diff --git a/R/cfr_rolling.R b/R/cfr_rolling.R index 3de503cf..9e22170b 100644 --- a/R/cfr_rolling.R +++ b/R/cfr_rolling.R @@ -22,7 +22,7 @@ #' confidence interval of the daily severity estimates, named #' "severity_estimate", "severity_low", and "severity_high", with one row for #' each day in the original data.frame. -#' +#' #' @details #' `cfr_rolling()` applies the internal function `.estimate_severity()` to an #' expanding time-series of total cases, total estimated outcomes, and total diff --git a/README.Rmd b/README.Rmd index 6e5629ec..80f24339 100644 --- a/README.Rmd +++ b/README.Rmd @@ -64,7 +64,7 @@ This example shows how to use _{{ packagename }}_ to estimate the overall case f library(cfr) # Load the Ebola 1976 data provided with the package -data("ebola1976") +data(ebola1976) # Calculate the static CFR without correcting for delays cfr_static(data = ebola1976) @@ -128,7 +128,7 @@ ggplot(data_cfr) + alpha = 0.2, show.legend = FALSE ) + geom_line( - aes(date, severity_mean, colour = method) + aes(date, severity_estimate, colour = method) ) + scale_colour_brewer( palette = "Dark2", diff --git a/vignettes/estimate_ascertainment.Rmd b/vignettes/estimate_ascertainment.Rmd index 26f3dfba..5a9897c1 100644 --- a/vignettes/estimate_ascertainment.Rmd +++ b/vignettes/estimate_ascertainment.Rmd @@ -169,8 +169,8 @@ df_reporting %>% ggplot() + geom_pointrange( aes( - x = fct_reorder(country, ascertainment_mean), - y = ascertainment_mean, + x = fct_reorder(country, ascertainment_estimate), + y = ascertainment_estimate, ymin = ascertainment_low, ymax = ascertainment_high ) diff --git a/vignettes/estimate_time_varying_severity.Rmd b/vignettes/estimate_time_varying_severity.Rmd index 50ce3e9e..6ffbfb8a 100644 --- a/vignettes/estimate_time_varying_severity.Rmd +++ b/vignettes/estimate_time_varying_severity.Rmd @@ -145,7 +145,7 @@ ggplot(df_covid_cfr_uk) + ) + geom_line( aes( - x = date, y = severity_mean, colour = method + x = date, y = severity_estimate, colour = method ) ) + scale_x_date( @@ -242,7 +242,7 @@ filter(df_covid_cfr, country %in% c("Brazil", "India", "United States")) %>% ) + geom_line( aes( - x = date, y = severity_mean, colour = country + x = date, y = severity_estimate, colour = country ) ) + scale_x_date(