README.md

This package is under development. It has not yet been exhaustively tested for all calls neither. Usage may also still change. If you have suggestions please use the issue tracker.

README

An R package to use the Breeding API (BrAPI) for accessing plant breeding data.

It can be installed using:

install.packages("devtools")
devtools::install_github("c5sire/brapi")

How to use the package

See tutorial.

Documentation of JSON response/requests

Follow the links in the table below or see the inst/apidocs directory for examples: apidocs

Implementation status

Out of 52 BrAPI calls currently 52 (100%) are implemented in this package.

group	name	R.function
Authentication	Authentication	ba_login
Authentication	Authentication	ba_logout
Calls	Calls	ba_calls
Crops	ListCrops	ba_crops
GenomeMaps	ListOfGenomeMap	ba_genomemaps
GenomeMaps	GenomeMapData	ba_genomemaps_data
GenomeMaps	GenomeMapDataByRangeOnLinkageGroup	ba_genomemaps_data_range
GenomeMaps	GenomeMapDetails	ba_genomemaps_details
Germplasm	GermplasmDetailsByGermplasmDbId	ba_germplasm_details
Germplasm	GermplasmDetailsListByStudyDbId	ba_germplasm_details_study
Germplasm	GermplasmMarkerprofile	ba_germplasm_markerprofiles
Germplasm	GermplasmPedigree	ba_germplasm_pedigree
Germplasm	GermplasmSearchGET	ba_germplasm_search
Germplasm	GermplasmSearchPOST	ba_germplasm_search
GermplasmAttributes	ListAttributesByAttributeCategoryDbId	ba_germplasmattributes
GermplasmAttributes	ListAttributeCategories	ba_germplasmattributes_categories
GermplasmAttributes	GermplasmAttributeValuesByGermplasmDbId	ba_germplasmattributes_details
Locations	ListLocations	ba_locations
MarkerProfiles	MarkerProfileAlleleMatrix	ba_markerprofiles_allelematrix_search
MarkerProfiles	ScoresThroughPOST	ba_markerprofiles_allelematrix_search
MarkerProfiles	MarkerProfileData	ba_markerprofiles_details
MarkerProfiles	MarkerProfileSearchPost	ba_markerprofiles_search
MarkerProfiles	MarkerProfileSearch	ba_markerprofiles_search
Markers	MarkerDetailsByMarkerDbId	ba_markers_details
Markers	MarkerSearch	ba_markers_search
ObservationVariables	VariableList	ba_observationvariables
ObservationVariables	VariableDataTypeList	ba_observationvariables_datatypes
ObservationVariables	VariableDetails	ba_observationvariables_details
ObservationVariables	VariableOntologyList	ba_observationvariables_ontologies
ObservationVariables	VariableSearch	ba_observationvariables_search
Phenotypes	PhenotypeSearch	ba_phenotype_search
Programs	ListPrograms	ba_programs
Programs	ProgramSearch	ba_programs_search
Samples	TakeASample	ba_samples_save
Samples	RetrieveSampleMetadata	ba_samples
Studies	StudyDetails	ba_studies_details
Studies	ListObservationLevels	ba_studies_observationlevels
Studies	GetObservationUnitsByObservationVariableId	ba_studies_observations
Studies	ObservationUnitDetails	ba_studies_observationunits
Studies	SaveOrUpdateObservationUnits	ba_studies_observationunits_save
Studies	StudyObservationVariables	ba_studies_observationvariables
Studies	ListStudySummaries	ba_studies_search
Studies	SearchStudie	ba_studies_search
Studies	ListSeasons	ba_studies_seasons
Studies	ListStudyTypes	ba_studies_studytypes
Studies	StudyObservationUnitsAsTable	ba_studies_table
Studies	PlotLayoutDetails	ba_studies_layout
Studies	StudyObservationUnitsAsTableSave	ba_studies_table_save
Traits	ListAllTraits	ba_traits
Traits	TraitDetails	ba_traits_details
Trials	ListTrialSummaries	ba_trials
Trials	GetTrialById	ba_trials_details