ggsurveillance is an R package with helpful tools and ggplot extensions for epidemiology, especially infectious disease surveillance and outbreak investigation. All functions provide tidy functional interfaces for easy integration with the tidyverse. For documentation and vignettes see: ggsurveillance.biostats.dev
This packages provides:
geom_epicurve() : A ggplot geom for plotting
epicurves
state_bin_date() for date interval (week,
month etc.) based binning of case numbers with perfect alignment with
i.e. reporting week.scale_y_cases_5er() for better (case) count
axis breaks and positioning.geom_vline_year(), which automatically
detects the turn of the year(s) from the date or datetime axis and draws
a vertical line.align_dates_seasonal() : Align surveillance data for
seasonal plots (e.g. flu season).
create_agegroups(): Create reproducible age groups
with highly customizable labels.
geom_epigantt() : A geom for epigantt plots. Helpful
to visualize overlapping time intervals for contact tracing
(i.e. hospital outbreaks). (Beta)
and more: geometric_mean() ,
expand_counts(),
library(ggplot2)
library(tidyr)
library(outbreaks)
library(ggsurveillance)
sars_canada_2003 |> #SARS dataset from outbreaks
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_x_date(date_labels = "W%V'%g", date_breaks = "2 weeks") +
scale_y_cases_5er() +
scale_fill_brewer(type = "qual", palette = 6) +
theme_classic()
library(ggplot2)
library(ggsurveillance)
influenza_germany |>
filter(AgeGroup == "00+") |>
align_dates_seasonal(dates_from = ReportingWeek,
date_resolution = "isoweek",
start = 28) -> df_flu_aligned
ggplot(df_flu_aligned, aes(x = date_aligned, y = Incidence)) +
stat_summary(
aes(linetype = "Historical Median (Min-Max)"), data = . %>% filter(!current_season),
fun.data = median_hilow, geom = "ribbon", alpha = 0.3) +
stat_summary(
aes(linetype = "Historical Median (Min-Max)"), data = . %>% filter(!current_season),
fun = median, geom = "line") +
geom_line(
aes(linetype = "2024/25"), data = . %>% filter(current_season), colour = "dodgerblue4", linewidth = 2) +
labs(linetype = "") +
scale_x_date(date_labels = "%b'%y") +
theme_bw() +
theme(legend.position = c(0.2,0.8))
Install the development version with:
devtools::install_github("biostats-dev/ggsurveillance")
# or directly with renv:
renv::install("biostats-dev/ggsurveillance")