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Issue #319: Fixes to Ebola vignette sex-district figures #326

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merged 4 commits into from
Sep 13, 2024
Merged

Issue #319: Fixes to Ebola vignette sex-district figures #326

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57c553d
Shorten title
athowes Sep 13, 2024
c25ff34
Don't think ` will work here either
athowes Sep 13, 2024
4ae6b54
Try making figure C bigger
athowes Sep 13, 2024
744ed0c
Fix facet and after_stat, make panel C bigger, put two word districts…
athowes Sep 13, 2024
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32 changes: 24 additions & 8 deletions vignettes/ebola.Rmd
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Original file line number Diff line number Diff line change
@@ -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
Expand Down Expand Up @@ -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)))) +
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labs(x = "", y = "", title = "Sex-stratified", tag = "B") +
facet_grid(. ~ sex) +
scale_x_continuous(limits = c(0, 30)) +
Expand All @@ -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"
Expand All @@ -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
Expand Down Expand Up @@ -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(
Expand All @@ -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
Expand Down
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