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hsquared: R Interface for Julia-Backed Quantitative-Genetic Models

Source: R/hsquared-package.R
hsquared-package.Rd

The hsquared package is the R-facing interface for heritability, breeding-value, G-matrix, and inheritance-structured quantitative-genetic models backed by the HSquared.jl Julia engine.

Details

v0.1 fits the univariate Gaussian animal model y ~ fixed + animal(1 | id, pedigree = ped) by REML (average-information) through the HSquared.jl engine: the default hsquared() call fits when a local Julia and HSquared.jl are available, and otherwise errors with install guidance. A cbind() multivariate Gaussian response also routes on that default path; multivariate is covered at validation scale and stays experimental. Narrow genomic GREML is an explicit experimental target (target = "genomic") and is covered at validation scale. The covered common-environment two-effect, independent multi-effect, direct-maternal, and k = 2 random-regression models remain opt-in. Repeatability, maternal two-effect, and non-Gaussian (poisson(log)/binomial(logit), Laplace marginal likelihood or hybrid variational-Laplace objective) models are opt-in and experimental; single-step stays opt-in partial. Factor-analytic G has a bounded experimental four-trait rank-one R control route; cov = fa() formula grammar stays planned. Genetic GLLVM has a bounded experimental three-trait, two-factor Poisson-log expert route. Neither R route is covered; see hs_control() for the required explicit controls and limits.

Current limitations

This package is an experimental 0.9.0 release; it is not production or 1.0.0, and CRAN availability is tracked separately. Default hsquared() fitting requires a local Julia installation and HSquared.jl; use hs_control() with engine = "validate" to check the model contract without fitting. Report point estimates only for covered routes; uncertainty intervals are experimental and not coverage-calibrated.

What you may report is listed on Can I fit and report this? – not in validation_status(). That article lists every covered route and its reporting scope. validation_status() is a developer evidence table of validation atoms; it is not the user-facing list. The model status and validation evidence articles are published on the package website rather than as installed vignettes.

See also

Useful links:

Author

Maintainer: Shinichi Nakagawa itchyshin@gmail.com (ORCID) [copyright holder]

Authors: