diff --git a/R/estimate_infections.R b/R/estimate_infections.R index b7524ce23..34b29ec19 100644 --- a/R/estimate_infections.R +++ b/R/estimate_infections.R @@ -131,8 +131,10 @@ #' #' #' # Plot output -#' report_plots(summarised_estimates = snapshot$summarised, -#' reported = snapshot_cases) +#' plots <- report_plots(summarised_estimates = snapshot$summarised, +#' reported = snapshot_cases) +#' +#' plots$summary #' #' ## Run model with stationary Rt assumption (likely to provide biased real-time estimates) #' stat <- estimate_infections(reported_cases, family = "negbin", @@ -144,8 +146,10 @@ #' #' #' # Plot output -#' report_plots(summarised_estimates = stat$summarised, -#' reported = reported_cases) +#' plots <- report_plots(summarised_estimates = stat$summarised, +#' reported = reported_cases) +#' +#' plots$summary #' #' # Run model with fixed Rt assumption #' fixed <- estimate_infections(reported_cases, family = "negbin", @@ -157,8 +161,10 @@ #' #' #' # Plot output -#' report_plots(summarised_estimates = fixed$summarised, -#' reported = reported_cases) +#' plots <- report_plots(summarised_estimates = fixed$summarised, +#' reported = reported_cases) +#' +#' plots$summary #' #' # Run model with breakpoints #' bkp <- estimate_infections(reported_cases, family = "negbin", @@ -170,8 +176,10 @@ #' #' #' # Plot output -#' report_plots(summarised_estimates = bkp$summarised, -#' reported = reported_cases) +#' plots <- report_plots(summarised_estimates = bkp$summarised, +#' reported = reported_cases) +#' +#' plots$summary #' #' # Run model with breakpoints but with constrained non-linear change over time #' # This formulation may increase the apparent effect of the breakpoint but needs to be tested using @@ -187,9 +195,11 @@ #' #' #' # Plot output -#' report_plots(summarised_estimates = cbkp$summarised, +#' plots <- report_plots(summarised_estimates = cbkp$summarised, #' reported = reported_cases) #' +#' plots$summary +#' #' # Pull out breakpoint summary #' cbkp$summarised[variable == "breakpoints"] #' @@ -205,9 +215,11 @@ #' #' #' # Plot output -#' report_plots(summarised_estimates = fbkp$summarised, +#' plots <- report_plots(summarised_estimates = fbkp$summarised, #' reported = reported_cases) #' +#' plots$summary +#' #' # Pull out breakpoint summary #' fbkp$summarised[variable == "breakpoints"] #' diff --git a/man/estimate_infections.Rd b/man/estimate_infections.Rd index da3b55b6d..9018cc592 100644 --- a/man/estimate_infections.Rd +++ b/man/estimate_infections.Rd @@ -181,8 +181,10 @@ snapshot <- estimate_infections(snapshot_cases, family = "negbin", # Plot output -report_plots(summarised_estimates = snapshot$summarised, - reported = snapshot_cases) +plots <- report_plots(summarised_estimates = snapshot$summarised, + reported = snapshot_cases) + +plots$summary ## Run model with stationary Rt assumption (likely to provide biased real-time estimates) stat <- estimate_infections(reported_cases, family = "negbin", @@ -194,8 +196,10 @@ stat <- estimate_infections(reported_cases, family = "negbin", # Plot output -report_plots(summarised_estimates = stat$summarised, - reported = reported_cases) +plots <- report_plots(summarised_estimates = stat$summarised, + reported = reported_cases) + +plots$summary # Run model with fixed Rt assumption fixed <- estimate_infections(reported_cases, family = "negbin", @@ -207,8 +211,10 @@ fixed <- estimate_infections(reported_cases, family = "negbin", # Plot output -report_plots(summarised_estimates = fixed$summarised, - reported = reported_cases) +plots <- report_plots(summarised_estimates = fixed$summarised, + reported = reported_cases) + +plots$summary # Run model with breakpoints bkp <- estimate_infections(reported_cases, family = "negbin", @@ -220,8 +226,10 @@ bkp <- estimate_infections(reported_cases, family = "negbin", # Plot output -report_plots(summarised_estimates = bkp$summarised, - reported = reported_cases) +plots <- report_plots(summarised_estimates = bkp$summarised, + reported = reported_cases) + +plots$summary # Run model with breakpoints but with constrained non-linear change over time # This formulation may increase the apparent effect of the breakpoint but needs to be tested using @@ -237,9 +245,11 @@ cbkp <- estimate_infections(reported_cases, family = "negbin", # Plot output -report_plots(summarised_estimates = cbkp$summarised, +plots <- report_plots(summarised_estimates = cbkp$summarised, reported = reported_cases) +plots$summary + # Pull out breakpoint summary cbkp$summarised[variable == "breakpoints"] @@ -255,9 +265,11 @@ fbkp <- estimate_infections(reported_cases, family = "negbin", # Plot output -report_plots(summarised_estimates = fbkp$summarised, +plots <- report_plots(summarised_estimates = fbkp$summarised, reported = reported_cases) +plots$summary + # Pull out breakpoint summary fbkp$summarised[variable == "breakpoints"]