Type checking for ODE-solvers is broken #2731
Description
Summary:
Some inputs to the ODE-solvers pass the Stan type check and fail on C++ compilation.
Description:
Data only argument status is not propagated correctly through function calls.
Reproducible Steps:
Try to compile
functions {
real[] two_pool_feedback(real t, real[] C, real[] theta,
real[] x_r, int[] x_i) {
real k1;
real k2;
real alpha21;
real alpha12;
real dC_dt[2];
k1 <- theta[1];
k2 <- theta[2];
alpha21 <- theta[3];
alpha12 <- theta[4];
dC_dt[1] <- -k1 * C[1] + alpha12 * k2 * C[2];
dC_dt[2] <- alpha21 * k1 * C[1] - k2 * C[2];
return dC_dt;
}
real[] evolved_CO2(int N_t, real t0, real[] ts,
real gamma, real totalC_t0,
real k1, real k2,
real alpha21, real alpha12,
real[] x_r, int[] x_i) {
real C_t0[2]; // initial state
real theta[4]; // ODE parameters
real C_hat[N_t,2]; // predicted pool content
real eCO2_hat[N_t];
C_t0[1] <- gamma * totalC_t0;
C_t0[2] <- (1 - gamma) * totalC_t0;
theta[1] <- k1;
theta[2] <- k2;
theta[3] <- alpha21;
theta[4] <- alpha12;
C_hat <- integrate_ode_bdf(two_pool_feedback,
C_t0, t0, ts, theta, x_r, x_i);
for (t in 1:N_t)
eCO2_hat[t] <- totalC_t0 - sum(C_hat[t]);
return eCO2_hat;
}
}
data {
real<lower=0> totalC_t0; // initial total carbon
int<lower=0> N_t; // number of measurement times
vector<lower=0>[N_t] eCO2mean; // measured cumulative evolved carbon
real<lower=0> eCO2sd[N_t]; // measured cumulative evolved carbon
}
transformed data {
real x_r[0]; // no real data for ODE system
int x_i[0]; // no integer data for ODE system
}
parameters {
real<lower=0> k1; // pool 1 decomposition rate
real<lower=0> k2; // pool 2 decomposition rate
real<lower=0> alpha21; // transfer coeff from pool 2 to 1
real<lower=0> alpha12; // transfer coeff from pool 1 to 2
real<lower=0,upper=1> gamma; // partitioning coefficient
real<lower=0> sigma; // observation std dev
real t0; // initial time
real<lower=t0> ts[N_t]; // measurement times
vector<lower=0>[N_t] eCO2; // evolved CO2
}
transformed parameters {
real eCO2_hat[N_t];
eCO2_hat <- evolved_CO2(N_t, t0, ts, gamma, totalC_t0,
k1, k2, alpha21, alpha12, x_r, x_i);
}
model {
gamma ~ beta(10,1); // identifies pools
k1 ~ normal(0,1); // weakly informative
k2 ~ normal(0,1);
alpha21 ~ normal(0,1);
alpha12 ~ normal(0,1);
sigma ~ normal(0,1);
// likelihood marginalizes out eCO2
// true eCO2 (unknown) generated from system plus noise
eCO2 ~ normal(eCO2_hat, sigma);
// measurement eCO2mean (observed) of true eCO2 value with
// measurement noise eCO2sd (observed)
eCO2mean ~ normal(eCO2, eCO2sd);
}
It passes stanc, but fails on C++ compilation. Same with any of the other ODE-solvers.
Current Output:
No stanc type checking error.
Expected Output:
A stanc type checking error.
Additional Information:
This should also be fixed in the manual.
Current Version:
v2.18.1