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hsquared

R interface · Julia engine · a twin, not a port

How much is genetic?

Formula first. The engine returns heritability, variance components, and breeding values on the routes that are covered — experimental 0.9.0 release, not production. CRAN availability is tracked separately.

Get started Choose a model Fit a model

Before you report anything

Warning — experimental 0.9.0 release. Not production. CRAN availability is tracked separately. There are 7 R-public covered routes; fitting needs local Julia and an HSquared.jl checkout. Julia engine-covered ≠ R-public covered. Report point estimates only within a covered route. No interval is nominally coverage-calibrated; named univariate pedigree intervals are only classified as directional-conservative. See Can I fit and report this?.

Your first analysis

1. Get started
Install or validate a first animal-model formula.
2. Choose a model
Check the route scope before fitting.
3. Fit
Run the smallest honest workflow.
4. Diagnose
Read fit diagnostics before extracting results.
5. Report
Use route-scoped point estimates only.

Start here

If you want to…	Read this
check a formula without installing Julia	Getting started (`control = hs_control(engine = "validate")`)
decide whether a number may go in a paper	Can I fit and report this?
see the seven R-public covered routes	Model status
set up the Julia engine	Installation
look up a function	Reference
understand evidence history without mistaking it for a release	Progression & evidence

Quick start — no Julia required

This four-animal pedigree is a syntax demo, not a number for a paper.

library(hsquared)

ped <- data.frame(
  id   = c("sire", "dam", "off1", "off2"),
  sire = c(NA, NA, "sire", "sire"),
  dam  = c(NA, NA, "dam", "dam")
)
dat <- data.frame(
  id     = c("sire", "dam", "off1", "off2"),
  sex    = c("m", "f", "m", "f"),
  weight = c(42, 38, 40, 37)
)

hsquared(
  weight ~ sex + animal(1 | id, pedigree = ped),
  data = dat,
  control = hs_control(engine = "validate")
)

Fitting — requires the Julia engine

With a local Julia, JuliaCall, and an HSquared.jl checkout (see Installation):

fit <- hsquared(
  weight ~ sex + animal(1 | id, pedigree = ped),
  data = dat
)
summary(fit)

Report only what Can I fit and report this? allows for the route you ran.

Installation

# install.packages("remotes")
remotes::install_github("itchyshin/hsquared")

Fitting also needs Julia, JuliaCall, and a local HSquared.jl tree. HSquared is not in the Julia General registry — do not use Pkg.add("HSquared") by name.

install.packages("JuliaCall")

Clone or point at your HSquared.jl checkout per the getting-started guide.

Authors

Shinichi Nakagawa (ORCID 0000-0002-7765-5182, itchyshin@gmail.com), Yefeng Yang (ORCID 0000-0002-8610-4016), Szymon Drobniak (ORCID 0000-0001-8101-6247).

Twin

hsquared is the applied R interface. HSquared.jl is the sparse engine. A twin, not a port.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.