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Reuse generation-time support grid across Rt Newton updates #1403

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Reuse generation-time support grid across Rt Newton updates #1403

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9eac792
Reuse Rt Newton support grid
ajh-oai May 12, 2026
8f131b0
Avoid exposed Rt helper overload collision
ajh-oai May 12, 2026
187de36
Document Rt Newton support grid
ajh-oai May 12, 2026
9ae081f
Document Rt Newton optimization
ajh-oai May 12, 2026
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14 changes: 10 additions & 4 deletions inst/stan/functions/rt.stan
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Original file line number Diff line number Diff line change
Expand Up @@ -98,15 +98,20 @@ void rt_lp(array[] real initial_infections_scale, vector bp_effects,
*
* @ingroup rt_estimation
*/
real R_to_r_newton_step(real R, real r, vector pmf) {
real R_to_r_newton_step(real R, real r, vector pmf, vector zero_series) {
int len = num_elements(pmf);
vector[len] zero_series = linspaced_vector(len, 0, len - 1);
vector[len] exp_r = exp(-r * zero_series);
real ret = (R * dot_product(pmf, exp_r) - 1) /
(- R * dot_product(pmf .* zero_series, exp_r));
return(ret);
}

real R_to_r_newton_step(real R, real r, vector pmf) {
int len = num_elements(pmf);
vector[len] zero_series = linspaced_vector(len, 0, len - 1);
return R_to_r_newton_step(R, r, pmf, zero_series);
}

/**
* Estimate the growth rate r from reproduction number R
*
Expand All @@ -128,11 +133,12 @@ real R_to_r_newton_step(real R, real r, vector pmf) {
real R_to_r(real R, vector gt_rev_pmf, real abs_tol) {
int gt_len = num_elements(gt_rev_pmf);
vector[gt_len] gt_pmf = reverse(gt_rev_pmf);
real mean_gt = dot_product(gt_pmf, linspaced_vector(gt_len, 0, gt_len - 1));
vector[gt_len] zero_series = linspaced_vector(gt_len, 0, gt_len - 1);
real mean_gt = dot_product(gt_pmf, zero_series);
real r = fmax((R - 1) / (R * mean_gt), -1);
real step = abs_tol + 1;
while (abs(step) > abs_tol) {
step = R_to_r_newton_step(R, r, gt_pmf);
step = R_to_r_newton_step(R, r, gt_pmf, zero_series);
r -= step;
}

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