ggsurveillance (version 0.3.0)

linelist_hospital_outbreak: Line list of a fictional hospital outbreak (Data)

Description

This hospital outbreak is inspired by typical hospital outbreaks with resistant 4MRGN bacterial pathogens. These outbreaks start silent, since they are not initially apparent from the symptoms of the patient.

Usage

linelist_hospital_outbreak

Format

A data frame with 8 rows and 9 columns:

• Patient - Patient ID (0-7)

• ward_name_1 - Name of first ward where patient stayed

• ward_start_of_stay_1 - Start date of stay in first ward

• ward_end_of_stay_1 - End date of stay in first ward

• ward_name_2 - Name of second ward where patient stayed (if applicable)

• ward_start_of_stay_2 - Start date of stay in second ward (if applicable)

• ward_end_of_stay_2 - End date of stay in second ward (if applicable)

• pathogen_detection_1 - Date of first positive pathogen test

• pathogen_detection_2 - Date of second positive pathogen test (if applicable)

Patient details:

• Patient 0: Index case (ICU), infected early on but detected June 30, 2024

• Patient 1-2: ICU patients, found during initial screening

• Patient 3: Case who moved from ICU to general ward prior to the detection of patient 0, potentially linking both outbreak clusters. Detected during extended case search

• Patient 4-6: General ward cases, found after Patient 3's detection

• Patient 7: General ward case, detected post-discharge by GP, who notified the hospital

Examples

library(dplyr)
library(tidyr)
library(ggplot2)

# Transform hospital outbreak line list 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

# Create Epi Gantt chart showing ward stays and test dates
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(legend.position = "bottom")