diff --git a/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiNow2.Rmd b/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiNow2.Rmd index ef5c6be..b0cc2ce 100644 --- a/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiNow2.Rmd +++ b/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiNow2.Rmd @@ -13,25 +13,8 @@ library(EpiNow2) ### Results ```{r rt-wrappers-prep} -# Approximate serial interval with gamma distribution since this is what EpiNow2 -# will use for generation_time -si_gamma <- epiparameter::extract_param( - type = "range", - values = c(median(si$prob_dist$r(1e3)), - min(si$prob_dist$r(1e3)), - max(si$prob_dist$r(1e3))), - distribution = params$si_dist, - samples = 1e3 -) -si_gamma <- epiparameter::convert_params_to_summary_stats( - distribution = "gamma", shape = si_gamma[[1]], scale = si_gamma[[2]]) - -generation_time <- list( - mean = si_gamma$mean, - mean_sd = 0, - sd = si_gamma$sd, - sd_sd = 0, - max = max(si_x) +generation_time <- generation_time_opts( + dist_spec(pmf = si$prob_dist$d(si_x)) ) ``` @@ -50,9 +33,10 @@ associated 95% credibility intervals # for a long time! res_epinow2_global <- dat_i_day %>% regroup() %>% - dplyr::rename( - confirm = .data[[count_var]], - date = date_index + dplyr::mutate( + confirm = count, + date = as.Date(date_index), + .keep = "unused" ) %>% epinow( generation_time = generation_time,