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Fixed rep phi #560

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Merged
merged 6 commits into from
Feb 20, 2024
Merged

Fixed rep phi #560

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8a46c11
bring phi specification in line with scale
sbfnk Feb 14, 2024
7998d04
support and deprecate legacy option
sbfnk Feb 14, 2024
72d4f47
update stan model
sbfnk Feb 14, 2024
ad80dfe
update tests
sbfnk Feb 14, 2024
e007e5e
add news item
sbfnk Feb 20, 2024
dc21eae
add PR number and reviewer
sbfnk Feb 20, 2024
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update stan model
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@sbfnk @seabbs
sbfnk authored and seabbs committed Feb 20, 2024
commit 72d4f478710d00165904f6e232d34c91404eee8d
6 changes: 4 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 @@ -77,8 +77,10 @@ void report_lp(array[] int cases, array[] int cases_time, vector reports,
obs_cases = cases;
}
if (model_type) {
real dispersion = 1 / pow(rep_phi[model_type], 2);
rep_phi[model_type] ~ normal(phi_mean, phi_sd) T[0,];
real dispersion = 1 / pow(phi_sd > 0 ? rep_phi[model_type] : phi_mean, 2);
if (phi_sd > 0) {
rep_phi[model_type] ~ normal(phi_mean, phi_sd) T[0,];
}
if (weight == 1) {
obs_cases ~ neg_binomial_2(obs_reports, dispersion);
} else {
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