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Plot Death vs Discharged Counts for Top Pathogens

Source: R/prep_eda_plots.R
plot_death_discharged.Rd

Produces a side-by-side (dodged) bar chart comparing Death and Discharged patient counts for the top n organisms. LAMA and Referred are excluded – only the two definitive outcomes are shown.

Usage

plot_death_discharged(
  data,
  n = 5,
  mode = c("faceted", "overall", "single"),
  center = NULL,
  resistance_filter = NULL,
  patient_col = "PatientInformation_id",
  organism_col = "organism_name",
  outcome_col = "final_outcome",
  center_col = "center_name",
  antibiotic_col = "antibiotic_name",
  value_col = "antibiotic_value",
  death_label = "Death",
  discharged_label = "Discharged",
  colours = NULL,
  bar_width = 0.65,
  ncol = 2,
  base_size = 14,
  title = NULL,
  syndrome_col = NULL,
  syndrome_name = NULL
)

Arguments

data

Data frame. Long-format AMR dataset.

n

Integer. Number of top organisms to show. Default 5.

mode

Character. One of "faceted", "overall", or "single". Default "faceted".

center

Character. Required when mode = "single". Exact centre name.

resistance_filter

Character or NULL. When "R", only patients who had at least one Resistant result for the organism are included (worst-phenotype rule: any R = R). When "S", only patients with exclusively Susceptible results are included. NULL (default) includes all patients regardless of resistance status.

patient_col

Character. Patient ID column. Default "PatientInformation_id".

organism_col

Character. Organism name column. Default "organism_name".

outcome_col

Character. Final outcome column. Default "final_outcome".

center_col

Character. Centre/facility column. Default "center_name".

antibiotic_col

Character. Antibiotic name column. Only used when resistance_filter is not NULL. Default "antibiotic_name".

value_col

Character. Susceptibility result column (R/S). Only used when resistance_filter is not NULL. Default "antibiotic_value".

death_label

Character. Exact string used for death in the outcome column. Default "Death".

discharged_label

Character. Exact string used for discharged. Default "Discharged".

colours

Named character vector with keys matching death_label and discharged_label. Default c("Death" = "#E74C3C", "Discharged" = "#2ECC71").

bar_width

Numeric. Width of each individual bar (0-1). Default 0.65.

ncol

Integer. Facet columns (mode = "faceted" only). Default 2.

base_size

Numeric. Base font size. Default 14.

title

Character. Custom title. Auto-generated if NULL. Default NULL.

syndrome_col

Character or NULL. Column name containing syndrome/infection category labels (e.g. "infectious_syndrome"). If NULL (default), no syndrome filtering is applied.

syndrome_name

Character or NULL. The syndrome value to retain (e.g. "BSI", "VAP"). Requires syndrome_col. If NULL (default), all syndromes are included.

Value

A ggplot object.

Details

Each bar is labelled with the count and the percentage that outcome represents out of all Death + Discharged patients for that organism (e.g. 45 (32%) on a Death bar means 45 patients died, which is 32% of the organism's known outcomes). This makes the mortality rate immediately readable without a separate calculation.

Deduplication: uses distinct(centre, patient, organism, outcome) – one record per patient per organism per outcome – consistent with the original EDA script.

Top N organisms are ranked by total unique patients with a known outcome (Death or Discharged). For mode = "faceted" the ranking is done independently per centre; for "overall" it is done globally.

Supports three display modes:

  • "faceted" (default) – one panel per centre.

  • "overall" – all centres pooled into one chart.

  • "single" – one specific centre.