What I’m trying to do is get the same values with RStan as I get with running the Stan C++ code directly.

With

stan::services:sample::hmc_nuts_diag_e_adapt()

you can specify:

chain_id

init_radius

num_warmup

num_samples

num_thin

save_warmup

refresh

stepsize

stepsize_jitter

max_depth

delta

gamma

kappa

t0

init_buffer

term_buffer

window

Using http://mc-stan.org/rstan/reference/stan.html#details

I’m tryng to specify all these through RStan, but one main thing stands in my way, I’m very new to R.

Here’s the parameter section:

//Where N = 2 in this case

parameters {

vector[N] param;

}

Can someone familar with RStan fill in the blanks to what I have?

control = list(adapt_engaged = TRUE, adapt_gamma = 0.04, adapt_delta = 0.9, adapt_kappa = 0.85, adapt_t0 = 4, adapt_init_buffer = 85, adapt_term_buffer = 40, adapt_window = 20)

fit = stan(file = ‘model.stan’, data=my_data, iter=2000, chains = 1, warmup = 250, thin = 1, seed = 1234, init = list(list(‘param[1]’ = 1.0, ‘param[2]’ = 1.0), algorithm = “NUTS”, control = control)

I’m looking to add:

stepsize

stepsize_jitter

metric (diag_e)

max_treedepth

chain_id (how is this specified if I have more than one chain?)

save_warmup

I’m pretty sure “init” is incorrect here as changing values has no effect.