Open innovative-simulator opened 3 years ago
Thanks for pointing this out — we are preparing a fix and correction to the article.
We don't expect this issue to affect our qualitative conclusions, specifically in terms of the relative impact of different interventions, and it has no impact upon the calculation of R values under different interventions, meaning that our conclusions regarding which interventions may be effective for controlling the UK epidemic will not change. This error occurred while preparing the manuscript for Lancet ID, so did not affect the modelling evidence originally submitted to government advisory bodies.
Thanks for submitting the feedback!
Nick
In UK.R simulations for intervention scenarios are being performed with the default seed_times (1 person on day 1), not the seed_times used for the base scenario (2 per day, for 28 days, starting at the randomly sampled seed_start, as per the Lancet paper).
To check, see UK.R:
Running with 1 seed infection, instead of 2*28, means many counties fail to have an epidemic. This is difficult to see from the aggregated output time series in the X-dynamics.qs file, but try:
The effects of the bug vary between runs, but in general are that interventions produce much bigger reductions in numbers of cases, beds, and deaths than they would if they received the same seed infections as the Base scenario.
The authors have been notified, so a bug fix should follow.
In the meantime, if you are using UK.R try the following correction. (I have concatenated the lines of code to preserve the line numbering.):
Line 372:
params = duplicate(parameters); initial_seed_times <- list(); initial_dist_seed_ages <- list(); # CW's addition: Setup lists to store populations' seed_times and dist_seed_ages
Lines: 376, 377:Line 446:
params$pop[[j]]$y = covy; params$pop[[j]]$seed_times = initial_seed_times[[j]]; params$pop[[j]]$dist_seed_ages = initial_dist_seed_ages[[j]]; # CW's addition: Re-use Base scenario's stored seed_times and dist_seed_ages.