Hello,

I am very new to STAN and I have been trying to use it to estimate parameters for my system of ODEs (three variables). I am using it via R with rstan package, where I give the model data and initial estimates for paramters.

One of my parameters, pM, depends on two others via a fixed value (not a parameter to be estimated), called Lm. At the moment I have added Lm to the transformed data section as it is not to be estimated, I have my other two paramters to be estimated in the paramters section, and then the dependent paramter in the transformed parameters section. I would like to be able to input the Lm as an input, rather than set it manually. This is because Lm appears in my r code more than once, so if I vary it in R I need to remeber to then edit it manually in STAN too, and that could lead to forgetting and mistakes.

The STAN code currently looks something like this (some bits omitted):

// The input data is a vector ‘y’ of length ‘N’.

data {

int<lower=0> T;

array[T] real t;

vector[3] y0; //initial conditions

array[T] vector[3] y_obs;

}transformed data {

real t0 = 0;

real L_m = 20;

}// The parameters accepted by the model.

parameters {

//

real<lower=0> sigma; //2

real kappa;

real<lower=0> p_Amax;

}transformed parameters {

//dependencies

real p_M = kappa*p_Amax/L_m;

}model {

sigma ~ normal(0, 1);// 2

kappa ~ beta(3, 2); // 0.86

p_Amax ~ normal(0, 1); // 282for (n in 1 : T) {

y_obs[n,1] ~ normal(y[n,1],sigma);

y_obs[n,2] ~ normal(y[n,2],sigma);

y_obs[n,3] ~ normal(y[n,3],sigma);

}

}