This repository contains information and code for replicating the analyses performed in the article below:
Article Title: Using Environmental Similarities to Design Training Sets
for Genomewide Selection
Journal: Crop Science (under review)
Authors: Jeffrey L. Neyhart, Lucía Gutiérrez, and Kevin P. Smith
Link to article
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 the Minnesota Supercomputing Institute.source_functions.R- loads additional functions into the environment.
R version 3.5.3 was used to complete analyses in this project.
The following packages (with version information) were used to complete this project:
|
package |
version |
|---|---|
|
agridat |
1.16 |
|
aqp |
1.17 |
|
boot |
1.3-20 |
|
broom |
0.5.2 |
|
car |
3.0-2 |
|
carData |
3.0-2 |
|
cluster |
2.0.8 |
|
cowplot |
0.9.4 |
|
crayon |
1.3.4 |
|
data.table |
1.12.2 |
|
dplyr |
0.8.0.1 |
|
effects |
4.1-0 |
|
flextable |
0.5.2 |
|
forcats |
0.4.0 |
|
foreign |
0.8-71 |
|
geosphere |
1.5-7 |
|
ggalt |
0.6.2 |
|
ggdendro |
0.1-20 |
|
ggplot2 |
3.2.1 |
|
ggrepel |
0.8.0 |
|
ggridges |
0.5.1 |
|
gridExtra |
2.3 |
|
kableExtra |
1.1.0 |
|
lattice |
0.20-38 |
|
lme4 |
1.1-21 |
|
lme4qtl |
0.1.10 |
|
lmerTest |
3.1-0 |
|
lubridate |
1.7.4 |
|
MASS |
7.3-51.3 |
|
Matrix |
1.2-17 |
|
mclust |
5.4.3 |
|
measurements |
1.3.0 |
|
modelr |
0.1.4 |
|
neyhart |
0.0.0.9000 |
|
officer |
0.3.3 |
|
optimx |
2018-7.10 |
|
patchwork |
0.0.1 |
|
pbr |
0.1.0 |
|
purrr |
0.3.2 |
|
raster |
2.8-19 |
|
readr |
1.3.1 |
|
readxl |
1.3.1 |
|
RevoUtils |
11.0.3 |
|
RevoUtilsMath |
11.0.0 |
|
rnoaa |
0.8.4 |
|
rrBLUP |
4.6 |
|
rvest |
0.3.3 |
|
slide |
0.0.0.9002 |
|
soilDB |
2.3.5 |
|
sommer |
3.9.3 |
|
sp |
1.3-1 |
|
stringr |
1.4.0 |
|
tibble |
2.1.1 |
|
tidyr |
0.8.3 |
|
tidyverse |
1.2.1 |
|
viridis |
0.5.1 |
|
viridisLite |
0.3.0 |
|
xml2 |
1.2.0 |