EpiCurves: epicurves in ggplot with ggsurveillance • ggsurveillance

Epi Curve examples

This vignette is still work in progress. But the examples are hopefully already helpful and inspiring.

Ebola Outbreak in Kikwit, Democratic Republic of the Congo 1995

ggplot(outbreaks::ebola_kikwit_1995, aes(x = date, weight = onset)) +
  geom_epicurve(date_resolution = "week") +
  scale_x_date(date_breaks = "2 weeks", date_labels = "%V'%g", name = "week") +
  scale_y_cases_5er() +
  theme_bw()

SARS Outbreak in Canada 2003

outbreaks::sars_canada_2003 |>
  pivot_longer(starts_with("cases"), names_prefix = "cases_", names_to = "origin") |>
  ggplot(aes(x = date, weight = value, fill = origin)) +
  geom_epicurve(date_resolution = "week") +
  scale_y_cases_5er() +
  theme_bw()

Influenza Data from Germany 2020-2025

align_dates_seasonal() defines the influenza seasons
geom_vline_year() marks the turn of the years
scale_y_cases_5er() creates a y-axis with more ticks and aligns 0 with the x-axis.

influenza_germany |>
  # Keep Age Groups 00-14, 15-59, 60+
  filter(AgeGroup != "00+") |>
  # Calc Influenza Seasons
  align_dates_seasonal(dates_from = ReportingWeek) |>
  ggplot(aes(x = ReportingWeek, weight = Cases, fill = season)) + # , weight = Cases
  geom_vline_year(color = "grey50") +
  geom_epicurve(color = NA, stat = "bin_date", date_resolution = "week") +
  scale_y_cases_5er() +
  theme_bw()

## Extra

influenza_germany |>
  # Calc Influenza Seasons
  align_dates_seasonal(dates_from = ReportingWeek) |>
  ggplot(aes(x = ReportingWeek, weight = Cases, color = AgeGroup)) + # , weight = Cases
  geom_line(stat = "bin_date", date_resolution = "month") +
  scale_y_cases_5er() +
  facet_wrap(~AgeGroup) +
  theme_bw()