Data, Code and Workflows Guideline

1. CERIS_EP.r and Sub_functions_bio.r are two R scripts for conducting Critical Environmental Regressor through Informed Search (CERIS) and Environic Prediction (EP).
2. 1Sorghum: The demo data for a sorghum multi-environment trial, which represents the scenerio of the number of tested indivdiuals is large.
3. 2Idaho: The demo data for a wheat multi-environment tria, which represents the scenerio of the number of environments is large.
4. README: Follow the demo example to format the necessary input files and run the CERIS_EP.r. The output file will be stored under 1Sorhgum or 2Idaho. The provided output folder under each demo contains the expected output from analysess.

Installation

• Running environment:

  • The workflow was constructed based on the Windows 10, and should be supported in iOS and Linux as long as R is supported.

• Required software and versions:

  • R 4.4.1 or Rstudio
    • rrBLUP and colorspace

Input Data

• Traits record: 1Sorghum/Traits_record.txt or 2Idaho/Traits_record.txt
• Cultural information: 1Sorghum/Env_meta_table.txt or 2Idaho/Env_meta_table.txt
• daily weather profile for each environment under 1Sorghum/dailyEnv/ or 2Idaho/dailyEnv/
• SNP file: 1Sorghum/Genotype.txt/

Major steps

The CERIS_EP.r has 6 blocks of codes, modify and run each block according to the protocol.

License

It is a free and open source software, licensed under (choose a license from the suggested list: GPLv3, MIT, or CC BY 4.0).