# adlaplace

Laplace approximations for hierarchical models using CppAD (via the
**RCppAD** R package) and trust-region optimization.

## Install

From [R-universe](https://eborgnine.r-universe.dev) (binaries when available):

```r
install.packages(
  c("RCppAD", "adlaplace"),
  repos = c("https://eborgnine.r-universe.dev", "https://cloud.r-project.org")
)
```

## Vignettes

Built HTML vignettes (from CI):

- [Index](https://eborgnine.github.io/adlaplace/)
- [Laplace Approximations with adlaplace](https://eborgnine.github.io/adlaplace/adlaplace/adlaplace.html)
- [Germany BYM example](https://eborgnine.github.io/adlaplace/adlaplace/germany.html)
- [GAMM examples](https://eborgnine.github.io/adlaplace/adlaplace/gamm.html)
- [Case-crossover models with adlaplace](https://eborgnine.github.io/adlaplace/adlaplace/casecrossover.html)
- [Bayesian Bernoulli mixed model for the bacteria data](https://eborgnine.github.io/adlaplace/adlaplace/bacteria.html)
- [Equivalence to Conditional Gamma-Poisson Model](https://eborgnine.github.io/adlaplace/adlaplace/dirichlet_multinom.html)

## Dependencies

- **RCppAD** — `Imports` + `LinkingTo`; provides `#include <cppad/cppad.hpp>`.
  Install RCppAD before building this package. No system CppAD /
  `libcppad_lib` is required.
- **OpenMP** — recommended (`SystemRequirements: OpenMP`); configure enables
  it when available. Without OpenMP, install still works and `num_threads`
  is ignored.

## Package layout

| Layer | R | C++ |
| ------- | --- | ----- |
| Model (formula, S4 terms) | `effects.R`, `term_data_setup.R`, term `*.R` | — |
| Laplace (AD handle, profile likelihood) | `ad_pack.R`, `density_data.R`, `log_lik.R`, … | `inner_opt`, … |
| Engine (eval, optimizer) | `R/RcppExports.R` | `src/`, `src/include/adlaplace/` |

Public headers for backend packages live in `inst/include/adlaplace/`.
Private engine headers are in `src/include/adlaplace/`.

Backend packages (e.g. `adlaplaceExample`, `adlaplaceFem`, `hpolcc`) should
also `LinkingTo` / `Imports` **RCppAD**, and typically link against the
installed `adlaplace` shared library.

See the monorepo root [`README.md`](../README.md) for install order.

## CRAN notes

Vignettes are abbreviated during `R CMD check` on CRAN (`NOT_CRAN` unset) to
keep rebuild time under 10 minutes; full HTML is built in CI and published at
<https://eborgnine.github.io/adlaplace/>.
No `-Wno-*` flags are used in `PKG_CXXFLAGS`. The Windows `-Wuninitialized`
report was a real uninitialized read in CppAD's `sparse_rc` move constructor,
fixed in RCppAD (>= 1.20260000.0-1).