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speed up generation of infections #416

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Merged
merged 3 commits into from
Jul 13, 2023
Merged

speed up generation of infections #416

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1622195
reduce number of exponential calls
sbfnk Jul 4, 2023
fefe19b
initialise vectors to zero
sbfnk Jul 4, 2023
b78843c
news item and version bump
sbfnk Jul 5, 2023
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initialise vectors to zero
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@sbfnk
sbfnk committed Jul 4, 2023
commit fefe19b4bada5c0abe228abcdcc816c9e4870953
10 changes: 5 additions & 5 deletions inst/stan/functions/infections.stan
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Original file line number Diff line number Diff line change
Expand Up @@ -27,9 +27,9 @@ vector generate_infections(vector oR, int uot, vector gt_rev_pmf,
int t = ot + uot;
vector[ot] R = oR;
real exp_adj_Rt;
vector[t] infections = rep_vector(1e-5, t);
vector[ot] cum_infections = rep_vector(0, ot);
vector[ot] infectiousness = rep_vector(1e-5, ot);
vector[t] infections = rep_vector(0, t);
vector[ot] cum_infections;
vector[ot] infectiousness;
// Initialise infections using daily growth
infections[1] = exp(initial_infections[1]);
if (uot > 1) {
Expand All @@ -44,13 +44,13 @@ vector generate_infections(vector oR, int uot, vector gt_rev_pmf,
}
// iteratively update infections
for (s in 1:ot) {
infectiousness[s] += update_infectiousness(infections, gt_rev_pmf, uot, s);
infectiousness[s] = update_infectiousness(infections, gt_rev_pmf, uot, s);
if (pop && s > nht) {
exp_adj_Rt = exp(-R[s] * infectiousness[s] / (pop - cum_infections[nht]));
exp_adj_Rt = exp_adj_Rt > 1 ? 1 : exp_adj_Rt;
infections[s + uot] = (pop - cum_infections[s]) * (1 - exp_adj_Rt);
}else{
infections[s + uot] += R[s] * infectiousness[s];
infections[s + uot] = R[s] * infectiousness[s];
}
if (pop && s < ot) {
cum_infections[s + 1] = cum_infections[s] + infections[s + uot];
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