Edit stan models using R

This package facilitates editing of stan model code using R. This includes adding/removing blocks, extracting variable names, and inserting/removing lines.

Development of this package was inspired by the <bi_model> class in the rbi package.

Installation

The stable version of the package can be installed using

install.packages("stanedit", repos = "https://epiforecasts.r-universe.dev/")

The development version can be installed using pak

pak::pak("epiforecasts/stanedit")

Example

First we load a stan model and prepare it for editing using the functionality in this package.

library("stanedit")
model_file_name <- system.file(package = "stanedit", "regression.stan")
reg <- stanedit(filename = model_file_name)
reg

## data {
##   int<lower=0> N;
##   vector[N] x;
##   vector[N] y;
## }
## parameters {
##   real alpha;
##   real beta;
##   real<lower=0> sigma;
## }
## model {
##   y ~ normal(alpha + beta * x, sigma);
## }

Let’s say we want to add standard normal priors for alpha and beta. We can do this using

insert_lines(reg,
  lines = c(
    "alpha ~ std_normal();",
    "beta ~ std_normal();"
  ),
  at_end_of = "model"
)

## data {
##   int<lower=0> N;
##   vector[N] x;
##   vector[N] y;
## }
## parameters {
##   real alpha;
##   real beta;
##   real<lower=0> sigma;
## }
## model {
##   y ~ normal(alpha + beta * x, sigma);
##   alpha ~ std_normal();
##   beta ~ std_normal();
## }

Contributors

All contributions to this project are gratefully acknowledged using the allcontributors package following the all-contributors specification. Contributions of any kind are welcome!

sbfnk