diff --git a/vignettes/ebola.Rmd b/vignettes/ebola.Rmd index 9d4ef04a7..e764eabb8 100644 --- a/vignettes/ebola.Rmd +++ b/vignettes/ebola.Rmd @@ -1,6 +1,6 @@ --- -title: "Using `epidist` to estimate stratified delays between symptom onset and positive test for the 2014-2016 Ebola outbreak in Sierra Leone" -description: "A more detailed guide to using the `epidist` R package" +title: "Using epidist to estimate delay between symptom onset and positive test for an Ebola outbreak in Sierra Leone" +description: "A more detailed guide to using the epidist R package" output: bookdown::html_document2: fig_caption: yes @@ -405,7 +405,7 @@ draws_sex_pmf <- obs_prep |> pmf_sex_figure <- draws_sex_pmf |> ggplot(aes(x = .prediction)) + - geom_bar(aes(y = after_stat(count / sum(count)))) + + geom_bar(aes(y = after_stat(count / ave(count, PANEL, FUN = sum)))) + labs(x = "", y = "", title = "Sex-stratified", tag = "B") + facet_grid(. ~ sex) + scale_x_continuous(limits = c(0, 30)) + @@ -418,8 +418,16 @@ draws_sex_district_pmf <- obs_prep |> add_predicted_draws(fit_sex_district, ndraws = 1000) pmf_sex_district_figure <- draws_sex_district_pmf |> + mutate( + district = case_when( + district == "Port Loko" ~ "Port\nLoko", + district == "Western Rural" ~ "Western\nRural", + district == "Western Urban" ~ "Western\nUrban", + .default = district + ) + ) |> ggplot(aes(x = .prediction)) + - geom_bar(aes(y = after_stat(count / sum(count)))) + + geom_bar(aes(y = after_stat(count / ave(count, PANEL, FUN = sum)))) + labs( x = "PMF with daily censoring and no truncation", y = "", title = "Sex-district-stratified", tag = "C" @@ -431,9 +439,9 @@ pmf_sex_district_figure <- draws_sex_district_pmf |> (ref:pmf) Posterior predictions of the discrete probability mass function for each of the fitted models. -```{r pmf, fig.cap="(ref:pmf)", fig.height = 9} +```{r pmf, fig.cap="(ref:pmf)", fig.height = 16} pmf_base_figure / pmf_sex_figure / pmf_sex_district_figure + - plot_layout(heights = c(1, 1.5, 3)) + plot_layout(heights = c(1, 1.5, 5.5)) ``` ### Continuous probability density function @@ -474,6 +482,14 @@ draws_sex_district_pdf <- obs_prep |> add_predicted_draws(fit_sex_district, ndraws = 1000) pdf_sex_district_figure <- draws_sex_district_pdf |> + mutate( + district = case_when( + district == "Port Loko" ~ "Port\nLoko", + district == "Western Rural" ~ "Western\nRural", + district == "Western Urban" ~ "Western\nUrban", + .default = district + ) + ) |> ggplot(aes(x = .prediction)) + geom_density() + labs( @@ -487,9 +503,9 @@ pdf_sex_district_figure <- draws_sex_district_pdf |> (ref:pdf) Posterior predictions of the continuous probability density function for each of the fitted models. -```{r pdf, fig.cap="(ref:pdf)", fig.height = 9} +```{r pdf, fig.cap="(ref:pdf)", fig.height = 16} pdf_base_figure / pdf_sex_figure / pdf_sex_district_figure + - plot_layout(heights = c(1, 1.5, 3)) + plot_layout(heights = c(1, 1.5, 5.5)) ``` # Conclusion