Package: heritable 0.1.0

Emi Tanaka

heritable: Heritability Estimation from Mixed Models

Reporting heritability estimates is an important to quantitative genetics studies and breeding experiments. Here we provide functions to calculate various broad-sense heritabilities from 'asreml' and 'lme4' model objects. All methods we have implemented in this package have extensively discussed in the article by Schmidt et al. (2019) <doi:10.1534/genetics.119.302134>.

Authors:Fonti Kar [aut, ctb], Yidi Deng [aut, ctb], Emi Tanaka [cre, aut, cph]

heritable_0.1.0.tar.gz
heritable_0.1.0.zip(r-4.7)heritable_0.1.0.zip(r-4.6)heritable_0.1.0.zip(r-4.5)
heritable_0.1.0.tgz(r-4.6-any)heritable_0.1.0.tgz(r-4.5-any)
heritable_0.1.0.tar.gz(r-4.7-any)heritable_0.1.0.tar.gz(r-4.6-any)
heritable_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
heritable/json (API)

# Install 'heritable' in R:

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

Bug tracker:https://github.com/anu-aagi/heritable/issues

Pkgdown/docs site:https://anu-aagi.github.io

Datasets:

lettuce_GRM - Molecular marker data and genomic relatedness matrix of 89 lettuce varieties
lettuce_markers - Molecular marker data and genomic relatedness matrix of 89 lettuce varieties
lettuce_phenotypes - Phenotypic data of 89 lettuce varieties
lizard_GRM - Molecular markers data and genomic relatedness matrix of Australian lizards
lizard_markers - Molecular markers data and genomic relatedness matrix of Australian lizards
lizard_phenotypes - Phenotypic data of Australian lizards

On CRAN:

6.30 score 7 stars 6 scripts 506 downloads 16 exports 177 dependencies

Last updated from:29d7ba58d8. Checks:7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	WARNING	206
source / vignettes	OK	242
linux-release-x86_64	WARNING	202
macos-release-arm64	WARNING	217
macos-oldrel-arm64	WARNING	230
windows-devel	WARNING	148
windows-release	WARNING	191
windows-oldrel	WARNING	129
wasm-release	OK	162

Exports:bootstrap_asreml get_fixed_fit_asreml H2 H2_Cullis H2_Cullis_parameters H2_Delta H2_Delta_by_genotype H2_Delta_pairwise h2_Delta_parameters H2_Delta_parameters H2_Oakey H2_Oakey_parameters H2_Piepho H2_Piepho_parameters H2_Standard H2_Standard_parameters

Dependencies:abind askpass asremlPlus backports base64enc bitops boot brew brio broom bslib cachem callr car carData caTools cli clipr codetools colorspace commonmark corrplot cowplot cpp11 crayon credentials curl dae DEoptimR Deriv desc devtools diffobj digest doBy doParallel downlit dplyr ellipsis emmeans estimability evaluate fansi farver fastmap fontawesome foreach forecast Formula fracdiff fs generics gert ggplot2 ggpubr ggrepel ggsci ggsignif gitcreds glue gridExtra gtable highr htmltools htmlwidgets httpuv httr2 ini isoband iterators jquerylib jsonlite knitr labeling later lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixModels memoise mgcv microbenchmark mime miniUI minqa modelr mvtnorm nlme nloptr nnet numDeriv opdisDownsampling openssl otel pak pbkrtest pbmcapply pillar pkgbuild pkgconfig pkgdown pkgload plyr polynom pracma praise prettyunits processx profvis promises ps purrr qqconf qqplotr quantreg R6 ragg rappdirs rbibutils rcmdcheck RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas reshape2 rlang rmarkdown robustbase roxygen2 rprojroot rstatix rstudioapi rversions S7 sass scales sessioninfo shiny sourcetools SparseM sticky stringi stringr survival sys systemfonts testthat textshaping tibble tidyr tidyselect timeDate tinytex tryCatchLog twosamples urca urlchecker usethis utf8 vctrs viridisLite waldo whisker withr xfun xml2 xopen xtable yaml zip zoo

heritable

Motivation | Installation | A demo | Broad-sense heritability | Alternative output formats

Rendered fromheritable.Rmdusingknitr::rmarkdown

Last update: 2026-02-02
Started: 2025-11-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Parametric bootstrap for an asreml model.	bootstrap_asreml
Bootstrap confidence interval for heritability	confint.heritable
Fixed-effects-only fitted values from an asreml model	get_fixed_fit_asreml
Calculate heritability from mixed model object	H2 h2
Calculate Cullis' heritability from model object	H2_Cullis
Calculate Cullis heritability using variance parameters	H2_Cullis_parameters
Calculate average heritability of differences between genotypes from model object	H2_Delta
Calculate heritability of differences for a given genotype from model object	H2_Delta_by_genotype
Calculate pairwise heritability of differences between genotypes from model object	H2_Delta_pairwise
Calculate heritability of pairwise differences using variance parameters	H2_Delta_parameters h2_Delta_parameters
Calculate Oakey's heritability from model object	H2_Oakey
Calculate Oakey's heritability using variance parameters	H2_Oakey_parameters
Calculate Piepho's heritability from model object Compute Piepho's heritability using variance differences between genotype BLUEs	H2_Piepho
Calculate Piepho's heritability using variance parameters	H2_Piepho_parameters
Calculate standard heritability from model object	H2_Standard
Calculate Standard heritability using variance parameters	H2_Standard_parameters
Molecular marker data and genomic relatedness matrix of 89 lettuce varieties	lettuce_GRM lettuce_markers
Phenotypic data of 89 lettuce varieties	lettuce_phenotypes
Molecular markers data and genomic relatedness matrix of Australian lizards	lizard_GRM lizard_markers
Phenotypic data of Australian lizards	lizard_phenotypes