Query the database SHiNeMaS throught an API and format data for specific R packages

Source: R/shinemas.R

shinemas queries the database SHiNeMaS throught an API and formats data for specific R packages

shinemas(db_url = "shinemas.local.seed", user = "wheat",
  password = "ppb", token = "1234",
  query_type = "PPBstats_data_agro", specie = NULL, project = NULL,
  variable = NULL, germplasm = NULL, germplasm_type = NULL,
  relation_type = NULL, location = NULL, year = NULL)

Arguments

db_url

url of the database
user

user name
password

password
token

token to connect to the database
query_type

name of the query. Possible values are

  • PPBstats

    • PPBstats_data_network_unipart_seed_lots

    • PPBstats_data_agro

    • PPBstats_data_agro_SR

    • PPBstats_data_agro_HA
specie

filter: specie to keep
project

filter: project to keep
variable

filter: variable to keep
germplasm

filter: germplasm to keep
germplasm_type

filter: germplasm type to keep
relation_type

filter: relation type to keep
location

filter: location to keep
year

filter: year to keep

Value

The function returns a dataframe formated for specific query type and packages

Details

  • SHiNeMaS: The database SHiNeMaS (Seed History and Network Management System) is available here: https://sourcesup.renater.fr/frs/?group_id=2295. The query is based on a webservice developped within SHiNeMaS v2 by Laetitia Courgey and Yannick de Oliveira. The token can be taken through the web interface of SHiNeMaS by cliking "Get Token" on the top left side of the page.

  • query_type: The query_type is under the format [package-name]_[query-name]. For example PPBstats_data_agro stands for data_agro format for package PPBstats.

  • Package supported:

    • See https://priviere.github.io/shinemas2R/#packages-supported for more details

    • PPBstats

      • For query_type = PPBstats_data_agro and PPBstats_data_agro_HA

        • filter year refers to sown year of seed-lot parent or year of selection of seed-lot parent

        • relation_type is either reproduction or selection

Examples

if (FALSE) {
data_agro = shinemas2R::shinemas(
  db_url = "shinemas.local.seed",
  user = "wheat",
  password = "ppb",
  token = "1234",
  query_type = "PPBstats_data_agro"
)

library(PPBstats)
data = format_data_PPBstats(data_agro, type = "data_agro")
}