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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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sqrt_phi -> dispersion
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@seabbs
seabbs authored Oct 24, 2023
commit c64d812e5bbc5e8b7dac700239580da8ade29674
4 changes: 2 additions & 2 deletions inst/stan/functions/observation_model.stan
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ void report_lp(array[] int cases, vector reports,
if (weight == 1) {
cases ~ neg_binomial_2(reports, dispersion);
} else {
target += neg_binomial_2_lpmf(cases | reports, sqrt_phi) * weight;
target += neg_binomial_2_lpmf(cases | reports, dispersion) * weight;
}
} else {
if (weight == 1) {
Expand Down Expand Up @@ -106,7 +106,7 @@ array[] int report_rng(vector reports, array[] real rep_phi, int model_type) {
if (sqrt_phi > 1e4) {
sampled_reports[s] = poisson_rng(reports[s] > 1e8 ? 1e8 : reports[s]);
} else {
sampled_reports[s] = neg_binomial_2_rng(reports[s] > 1e8 ? 1e8 : reports[s], sqrt_phi);
sampled_reports[s] = neg_binomial_2_rng(reports[s] > 1e8 ? 1e8 : reports[s], dispersion);
}
}
}
Expand Down