Home field advantage (HFA) - Analysis of local adaptation in crop populations.

Home Field Advantage (HFA) is the fitness gain an entry (genotype) realizes by growing in its home location, which is empirically defined as the location of highest fitness relative to other entries (Ewing et al., 2019).

Requirements

Input data should be analogous to common gardens. Ex. breeding trials, multi-environment trials, yield trials.

Brief how-to:

1. permute_hfa() to run hfa analysis. This will work at the population, genotype, site, and year level.
2. id_home() to return the home site of each genotype
3. specialist_test() and generalist_test() to identify specialists and generalists.

The rHFA Guide vignette contains a step-by-step analysis of sample data. When installing the package from github, use this command to ensure the vignette is included.

> remotes::install_github("PatrickEwing-USDA/rHFA", build_vignettes = TRUE)

See analysis code for publications below and methods described in those publications - especially Ewing et al. (2019).

Of course, message with questions.

Publications:

• Ewing, P. M., Runck, B. C., Kono, T. Y., & Kantar, M. B. (2019). The home field advantage of modern plant breeding. PloS one 14(12), e0227079. Link
• MacQueen, Alice H., et al. (2022). "Local to continental‐scale variation in fitness and heritability in common bean." Crop Science 62(2): 767-779. Link Code
• Ewing, P. M., et al. (2024). Local adaptation and broad performance are synergistic to productivity in modern barley. Crop Science, 64(1), 192-199. Link Code

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