Add Stan support as alternative Bayesian modeling backend

[Copilot]

Implements Stan/cmdstanr support alongside existing JAGS implementation, allowing users to choose their preferred Bayesian MCMC backend.

Changes

Stan Model Files

• inst/extdata/model.stan - Main antibody dynamics model with:
  • Precision→covariance matrix conversions (JAGS uses precision, Stan uses covariance)
  • Wishart→inverse Wishart transformation for subject-level variance priors
  • Explicit block structure (data, parameters, transformed parameters, model)
  • Conditional infection phase logic (active vs recovery) using if/else instead of JAGS step()
• inst/extdata/model.dobson.stan - Simple Bernoulli example

R Functions

• run_mod_stan() - Stan equivalent of run_mod(), returns same sr_model output format
• prep_data_stan() - Handles Stan array padding requirements (no ragged arrays)
• prep_priors_stan() - Prior specification interface matching prep_priors()

Dependencies

• Added cmdstanr to Suggests (not Imports) - Stan support is optional
• Runtime check with informative error if cmdstanr unavailable

Usage

# Existing JAGS workflow (unchanged)
run_mod(data, file_mod = "model.jags", nchain = 4, nadapt = 100, niter = 1000)

# New Stan workflow (identical interface)
run_mod_stan(data, file_mod = "model.stan", nchain = 4, nadapt = 500, niter = 1000)

Both return compatible outputs for existing analysis/plotting functions.

Installation (Stan)

install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev", getOption("repos")))
cmdstanr::install_cmdstan()

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• cloud.r-project.org
  • Triggering command: /opt/R/4.5.2/lib/R/bin/exec/R /opt/R/4.5.2/lib/R/bin/exec/R -e install.packages('cmdstanr',~+~repos~+~=~+~c('REDACTED',~+~'REDACTED')) (dns block)
• stan-dev.r-universe.dev
  • Triggering command: /opt/R/4.5.2/lib/R/bin/exec/R /opt/R/4.5.2/lib/R/bin/exec/R -e install.packages('cmdstanr',~+~repos~+~=~+~c('REDACTED',~+~'REDACTED')) (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

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This section details on the original issue you should resolve

<issue_title>convert jags model to stan</issue_title>
<issue_description></issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes convert jags model to stan #174

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[d-morrison]

fix failing workflow checks

[d-morrison]

address workflow check failures