [ "get_study_data" ] }, { "page": "get_study_info", "title": "Get the Details/Metadata of the Current Active Study", "topics": [ "get_study_info" ] }, { "page": "get_terraclimate", "title": "Get TerraClimate Data for a Given Coordinate(s)", "topics": [ "get_terraclimate" ] }, { "page": "get_trial_data", "title": "Get the Observations Data of the Current Active Trial", "topics": [ "get_trial_data" ] }, { "page": "get_trial_obs_ontology", "title": "Get the Traits Ontology/Metadata of the Current Active Trial", "topics": [ "get_trial_obs_ontology" ] }, { "page": "get_trial_pedigree", "title": "Get the Pedigree table for the Selected Trial", "topics": [ "get_trial_pedigree" ] }, { "page": "get_variants", "title": "Get Marker Matrix from the Selected Variant Set", "topics": [ "get_variants" ] }, { "page": "get_variantset", "title": "Get Marker Matrix from the Selected Variant Set", "topics": [ "get_variantset" ] }, { "page": "gigwa_get_allelematrix", "title": "Get Markers Matrix in the Selected GIGWA Run", "topics": [ "gigwa_get_allelematrix" ] }, { "page": "gigwa_get_markers", "title": "Get Markers Map in the Selected GIGWA Run", "topics": [ "gigwa_get_markers" ] }, { "page": "gigwa_get_metadata", "title": "Get the Metadata of the Current Active GIGWA Run", "topics": [ "gigwa_get_metadata" ] }, { "page": "gigwa_get_samples", "title": "Get the Samples List of the Current Active GIGWA Project", "topics": [ "gigwa_get_samples" ] }, { "page": "gigwa_get_sequences", "title": "Get the Sequences of the Current Active GIGWA Project", "topics": [ "gigwa_get_sequences" ] }, { "page": "gigwa_get_variants", "title": "Get Available Variants in the Selected GIGWA Run", "topics": [ "gigwa_get_variants" ] }, { "page": "gigwa_list_dbs", "title": "List GIGWA Databases", "topics": [ "gigwa_list_dbs" ] }, { "page": "gigwa_list_projects", "title": "Get the List of All Projects in the Selected GIGWA Database", "topics": [ "gigwa_list_projects" ] }, { "page": "gigwa_list_runs", "title": "Get the List of the Run Names Available in the Selected GIGWA Project", "topics": [ "gigwa_list_runs" ] }, { "page": "gigwa_set_db", "title": "Set the Current Active GIGWA Database by Name", "topics": [ "gigwa_set_db" ] }, { "page": "gigwa_set_project", "title": "Set the Current Active GIGWA Project", "topics": [ "gigwa_set_project" ] }, { "page": "gigwa_set_run", "title": "Set the Current Active GIGWA Run", "topics": [ "gigwa_set_run" ] }, { "page": "ini_hwsd2", "title": "Download and Setup HWSD v2.0 Data Files to Extract their Data Offline", "topics": [ "ini_hwsd2" ] }, { "page": "ini_terraclimate", "title": "Download TerraClimate netCDF Data Files to Extract their Data Offline", "topics": [ "ini_terraclimate" ] }, { "page": "list_crops", "title": "Retrieve Supported Crops from the Server", "topics": [ "list_crops" ] }, { "page": "list_locations", "title": "Get the List of Locations Information of the Current Selected Crop", "topics": [ "list_locations" ] }, { "page": "list_programs", "title": "Retrieve Breeding Programs for the Active Crop", "topics": [ "list_programs" ] }, { "page": "list_studies", "title": "Get the List of Studies in the Current Active Trial", "topics": [ "list_studies" ] }, { "page": "list_trials", "title": "List Trials in the Current Active Breeding Program", "topics": [ "list_trials" ] }, { "page": "list_variantsets", "title": "List Variant Sets in the Selected Study", "topics": [ "list_variantsets" ] }, { "page": "login", "title": "Login to a BrAPI Server", "topics": [ "login" ] }, { "page": "login_bms", "title": "Login to the Server", "topics": [ "login_bms" ] }, { "page": "login_breedbase", "title": "Login to the BreedBase Server", "topics": [ "login_breedbase" ] }, { "page": "login_germinate", "title": "Login to the Germinate Server", "topics": [ "login_germinate" ] }, { "page": "login_gigwa", "title": "Login to the GIGWA Server", "topics": [ "login_gigwa" ] }, { "page": "login_oauth2", "title": "Login using OAuth 2.0 Authentication", "topics": [ "login_oauth2" ] }, { "page": "rbindlistx", "title": "Make One Data.Table from a List of Many", "topics": [ "rbindlistx" ] }, { "page": "rbindx", "title": "Combine Data Frames by Row, Filling in Missing Columns", "topics": [ "rbindx" ] }, { "page": "scan_brapi_endpoints", "title": "Scan BrAPI Endpoints", "topics": [ "scan_brapi_endpoints" ] }, { "page": "set_crop", "title": "Set the Current Active Crop", "topics": [ "set_crop" ] }, { "page": "set_program", "title": "Set the Current Active Breeding Program", "topics": [ "set_program" ] }, { "page": "set_qbms_config", 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