Get Timeseries from EpiNow

Get Timeseries from EpiNow

get_timeseries(results_dir = NULL, date = NULL, summarised = FALSE)

Arguments

results_dir	A character string indicating the folder containing the EpiNow results to extract.
date	A Character string (in the format "yyyy-mm-dd") indicating the date to extract data for. Defaults to "latest" which finds the latest results available.
summarised	Logical, defaults to FALSE. Should full or summarised results be returned.

Value

A list of reproduction number estimates and nowcast cases

Examples

if (FALSE) {
## Assuming epiforecasts/covid is one repo higher
## Summary results
get_timeseries("../covid/_posts/global/nowcast/results/", 
               summarised = TRUE)

## Simulations
get_timeseries("../covid/_posts/global/nowcast/results/")
}
## Code
get_timeseries
#> function (results_dir = NULL, date = NULL, summarised = FALSE) 
#> {
#>     if (is.null(date)) {
#>         date <- "latest"
#>     }
#>     if (summarised) {
#>         nowcast <- "summarised_nowcast.rds"
#>         rt_index <- 1
#>     }
#>     else {
#>         nowcast <- "nowcast.rds"
#>         rt_index <- 3
#>     }
#>     regions <- list.files(results_dir)
#>     names(regions) <- regions
#>     load_data <- purrr::safely(EpiNow::load_nowcast_result)
#>     rt <- purrr::map_dfr(regions, ~load_data("time_varying_params.rds", 
#>         ., result_dir = results_dir, date = date)[[1]][[rt_index]], 
#>         .id = "region")
#>     incidence <- purrr::map_dfr(regions, ~load_data(nowcast, 
#>         ., result_dir = results_dir, date = date)[[1]], .id = "region")
#>     out <- list(rt, incidence)
#>     names(out) <- c("rt", "incidence")
#>     return(out)
#> }
#> <bytecode: 0x7fdc07307d90>
#> <environment: namespace:EpiNow>