Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

speed up generation of infections #416

Merged
merged 3 commits into from
Jul 13, 2023
Merged

speed up generation of infections #416

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ Type: Package
Package: EpiNow2
Title: Estimate Real-Time Case Counts and Time-Varying
Epidemiological Parameters
Version: 1.3.6.8000
Version: 1.3.6.9000
Authors@R:
c(person(given = "Sam",
family = "Abbott",
Expand Down
1 change: 1 addition & 0 deletions NEWS.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ This release is in development. For a stable release install 1.3.5 from CRAN.
* `dist_fit()`'s `samples` argument now takes a default value of 1000 instead of NULL. If a supplied `samples` is less than 1000, it is changed to 1000 and a warning is thrown to indicate the change. By @jamesmbazam in #389 and reviewed by @seabbs.
* The internal distribution interface has been streamlined to reduce code duplication. By @sbfnk in #363 and reviewed by @seabbs.
* A small bug has been fixed where the seeding time was too long. When a single delay is used this shortens the seeding time by one day and when more delays are used it shortens the seeding time by n days where n is the number of delays used e.g. for two parametric delays it's two days. By @sbfnk in #413 and reviewed by @seabbs.
* Some tuning was done to speed up the renewal model. By @sbfnk in #416.

# EpiNow2 1.3.5

Expand Down
13 changes: 7 additions & 6 deletions inst/stan/functions/infections.stan
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,14 +27,15 @@ 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) {
real growth = exp(initial_growth[1]);
for (s in 2:uot) {
infections[s] = exp(initial_infections[1] + initial_growth[1] * (s - 1));
infections[s] = infections[s - 1] * growth;
}
}
// calculate cumulative infections
Expand All @@ -43,13 +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];
Expand Down