Hi all,

Just wondering if it’s possible to use chkpt_brms() with the “data2” argument from the normal brms function. I normally use it to specifiy the correlation matrix for a random effect, but I can’t see how I can add it to the chkpt_brms() function.

I’ve added in a simple example of the model formula that I currently use (but takes too long to run).

```
# Model formula.
model_formula <- paste0("habitat_density ~ seasonality + (1|gr(tree_tip, cov=A))")
# brms formula.
brms_formula <- brmsformula(model_formula, family = cumulative(threshold = "equidistant"))
# # Add priors.
normal_priors <- c(prior(normal(0,1), class="Intercept"),
prior(normal(0,1), class="b"),
prior(gamma(2,1), "sd"))
brms_model <- brm(
brms_formula,
data = model_data,
data2 = list(A=model_covar),
prior = normal_priors,
iter = 10000,
warmup = 5000,
chains = 2,
thin = 20,
cores = 32,
init = 0,
file = model_pathway,
normalize = FALSE,
backend = "cmdstanr",
threads = threading(16),
)
```

In the above code, I specify the co-variance matrix using the data2 arguement with “list(A = model_covar)”, which responds to “(1|gr(tree_tip, cov=A))” in the formula.

If I try and test code on a smaller sample of data using chkpt_brms() i get an error.

This is my checkpoint code:

```
# Run brms checkpoint model.
brms_model <- chkpt_brms(
brms_formula,
data = model_data,
data2 = list(A=model_covar),
prior = normal_priors,
iter_sampling = 1000,
iter_warmup = 500,
iter_per_chkpt = 100,
parallel_chains = 2,
threads_per = 2,
path = model_pathway)
```

The output looks normal to begin with but has an error at the end:

```
Initial Warmup (Typical Set)
Chkpt: 1 / 15; Iteration: 100 / 1500 (warmup)
Chkpt: 2 / 15; Iteration: 200 / 1500 (warmup)
Chkpt: 3 / 15; Iteration: 300 / 1500 (warmup)
Chkpt: 4 / 15; Iteration: 400 / 1500 (warmup)
Chkpt: 5 / 15; Iteration: 500 / 1500 (warmup)
Chkpt: 6 / 15; Iteration: 600 / 1500 (sample)
Chkpt: 7 / 15; Iteration: 700 / 1500 (sample)
Chkpt: 8 / 15; Iteration: 800 / 1500 (sample)
Chkpt: 9 / 15; Iteration: 900 / 1500 (sample)
Chkpt: 10 / 15; Iteration: 1000 / 1500 (sample)
Chkpt: 11 / 15; Iteration: 1100 / 1500 (sample)
Chkpt: 12 / 15; Iteration: 1200 / 1500 (sample)
Chkpt: 13 / 15; Iteration: 1300 / 1500 (sample)
Chkpt: 14 / 15; Iteration: 1400 / 1500 (sample)
Chkpt: 15 / 15; Iteration: 1500 / 1500 (sample)
Checkpointing complete
Error: Object 'A' was not found in 'data2'.
```

I’m not sure how to diagnose the problem, so please let me know if there’s extra info I need to supply as well.

Any help would be very appreciated!