README.md

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

shinemas2R

shinemas2R is a R package that queries the database SHiNeMaS (Seeds History and Network Management System) and format data for specific R packages.

Install

library(devtools)
devtools::install_github("priviere/shinemas2R")

Usage

shinemas2R has one function shinemas() which queries SHiNeMaS and formats data for specific R packages. The query is based on a webservice developped within SHiNeMaS v2 by Laetitia Courgey and Yannick de Oliveira from ABI-Soft team at GQE-Le Moulon. The following information are needed to connect to the database: db_url, user, password and token. The token can be taken through the web interface of SHiNeMaS by cliking "Get Token" on the top left side of the page.

Packages supported

PPBstats

PPBstats is a R package for Participatory Plant Breeding statisticial analyses.

Four queries are supported:

• PPBstats_data_network_unipart_seed_lots, for network analysis on unipart network for seed lots analysis, unipart network for location analysis and bipart network analysis.
• PPBstats_data_agro, for agronomic analysis
• PPBstats_data_agro_SR, for response to selection analysis
• PPBstats_data_agro_HA, for local adaptation analysis

Examples

For example, first get the formated data set

library(shinemas2R)
data_agro = shinemas2R::shinemas(
  db_url = "shinemas.local.seed",
  user = "wheat",
  password = "ppb",
  token = "1234",
  query = "PPBstats_data_agro"
  )

and then transform if for PPBstats format.

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

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