get_rep_sample_fun.RdThis connects to the Google Sheet containing the collated linelist; the first time this is run, it may require authentiction with Google
get_rep_sample_fun()
a function that takes one parameter, n, the number of reporting
delays to randomly sample
## Example if (FALSE) { get_rep_sample_fun() } ## Code get_rep_sample_fun#> function () #> { #> delay_confirmation <- NULL #> country <- NULL #> . <- NULL #> message("Downloading linelist") #> confirmation_delays <- get_linelist() %>% dplyr::filter(!is.na(delay_confirmation), #> country == "China") %>% .$delay_confirmation %>% as.integer() #> test_distributions <- c("geom", "pois", "nbinom") #> fits <- lapply(stats::setNames(test_distributions, test_distributions), #> function(x) { #> fitdistrplus::fitdist(confirmation_delays, x) #> }) #> gof <- fitdistrplus::gofstat(fits, fitnames = names(fits)) #> best_fit <- names(which.min(gof$aic)) #> message("Best fitting distribution: ", best_fit) #> good_fit <- (gof$chisqpvalue[best_fit] > 0.05) #> if (!good_fit) { #> message("Fit below threshold. Sampling from data.") #> sample_function <- function(n) { #> sample(confirmation_delays, n, replace = TRUE) #> } #> } #> else { #> pars <- fits[[best_fit]]$estimate #> sample_function <- function(n) { #> do.call(paste0("r", best_fit), c(list(n = n), as.list(pars))) #> } #> } #> return(sample_function) #> } #> <bytecode: 0x55a6b7118250> #> <environment: namespace:WuhanSeedingVsTransmission>