shinemas: Query the database SHiNeMaS throught an API and format data...

In priviere/shinemas2R: A R package to query the database SHiNeMaS

Description

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

Usage

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

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

Value

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

Author(s)

Pierre Riviere

Examples

## Not run: 
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")

## End(Not run)

priviere/shinemas2R documentation built on Jan. 28, 2021, 1:12 a.m.