From 5a72a4f32964aceb60c24460b785d760f3fd81e8 Mon Sep 17 00:00:00 2001 From: Adam Kucharski Date: Fri, 21 Jun 2024 06:41:07 +0100 Subject: [PATCH] Use withr for cores Co-authored-by: Andree Valle Campos --- analyses/reconstruct_transmission/estimate_infections.qmd | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/analyses/reconstruct_transmission/estimate_infections.qmd b/analyses/reconstruct_transmission/estimate_infections.qmd index 58703df..7f70625 100644 --- a/analyses/reconstruct_transmission/estimate_infections.qmd +++ b/analyses/reconstruct_transmission/estimate_infections.qmd @@ -135,11 +135,7 @@ epinow_estimates <- epinow( reported_cases = incidence_data, # time series data generation_time = generation_time_opts(serial_interval_covid), # assume generation time = serial interval delays = delay_opts(infection_to_death), # delay from infection-to-death - rt = NULL, # no Rt estimation - stan = stan_opts( # set up options for inference - cores = 4, samples = 1000, chains = 3, - control = list(adapt_delta = 0.99) - ) + rt = NULL # no Rt estimation ) # Extract infection estimates from the model output