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Merged
merged 12 commits into from
Oct 25, 2023
Merged

Update phi parameterisation #487

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85d5563
Update observation_model.stan
seabbs Oct 24, 2023
daf7e5d
Update NEWS.md
seabbs Oct 24, 2023
7b99861
Update inst/stan/functions/observation_model.stan
seabbs Oct 24, 2023
38a520a
Update inst/stan/functions/observation_model.stan
seabbs Oct 24, 2023
bb5f8aa
Update inst/stan/functions/observation_model.stan
seabbs Oct 24, 2023
e63595b
Update inst/stan/functions/observation_model.stan
seabbs Oct 24, 2023
6e1e54b
Update inst/stan/functions/observation_model.stan
seabbs Oct 24, 2023
9505d04
Update inst/stan/functions/observation_model.stan
seabbs Oct 24, 2023
66808b8
Update inst/stan/functions/observation_model.stan
seabbs Oct 24, 2023
c64d812
sqrt_phi -> dispersion
seabbs Oct 24, 2023
62b5b8e
Catch another sqrt_phi
seabbs Oct 24, 2023
e02e300
Update NEWS.md
seabbs Oct 24, 2023
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Update observation_model.stan
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@seabbs
seabbs authored Oct 24, 2023
commit 85d5563015004d1ba4c97b5d905887083e71a37d
6 changes: 3 additions & 3 deletions inst/stan/functions/observation_model.stan
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ void report_lp(array[] int cases, vector reports,
if (model_type) {
real sqrt_phi; // the reciprocal overdispersion parameter (phi)
rep_phi[model_type] ~ normal(phi_mean, phi_sd) T[0,];
sqrt_phi = 1 / sqrt(rep_phi[model_type]);
sqrt_phi = 1 / pow(rep_phi[model_type], 2);
if (weight == 1) {
cases ~ neg_binomial_2(reports, sqrt_phi);
} else {
Expand All @@ -83,7 +83,7 @@ vector report_log_lik(array[] int cases, vector reports,
log_lik[i] = poisson_lpmf(cases[i] | reports[i]) * weight;
}
} else {
real sqrt_phi = 1 / sqrt(rep_phi[model_type]);
real sqrt_phi = 1 / pow(rep_phi[model_type], 2);
for (i in 1:t) {
log_lik[i] = neg_binomial_2_lpmf(cases[i] | reports[i], sqrt_phi) * weight;
}
Expand All @@ -96,7 +96,7 @@ array[] int report_rng(vector reports, array[] real rep_phi, int model_type) {
array[t] int sampled_reports;
real sqrt_phi = 1e5;
if (model_type) {
sqrt_phi = 1 / sqrt(rep_phi[model_type]);
sqrt_phi = 1 / pow(rep_phi[model_type], 2);
}

for (s in 1:t) {
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