Package: QBMS 1.5.0

Khaled Al-Shamaa

QBMS: Query the Breeding Management System(s)

This R package assists breeders in linking data systems with their analytic pipelines, a crucial step in digitizing breeding processes. It supports querying and retrieving phenotypic and genotypic data from systems like 'EBS' <https://ebs.excellenceinbreeding.org/>, 'BMS' <https://bmspro.io>, 'BreedBase' <https://breedbase.org>, and 'GIGWA' <https://github.com/SouthGreenPlatform/Gigwa2> (using 'BrAPI' <https://brapi.org> calls). Extra helper functions support environmental data sources, including 'TerraClimate' <https://www.climatologylab.org/terraclimate.html> and 'FAO' 'HWSDv2' <https://gaez.fao.org/pages/hwsd> soil database.

Authors:Khaled Al-Shamaa [aut, cre], Mariano Omar Crimi [ctb], Zakaria Kehel [ctb], Johan Aparicio [ctb], ICARDA [cph]

QBMS_1.5.0.tar.gz
QBMS_1.5.0.zip(r-4.5)QBMS_1.5.0.zip(r-4.4)QBMS_1.5.0.zip(r-4.3)
QBMS_1.5.0.tgz(r-4.4-any)QBMS_1.5.0.tgz(r-4.3-any)
QBMS_1.5.0.tar.gz(r-4.5-noble)QBMS_1.5.0.tar.gz(r-4.4-noble)
QBMS_1.5.0.tgz(r-4.4-emscripten)QBMS_1.5.0.tgz(r-4.3-emscripten)
QBMS.pdf |QBMS.html✨
QBMS/json (API)
NEWS

# Install 'QBMS' in R:
install.packages('QBMS', repos = c('https://icarda-git.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/icarda-git/qbms/issues

On CRAN:

8.00 score 8 stars 1 packages 26 scripts 440 downloads 44 exports 36 dependencies

Last updated 1 months agofrom:fa2ae20779. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 23 2024
R-4.5-winWARNINGOct 23 2024
R-4.5-linuxWARNINGOct 23 2024
R-4.4-winWARNINGOct 23 2024
R-4.4-macWARNINGOct 23 2024
R-4.3-winWARNINGOct 23 2024
R-4.3-macWARNINGOct 23 2024

Exports:calc_biovarsdebug_qbmsget_germplasm_attributesget_germplasm_dataget_germplasm_listget_hwsd2get_pedigree_tableget_program_studiesget_qbms_connectionget_study_dataget_study_infoget_terraclimateget_trial_dataget_trial_obs_ontologygigwa_get_allelematrixgigwa_get_markersgigwa_get_metadatagigwa_get_samplesgigwa_get_sequencesgigwa_get_variantsgigwa_list_dbsgigwa_list_projectsgigwa_list_runsgigwa_set_dbgigwa_set_projectgigwa_set_runini_hwsd2ini_terraclimatelist_cropslist_programslist_studieslist_trialslogin_bmslogin_breedbaselogin_gigwalogin_oauth2scan_brapi_endpointsset_cropset_programset_qbms_configset_qbms_connectionset_studyset_tokenset_trial

Dependencies:askpassbitbit64blobcachemclicodetoolscpp11curlDBIdigestfastmapfuturefuture.applyglobalsgluehttr2jsonlitelifecyclelistenvmagrittrmemoiseopensslparallellypkgconfigplogrR6rappdirsRcpprlangRNetCDFRSQLitesysterravctrswithr

BMS Example

Khaled Al-Shamaa

Rendered frombms_example.Rmdusingknitr::rmarkdownon Oct 23 2024.

Last update: 2024-03-07
Started: 2022-05-18

BreedBase Example

Khaled Al-Shamaa

Rendered frombreedbase_example.Rmdusingknitr::rmarkdownon Oct 23 2024.

Last update: 2024-03-07
Started: 2022-02-28

EBS Example

Khaled Al-Shamaa

Rendered fromebs_example.Rmdusingknitr::rmarkdownon Oct 23 2024.

Last update: 2024-03-07
Started: 2023-12-16

FAO HWSD v2 Example

Khaled Al-Shamaa

Rendered fromhwsd2_example.Rmdusingknitr::rmarkdownon Oct 23 2024.

