Plot density plots of the basic reproduction number

Plot density plots of the basic reproduction number

plot_R0_density(sims = NULL)

Arguments

sims	A data.table from scenario_analysis.

Value

A ggplot2 plot of R0 density over the scenarios explored

Examples

## Code
plot_R0_density
#> function (sims = NULL) 
#> {
#>     scenario <- NULL
#>     time <- NULL
#>     event_size <- NULL
#>     x <- NULL
#>     R0 <- NULL
#>     serial_type <- NULL
#>     plot <- sims %>% dplyr::group_by(scenario, sample) %>% dplyr::filter(time == 
#>         max(time)) %>% dplyr::ungroup() %>% dplyr::mutate(serial_type = serial_type %>% 
#>         stringr::str_replace_all("initial SARS-like", "pre-intervention SARS-like") %>% 
#>         factor(levels = c("MERS-like", "SARS-like", "pre-intervention SARS-like"))) %>% 
#>         ggplot2::ggplot(ggplot2::aes(x = R0, y = factor(event_size), 
#>             fill = stat(x))) + ggridges::geom_density_ridges_gradient(quantile_lines = TRUE, 
#>         quantiles = c(0.05, 0.95)) + ggplot2::facet_grid(serial_type ~ 
#>         event_duration) + ggplot2::scale_fill_continuous(type = "viridis", 
#>         direction = 1) + ggplot2::theme_minimal() + ggplot2::labs(x = "Reproduction number (R0)", 
#>         y = "Transmission event size") + ggplot2::theme(legend.position = "bottom") + 
#>         ggplot2::guides(fill = ggplot2::guide_colorbar(title = "R0"))
#>     return(suppressWarnings(suppressMessages(plot)))
#> }
#> <bytecode: 0x55a6b3fe4420>
#> <environment: namespace:WuhanSeedingVsTransmission>