This repository contains information and code for replicating the analyses performed in the article below:
Article Title: Accurate predictions of barley phenotypes using
genomewide markers and environmental covariates
Journal: Crop Science
Authors: Jeffrey L. Neyhart, Kevin A.T. Silverstein, and Kevin P.
Smith
Article doi:
https://acsess.onlinelibrary.wiley.com/doi/10.1002/csc2.20782
Data used in this study are available from the Triticeae Toolbox. See this README for instructions on accessing this data.
Scripts used to complete the analysis and generate figures outlined in the article above are available in the “Scripts” subfolder. See this README for information on the scripts and their intended execution order.
Three scripts in this directory are used by all other scripts:
source.R- loads packages, creates directory links, and loads data.source_MSI.R- runs script #1 with modifications for high-performance computing supported by the Minnesota Supercomputing Institute.source_functions.R- loads additional functions into the environment.
The figures.R script in the “Scripts” subfolder produces the figures
found in the paper.
R version 4.0.2 was used to complete analyses in this project.
The following packages (with version information) were used to complete this project:
| package | version |
|---|---|
| APSIM | 0.9.3 |
| broom | 1.0.1 |
| car | 3.0-10 |
| cowplot | 1.1.1 |
| daymetr | 1.5 |
| dbplyr | 2.1.1 |
| dplyr | 1.0.10 |
| ggdendro | 0.1.22 |
| ggrepel | 0.9.1 |
| ggsn | 0.5.0 |
| glmnet | 4.1-1 |
| lme4 | 1.1-27 |
| lmerTest | 3.1-3 |
| lubridate | 1.8.0 |
| maps | 3.3.0 |
| maptools | 1.1-1 |
| modelr | 0.1.8 |
| nasapower | 1.1.3 |
| paletteer | 1.3.0 |
| parallel | 4.0.2 |
| patchwork | 1.1.1 |
| purrr | 0.3.4 |
| raster | 3.4-10 |
| readr | 2.1.3 |
| rgeos | 0.5-5 |
| rhwsd | 1.0 |
| RSQLite | 2.2.7 |
| rvest | 1.0.3 |
| sp | 1.4-5 |
| spdep | 1.1-8 |
| stringr | 1.4.0 |
| tibble | 3.1.8 |
| tidyr | 1.2.0 |