Last update: 2024-03-07
Started: 2023-12-16

GIGWA Example

Khaled Al-Shamaa

Rendered fromgigwa_example.Rmdusingknitr::rmarkdownon Oct 23 2024.

Last update: 2024-09-03
Started: 2022-05-18

TerraClimate Example

Khaled Al-Shamaa

Rendered fromterraclimate_example.Rmdusingknitr::rmarkdownon Oct 23 2024.

Last update: 2024-03-07
Started: 2022-06-29

Readme and manuals

Help Manual

Help pageTopics
Internal Function for Core BrAPI GET Callsbrapi_get_call
Generate Common HTTP Headers for API Requestsbrapi_headers
BrAPI Mapping Tablebrapi_map
Internal Function Used for Core BrAPI POST Calls (Allele Matrix Search)brapi_post_search_allelematrix
Internal Function Used for Core BrAPI POST Callsbrapi_post_search_call
Building Pedigree Table Recursivelybuild_pedigree_table
Calculate the Bioclimatic Variablescalc_biovars
Debug Internal QBMS Status Objectdebug_qbms
Asynchronously Fetch a Single API Pageget_async_page
Asynchronously Fetch Multiple API Pagesget_async_pages
Get the BrAPI Endpoint URL for a given QBMS functionget_brapi_url
Retrieve Attributes for a Specified Germplasmget_germplasm_attributes
Retrieve Observations Data for a Specified Germplasm.get_germplasm_data
Get Germplasm ID for a Specified Germplasm Nameget_germplasm_id
Get the Germplasm List of the Current Active Studyget_germplasm_list
Get HWSD v2 Soil Data for a Given Location(s)get_hwsd2
Login Pop-Up Windowget_login_details
Get Direct Parentsget_parents
Get the Pedigree Tableget_pedigree_table
Get the List of Trials, Studies, and Locations Information for the Current Selected Programget_program_studies
Retrieve the List of Trials for the Active Breeding Programget_program_trials
Get the QBMS Connectionget_qbms_connection
Get the Observations Data of the Current Active Studyget_study_data
Get the Details/Metadata of the Current Active Studyget_study_info
Get TerraClimate Data for a Given Coordinate(s)get_terraclimate
Get the Observations Data of the Current Active Trialget_trial_data
Get the Traits Ontology/Metadata of the Current Active Trialget_trial_obs_ontology
Get Markers Matrix in the Selected GIGWA Rungigwa_get_allelematrix
Get Markers Map in the Selected GIGWA Rungigwa_get_markers
Get the Metadata of the Current Active GIGWA Rungigwa_get_metadata
Get the Samples List of the Current Active GIGWA Projectgigwa_get_samples
Get the Sequences of the Current Active GIGWA Projectgigwa_get_sequences
Get Available Variants in the Selected GIGWA Rungigwa_get_variants
List GIGWA Databasesgigwa_list_dbs
Get the List of All Projects in the Selected GIGWA Databasegigwa_list_projects
Get the List of the Run Names Available in the Selected GIGWA Projectgigwa_list_runs
Set the Current Active GIGWA Database by Namegigwa_set_db
Set the Current Active GIGWA Projectgigwa_set_project
Set the Current Active GIGWA Rungigwa_set_run
Download and Setup HWSD v2.0 Data Files to Extract their Data Offlineini_hwsd2
Download TerraClimate netCDF Data Files to Extract their Data Offlineini_terraclimate
Retrieve Supported Crops from the Serverlist_crops
Get the List of Locations Information of the Current Selected Croplist_locations
Retrieve Breeding Programs for the Active Croplist_programs
Get the List of Studies in the Current Active Triallist_studies
List Trials in the Current Active Breeding Programlist_trials
Login to the Serverlogin_bms
Login to the BreedBase Serverlogin_breedbase
Login to the GIGWA Serverlogin_gigwa
Login using OAuth 2.0 Authenticationlogin_oauth2
Make One Data.Table from a List of Manyrbindlistx
Combine Data Frames by Row, Filling in Missing Columnsrbindx
Scan BrAPI Endpointsscan_brapi_endpoints
Set the Current Active Cropset_crop
Set the Current Active Breeding Programset_program
Configure BMS Server Settingsset_qbms_config
Set the QBMS Connectionset_qbms_connection
Set the Current Active Studyset_study
Set Access Token Responseset_token
Set the Current Active Trialset_trial