inst/doc/Epigantt_with_ggsurveillance.R

In ggsurveillance: Tools for Outbreak Investigation/Infectious Disease Surveillance

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  warning = FALSE,
  message = FALSE,
  fig.width = 7,
  fig.height = 4
)

## ----setup, echo = FALSE------------------------------------------------------
library(ggplot2)
library(dplyr)
library(tidyr)
library(outbreaks)
library(ggsurveillance)

## ----echo=FALSE---------------------------------------------------------------
# Transform to long format
linelist_hospital_outbreak |>
  pivot_longer(
    cols = starts_with("ward"),
    names_to = c(".value", "num"),
    names_pattern = "ward_(name|start_of_stay|end_of_stay)_([0-9]+)",
    values_drop_na = TRUE
  ) -> df_stays_long

linelist_hospital_outbreak |>
  pivot_longer(cols = starts_with("pathogen"), values_to = "date") -> df_detections_long

# Plot
ggplot(df_stays_long) +
  geom_epigantt(aes(y = Patient, xmin = start_of_stay, xmax = end_of_stay, color = name)) +
  geom_point(aes(y = Patient, x = date, shape = "Date of pathogen detection"), data = df_detections_long) +
  scale_y_discrete_reverse() +
  theme_bw() +
  theme_mod_legend_bottom()

## -----------------------------------------------------------------------------
linelist_hospital_outbreak

## -----------------------------------------------------------------------------
linelist_hospital_outbreak |>
  pivot_longer(
    cols = starts_with("ward"),
    names_to = c(".value", "num"),
    names_pattern = "ward_(name|start_of_stay|end_of_stay)_([0-9]+)",
    values_drop_na = TRUE
  ) -> df_stays_long
df_stays_long |> select(Patient, num:end_of_stay)

linelist_hospital_outbreak |>
  pivot_longer(cols = starts_with("pathogen"), values_to = "date", values_drop_na = TRUE) -> df_detections_long
df_detections_long |> select(Patient, name, date)

## -----------------------------------------------------------------------------
ggplot(df_stays_long) +
  geom_epigantt(aes(y = Patient, xmin = start_of_stay, xmax = end_of_stay, color = name)) +
  geom_point(aes(y = Patient, x = date, shape = "Date of pathogen detection"), data = df_detections_long) +
  scale_y_discrete_reverse() +
  theme_bw() +
  theme_mod_legend_bottom()

## -----------------------------------------------------------------------------
outbreaks::varicella_sim_berlin |>
  filter(center1 == "Platz der Luftbruecke") |>
  arrange(onset) |>
  slice_head(n = 20) |>
  mutate(
    fullname = paste(firstname, lastname),
    fullname = factor(fullname, levels = rev(fullname))
  ) |>
  pivot_longer(
    cols = starts_with(c("arrival", "leave", "center")),
    names_to = c(".value", "group"),
    names_pattern = "(\\w+)(\\d+)"
  ) |>
  ggplot(aes(y = fullname)) +
  geom_epigantt(aes(xmin = arrival, xmax = leave, colour = center), lw_scaling_factor = 100) + # linewidth = 4
  # geom_point(aes(x = onset)) +
  scale_x_date() +
  theme_bw() +
  theme_mod_legend_top()

## -----------------------------------------------------------------------------
ggplot(outbreaks::measles_hagelloch_1861, aes(y = case_ID, xmin = date_of_prodrome, xmax = date_of_rash, fill = class)) +
  geom_vline_year(color = "grey50") +
  geom_epigantt() +
  scale_x_date(date_breaks = "2 weeks", date_labels = "W%V'%G") +
  theme_bw()