Package: hsquared 0.9.0

Shinichi Nakagawa

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

Provides an interface for quantitative-genetic models in 'R', backed by the 'HSquared.jl' engine for 'Julia'. Fits Gaussian pedigree animal models by restricted maximum likelihood, using average-information restricted maximum likelihood (AI-REML; Gilmour et al. (1995) <doi:10.2307/2533274>) for the univariate model. Returns heritability, variance components, breeding values, and covariance and correlation matrices for multivariate models. Formula and pedigree validation can run without 'Julia'. Model fitting requires a local 'Julia' and 'HSquared.jl'; use hs_control(engine = "validate") to preview the model contract without fitting. What you may report is listed on the package article 'Can I fit and report this?', not in validation_status(), which is a developer evidence table. Model-specific restrictions are documented in that article. Uncertainty intervals are not coverage-calibrated.

Authors:Shinichi Nakagawa [aut, cre, cph], Yefeng Yang [aut, cph], Szymon Drobniak [aut, cph]

hsquared_0.9.0.tar.gz
hsquared_0.9.0.zip(r-4.7-any)hsquared_0.9.0.zip(r-4.6-any)
hsquared_0.9.0.tar.gz(r-4.7-any)hsquared_0.9.0.tar.gz(r-4.6-any)
hsquared_0.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
hsquared/json (API)

# Install 'hsquared' in R:

install.packages('hsquared', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/itchyshin/hsquared/issues

Pkgdown/docs site:https://itchyshin.github.io

On CRAN:

3.04 score 22 scripts 96 exports 19 dependencies

Last updated from:0b9138d212. Checks:6 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	218
source / vignettes	OK	198
linux-release	OK	160
windows-devel	OK	150
windows-release	OK	136
wasm-release	OK	104

Exports:accuracy animal autonomy autoplot backend_info BLUP breeding_values common_env common_env_effects common_env_proportion common_env_proportion_interval conditional_evolvability covariance_standard_errors covariance_structure_lrt cytoplasmic data_status direct_heritability direct_maternal_covariance direct_variance dominance EBV eigen_G epistasis eqtl_table evolvability fit_diagnostics fixef formula_status G_matrix g_max gamma_matrix genetic_correlation genetic_covariance genetic_loadings genomic group gwas gwas_table heritability heritability_interval heritability_standard_error hs_control hs_data hs_recovery_forest hsquared imprinting inbreeding latent_breeding_values lod_scores marker_effects marker_scan marker_variance_explained markers maternal_effects maternal_env maternal_genetic maternal_proportion maternal_proportion_interval mean_evolvability metafounder metafounder_effects metafounder_groups model_spec partner_variance paternal_env paternal_genetic permanent permanent_effects precision prediction_error_variance qtl_scan qtl_table R_matrix random_coefficients ranef reliability relmat repeatability repeatability_interval residual_correlation residual_covariance respondability rr_correlation rr_covariance rr_eigenfunctions rr_genetic_variance rr_heritability single_step specific_variance theme_hsquared total_heritability unknown_parent_group validation_status variance_along_gradient variance_component_standard_errors variance_components

Dependencies:cli cpp11 farver ggplot2 glue gtable isoband labeling lattice lifecycle Matrix R6 RColorBrewer rlang S7 scales vctrs viridisLite withr

Getting started with hsquared

Check the model (no Julia) | Fit (needs the Julia engine) | After this works | Twin-package flow

Rendered fromhsquared.Rmdusingknitr::rmarkdown

Last update: 2026-10-21
Started: 2026-10-21

Help page	Topics
Animal-model formula marker	animal
Inspect planned compute backends	backend_info
Extract breeding values	BLUP breeding_values EBV
Extract common-environment effects	common_env_effects
Extract the common-environment variance ratio (c2)	common_env_proportion
Extract an experimental common-environment / maternal variance-ratio interval	common_env_proportion_interval maternal_proportion_interval
Extract experimental multivariate covariance standard errors	covariance_standard_errors
Likelihood-ratio test for genetic covariance structure	covariance_structure_lrt
Inspect hsquared data-container status	data_status
Direct-maternal correlated model extractors	direct_heritability direct_maternal_covariance direct_maternal_extractors direct_variance partner_variance total_heritability
Reserved factor-analytic and G-matrix extractors	factor_g_extractors genetic_loadings latent_breeding_values specific_variance
Inspect fitted-model diagnostics	fit_diagnostics
Extract fixed effects	fixef
Inspect formula grammar status	formula_status
G-matrix geometry and evolvability	autonomy conditional_evolvability eigen_G evolvability g_matrix_geometry g_max mean_evolvability respondability variance_along_gradient
Extract a supplied metafounder Gamma matrix	gamma_matrix
Genomic and QTL formula markers	genomic genomic_markers markers marker_scan qtl_scan single_step
Post-fit relatedness-corrected marker scan (GWAS)	gwas
Extract heritability estimates	heritability
Extract an experimental heritability confidence interval	heritability_interval
Create hsquared control options	hs_control
Create an hsquared data container	hs_data
Forest plot of a known-truth recovery study	hs_recovery_forest
Fit a quantitative-genetic model	hsquared
ggplot2 visualizations for hsquared results	autoplot.hsquared_fit autoplot.hs_gwas hsquared-autoplot
Block unsupported likelihood-inference helpers	anova.hsquared_fit confint.hsquared_fit inference_blocks profile.hsquared_fit vcov.hsquared_fit
Extract planned marker, QTL, GWAS, and eQTL results	eqtl_table gwas_table lod_scores marker_effects marker_extractors marker_variance_explained qtl_table
Extract maternal genetic effects	maternal_effects
Extract the maternal variance ratio (m2)	maternal_proportion
Reserved metafounder effect extractor	metafounder_effects
Extract supplied metafounder group assignments	metafounder_groups
Inspect a parsed hsquared model specification	model_spec
Extract multivariate covariance and correlation matrices	genetic_correlation genetic_covariance G_matrix multivariate_extractors residual_correlation residual_covariance R_matrix
Extract permanent-environment effects	permanent_effects
Diagnostic plots for a fitted animal model	plot.hsquared_fit
Extract prediction error variances	prediction_error_variance
Quantitative-genetic formula markers	common_env cytoplasmic dominance epistasis group imprinting inbreeding maternal_env maternal_genetic metafounder paternal_env paternal_genetic permanent precision qg_effect_markers relmat unknown_parent_group
Random-regression (reaction-norm) extractors	random_coefficients random_regression_extractors rr_correlation rr_covariance rr_eigenfunctions rr_genetic_variance rr_heritability
Extract random effects	ranef
Extract reliability and accuracy estimates	accuracy reliability
Extract repeatability estimates	repeatability
Extract an experimental repeatability confidence interval	repeatability_interval
Response-scale prediction helpers	fitted.hsquared_fit predict.hsquared_fit residuals.hsquared_fit response_scale_methods
hsquared ggplot2 theme	theme_hsquared
Inspect validation evidence status	validation_status
Extract experimental variance-component and heritability standard errors	heritability_standard_error variance_component_standard_errors
Extract variance components	variance_components

Package: hsquared 0.9.0

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

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