Overall question: Is there a way to pass an argument from the command line into `.stan`

model code, to alter a function that’s being used in the transformed parameters block? I don’t think I’m asking this correctly, but hopefully the below background helps get at what I’m asking.

I’m running a bunch of models that are essentially the same, except they each use a different function in the transformed parameters block. Currently, I have a different `.stan`

file for each, where the function `logistic_gauge`

would be replaced by one of five other functions, depending on the model:

```
#include fcns_data_params_marg.stan
transformed parameters {
vector[n0] beta;
for (n in 1:n0) {
beta[n] = logistic_gauge(W_trunc[n], dep);
}
}
#include model_gq_marg.stan
```

(For reference, I’ve included the code for the `#include`

statements at the end of this post.)

I kick off each of these models from the command line with the following code:

```
#!/bin/zsh
#
trap '' HUP
stanc_exe="/opt/homebrew/Caskroom/miniconda/base/envs/stan/bin/cmdstan/bin/stanc"
# compile model and link c++
inc_path="stan/trunc/"
for gauge_name in "gauss" "logistic" "inv_log" "asym_log" "dirichlet" "rectangular"
do
object="stan/trunc/bivar_${gauge_name}_${threshold}"
${stanc_exe} ${object}.stan --include-paths=${inc_path}
cmdstan_model ${object}
for level in "low" "mid" "high"
do
for i in {1..100}
do
export gauge_name level i
nohup ./shell_scripts/sampling_trunc_calibrate.sh > shell_scripts/console_output/calibrate/${gauge_name}_${level}_${i}.txt 2>&1&
sleep 10
done
sleep 10
done
sleep 10
done
```

Where `sampling_trunc_calibrate.sh`

is:

```
#!/bin/zsh
# model run
trap '' HUP
datafile="../data/${gauge_name}/${level}_${i}.json"
basedir="./stan/"
cd ${basedir}
model="trunc/bivar_${gauge_name}"
outbase="csv_fits/calibrate/${gauge_name}/${level}_${i}_trunc"
# run model with 3 chains
./${model} sample num_chains=3 \
data file=${datafile} \
output file=${outbase}.csv \
num_threads=3
echo "Model has finished running all 3 chains"
```

Is there a way for me to have one `.stan`

file (instead of six) and pass in the `gauge_name`

argument from the command line to alter the function that’s used in the transformed parameters block? I can’t think of an obvious way to do this, which is why I currently have six different `.stan`

files.

Thank you in advance for your help!! I really appreciate it.

Code for `#include`

statements:

`fcns_data_params_marg.stan`

file:

```
// shared functions, data input values and shared parameter declaration
functions {
#include ../gauge_fcns.stanfunctions
#include truncGamma.stanfunctions
}
data {
int<lower=1> N;
int<lower=1> n0;
array[N] real<lower=0> R;
array[N] real<lower=0, upper=1> W;
array[N] real<lower=0> r0_w;
array[n0] int<lower=1> idx;
}
transformed data {
array[n0] real<lower=0> R_trunc = R[idx];
array[n0] real<lower=0, upper=1> W_trunc = W[idx];
array[n0] real<lower=0> r0_w_trunc = r0_w[idx];
}
parameters {
real<lower=0> alpha;
real<lower=0, upper =1> dep;
}
```

`model_gq_marg.stan`

file:

```
// same model and gen_quant declarations across differing gauge functions
model {
// alpha ~ student_t(4, 0, 2.5);
alpha ~ gamma(4, 2);
dep ~ uniform(0, 1);
for (n in 1:n0) {
target += trunc_gamma_lpdf(R_trunc[n] | r0_w_trunc[n], alpha, beta[n]);
}
}
generated quantities {
vector[n0] log_lik;
for (n in 1:n0) {
log_lik[n] = trunc_gamma_lpdf(R_trunc[n] | r0_w_trunc[n], alpha, beta[n]);
}
}
```

I can upload the custom functions if that would be helpful, but I didn’t want to make this post longer than it already is. Thank you for taking the time to read through this!