'R' Interface for 'Julia'-Backed Quantitative-Genetic Models
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Documentation for package ‘hsquared’ version 0.9.0
Help Pages
A B C D E F G H I L M P Q R S T U V
-- A --
| accuracy | Extract reliability and accuracy estimates |
| animal | Animal-model formula marker |
| anova.hsquared_fit | Block unsupported likelihood-inference helpers |
| autonomy | G-matrix geometry and evolvability |
| autoplot.hsquared_fit | ggplot2 visualizations for hsquared results |
| autoplot.hs_gwas | ggplot2 visualizations for hsquared results |
-- B --
| backend_info | Inspect planned compute backends |
| BLUP | Extract breeding values |
| breeding_values | Extract breeding values |
-- C --
| common_env | Quantitative-genetic formula markers |
| common_env_effects | Extract common-environment effects |
| common_env_proportion | Extract the common-environment variance ratio (c2) |
| common_env_proportion_interval | Extract an experimental common-environment / maternal variance-ratio interval |
| conditional_evolvability | G-matrix geometry and evolvability |
| confint.hsquared_fit | Block unsupported likelihood-inference helpers |
| covariance_standard_errors | Extract experimental multivariate covariance standard errors |
| covariance_structure_lrt | Likelihood-ratio test for genetic covariance structure |
| cytoplasmic | Quantitative-genetic formula markers |
-- D --
| data_status | Inspect hsquared data-container status |
| direct_heritability | Direct-maternal correlated model extractors |
| direct_maternal_covariance | Direct-maternal correlated model extractors |
| direct_maternal_extractors | Direct-maternal correlated model extractors |
| direct_variance | Direct-maternal correlated model extractors |
| dominance | Quantitative-genetic formula markers |
-- E --
| EBV | Extract breeding values |
| eigen_G | G-matrix geometry and evolvability |
| epistasis | Quantitative-genetic formula markers |
| eqtl_table | Extract planned marker, QTL, GWAS, and eQTL results |
| evolvability | G-matrix geometry and evolvability |
-- F --
| factor_g_extractors | Reserved factor-analytic and G-matrix extractors |
| fitted.hsquared_fit | Response-scale prediction helpers |
| fit_diagnostics | Inspect fitted-model diagnostics |
| fixef | Extract fixed effects |
| formula_status | Inspect formula grammar status |
-- G --
| gamma_matrix | Extract a supplied metafounder Gamma matrix |
| genetic_correlation | Extract multivariate covariance and correlation matrices |
| genetic_covariance | Extract multivariate covariance and correlation matrices |
| genetic_loadings | Reserved factor-analytic and G-matrix extractors |
| genomic | Genomic and QTL formula markers |
| genomic_markers | Genomic and QTL formula markers |
| group | Quantitative-genetic formula markers |
| gwas | Post-fit relatedness-corrected marker scan (GWAS) |
| gwas_table | Extract planned marker, QTL, GWAS, and eQTL results |
| G_matrix | Extract multivariate covariance and correlation matrices |
| g_matrix_geometry | G-matrix geometry and evolvability |
| g_max | G-matrix geometry and evolvability |
-- H --
| heritability | Extract heritability estimates |
| heritability_interval | Extract an experimental heritability confidence interval |
| heritability_standard_error | Extract experimental variance-component and heritability standard errors |
| hsquared | Fit a quantitative-genetic model |
| hsquared-autoplot | ggplot2 visualizations for hsquared results |
| hs_control | Create hsquared control options |
| hs_data | Create an hsquared data container |
| hs_recovery_forest | Forest plot of a known-truth recovery study |
-- I --
| imprinting | Quantitative-genetic formula markers |
| inbreeding | Quantitative-genetic formula markers |
| inference_blocks | Block unsupported likelihood-inference helpers |
-- L --
| latent_breeding_values | Reserved factor-analytic and G-matrix extractors |
| lod_scores | Extract planned marker, QTL, GWAS, and eQTL results |
-- M --
| markers | Genomic and QTL formula markers |
| marker_effects | Extract planned marker, QTL, GWAS, and eQTL results |
| marker_extractors | Extract planned marker, QTL, GWAS, and eQTL results |
| marker_scan | Genomic and QTL formula markers |
| marker_variance_explained | Extract planned marker, QTL, GWAS, and eQTL results |
| maternal_effects | Extract maternal genetic effects |
| maternal_env | Quantitative-genetic formula markers |
| maternal_genetic | Quantitative-genetic formula markers |
| maternal_proportion | Extract the maternal variance ratio (m2) |
| maternal_proportion_interval | Extract an experimental common-environment / maternal variance-ratio interval |
| mean_evolvability | G-matrix geometry and evolvability |
| metafounder | Quantitative-genetic formula markers |
| metafounder_effects | Reserved metafounder effect extractor |
| metafounder_groups | Extract supplied metafounder group assignments |
| model_spec | Inspect a parsed hsquared model specification |
| multivariate_extractors | Extract multivariate covariance and correlation matrices |
-- P --
| partner_variance | Direct-maternal correlated model extractors |
| paternal_env | Quantitative-genetic formula markers |
| paternal_genetic | Quantitative-genetic formula markers |
| permanent | Quantitative-genetic formula markers |
| permanent_effects | Extract permanent-environment effects |
| plot.hsquared_fit | Diagnostic plots for a fitted animal model |
| precision | Quantitative-genetic formula markers |
| predict.hsquared_fit | Response-scale prediction helpers |
| prediction_error_variance | Extract prediction error variances |
| profile.hsquared_fit | Block unsupported likelihood-inference helpers |
-- Q --
| qg_effect_markers | Quantitative-genetic formula markers |
| qtl_scan | Genomic and QTL formula markers |
| qtl_table | Extract planned marker, QTL, GWAS, and eQTL results |
-- R --
| random_coefficients | Random-regression (reaction-norm) extractors |
| random_regression_extractors | Random-regression (reaction-norm) extractors |
| ranef | Extract random effects |
| reliability | Extract reliability and accuracy estimates |
| relmat | Quantitative-genetic formula markers |
| repeatability | Extract repeatability estimates |
| repeatability_interval | Extract an experimental repeatability confidence interval |
| residuals.hsquared_fit | Response-scale prediction helpers |
| residual_correlation | Extract multivariate covariance and correlation matrices |
| residual_covariance | Extract multivariate covariance and correlation matrices |
| respondability | G-matrix geometry and evolvability |
| response_scale_methods | Response-scale prediction helpers |
| rr_correlation | Random-regression (reaction-norm) extractors |
| rr_covariance | Random-regression (reaction-norm) extractors |
| rr_eigenfunctions | Random-regression (reaction-norm) extractors |
| rr_genetic_variance | Random-regression (reaction-norm) extractors |
| rr_heritability | Random-regression (reaction-norm) extractors |
| R_matrix | Extract multivariate covariance and correlation matrices |
-- S --
| single_step | Genomic and QTL formula markers |
| specific_variance | Reserved factor-analytic and G-matrix extractors |
-- T --
| theme_hsquared | hsquared ggplot2 theme |
| total_heritability | Direct-maternal correlated model extractors |
-- U --
| unknown_parent_group | Quantitative-genetic formula markers |
-- V --
| validation_status | Inspect validation evidence status |
| variance_along_gradient | G-matrix geometry and evolvability |
| variance_components | Extract variance components |
| variance_component_standard_errors | Extract experimental variance-component and heritability standard errors |
| vcov.hsquared_fit | Block unsupported likelihood-inference helpers |