implement s7 classes

[vandenman]

Fixes https://github.com/Bayesian-Graphical-Modelling-Lab/issues/issues/79

Description

Provide a concise summary of the changes.

Problem / Motivation

This fixes the fragile S3 methods with cache for lazy computations, those are now implemented like so:

bgms_class = new_class("bgms",
  package = NULL,
  properties = list(
    # --- Core (always present) ---
    arguments = new_property(class_any),
    raw_samples = new_property(class_any),
    cache = new_property(class_any),

    # --- Posterior means (set during construction, immutable) ---
    posterior_mean_main = new_property(class_any, default = NULL),

# < omitted stuff >

    # --- Lazy MCMC diagnostics (computed on first access via getter) ---
    posterior_summary_main = new_property(
      class = class_any,
      getter = function(self) {
        ensure_summaries(self)
        self@cache[["posterior_summary_main"]]
      }
    ),

# < omitted stuff >

)

So there is a proper getter method that does the computation.

Note that we have a lot of class_any. This could be a more constrained type, but for now this is fine I think.

Key difference for users

# Old behaviour
data("Wenchuan")
fit <- bgm(Wenchuan)
class(fit) # "bgms"
fit$posterior_mean_main # <- uses '$'

# New behaviour
data("Wenchuan")
fit <- bgm(Wenchuan)
class(fit) # "bgms"      "S7_object"
fit@posterior_mean_main # <- uses '@'

However, if users do/ did extract_main_effects then nothing changed.

Type of Change

• Bug fix
• New feature
• Breaking change
• Documentation update
• Performance optimization
• Statistical / methodological update

Documentation and Release Notes

• Updated function documentation for any signature or behaviour changes
• Regenerated man/*.Rd files if roxygen comments changed
• Updated _pkgdown.yml if adding a new exported function
• Added or updated NEWS.md entry if the change affects users

Testing and Validation

Describe the checks you ran and the main results.

• Added or updated tests in tests/testthat/ when needed
• Ran the project styler

source("inst/styler/bgms_style.R")
styler::style_pkg(style = bgms_style)

• Checked test files for styled result = captures that must be reverted to result <-
• Ran lintr::lint_package()
• Ran roxygen2::roxygenise() if roxygen comments changed
• Ran rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran")) for non-trivial changes
• Verified numerical behaviour where relevant

[vandenman]

The R devel check fails because some other R package could not be installed.