Package: genesysr 2.2.0

genesysr: Genesys PGR Client

Access data on plant genetic resources from genebanks around the world published on Genesys (<https://www.genesys-pgr.org>). Your use of data is subject to terms and conditions available at <https://www.genesys-pgr.org/content/legal/terms>.

Authors:Global Crop Diversity Trust [cph], Matija Obreza [aut, cre], Nora Castaneda [ctb]

genesysr_2.2.0.tar.gz
genesysr_2.2.0.zip(r-4.7-any)genesysr_2.2.0.zip(r-4.6-any)genesysr_2.2.0.zip(r-4.5-any)
genesysr_2.2.0.tgz(r-4.6-any)genesysr_2.2.0.tgz(r-4.5-any)
genesysr_2.2.0.tar.gz(r-4.7-any)genesysr_2.2.0.tar.gz(r-4.6-any)
genesysr_2.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
genesysr/json (API)

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

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.00 score 8 scripts 403 downloads 28 exports 32 dependencies

Last updated from:db078393f2. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK133
source / vignettesOK180
linux-releaseOK118
macos-releaseOK158
macos-oldrelOK142
windows-develOK92
windows-releaseOK79
windows-oldrelOK74
wasm-releaseOK98

Exports:api2_urlauthorizationcheck_countrycheck_landorseacheck_taxonomyclient_logindownload_mcpddownload_pdcifilter_DOIfilter_GENUSfilter_INSTCODEfilter_ORIGCTYfilter_SAMPSTATfilter_SPECIESget_accessionslist_cropslist_instituteslist_speciesmcpd_filtermeprint_setupSELECT_ALL_FIELDSSELECT_GEO_FIELDSSELECT_INFO_FIELDSsetupsetup_productionsetup_sandboxuser_login

Dependencies:askpassbitbit64clicliprcpp11crayoncurldplyrgenericsgluehmshttr2jsonlitelifecyclemagrittropensslpillarpkgconfigprettyunitsprogressR6readrrlangsystibbletidyselecttzdbutf8vctrsvroomwithr

genesysr Tutorial
Querying Genesys PGR | For the impatient | Processing fetched data | Filters | Taxonomy | Origin of material | Holding institute | Selecting columns | Step-by-step example | Downloading all non-historical records
Rendered fromtutorial.Rmdusingknitr::rmarkdown

Last update: 2025-08-19
Started: 2018-06-14

Validating passport data
Scientific names spell-check | Checking coordinates
Rendered fromvalidation.Rmdusingknitr::rmarkdown

Last update: 2025-08-19
Started: 2019-11-22

Readme and manuals

Help Manual

Help pageTopics
Get partial API v2 URL for the provided pathapi2_url
Provide OAuth2 token to use for authorization with Genesysauthorization
Run Land-or-Sea check on MCPD data. Uploads only rows where ORIGCTY, DECLATITUDE and DECLONGITUDE are provided.check_country
Run Land-or-Sea check on MCPD data using https://validator.genesys-pgr.org. Uploads only rows where DECLATITUDE and DECLONGITUDE are provided. In practice it is better to use `check_country` if ORIGCTY data exists.check_landorsea
Check MCPD taxonomic data (GENUS, SPECIES, SPAUTHOR, SUBTAXA, SUBTAUTHOR) using https://validator.genesys-pgr.org.check_taxonomy
Login to Genesys as a service client (system-to-system)client_login
Download passport data for one genebank in Excel format and save it to diskdownload_mcpd
Download PDCI data for one genebank in Excel format and save it to disk.download_pdci
Add filter on accession DOIfilter_DOI
Add filter by genusfilter_GENUS
Add filter by genusfilter_INSTCODE
Add filter on Country of origin of materialfilter_ORIGCTY
Add filter on Biological status of samplefilter_SAMPSTAT
Add filter on specific epithetfilter_SPECIES
Get accession passport data as a data table.get_accessions
Fetch Genesys crops. Note that the list of Genesys crops does not fully correspond with various CROPNAME in MCPD provided by genebanks.list_crops
List FAO WIEWS institutes.list_institutes
Fetch taxonomic data of selected accessions.list_species
Make or adjust filter using MCPD terminologymcpd_filter
Who am i? Loads and prints the user profile from Genesys as JSON. You need to be logged in.me
Print Genesys client configurationprint_setup
List of all supported passport data fieldsSELECT_ALL_FIELDS
List of passport data fields relevant for GIS analysisSELECT_GEO_FIELDS
List of basic passport data fieldsSELECT_INFO_FIELDS
Configure the Genesys environmentsetup
Setup for Genesys Productionsetup_production
Setup for Genesys Sandboxsetup_sandbox
Login to Genesys as a useruser_login