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Plot Distribution of Final Outcomes

Source: R/prep_eda_plots.R
plot_outcome_distribution.Rd

Produces a bar chart of final outcome counts per centre, with each bar labelled with the count and percentage of that centre's (or overall) unique patients. Bars are coloured by outcome category.

Usage

plot_outcome_distribution(
  data,
  mode = c("faceted", "overall", "single"),
  center = NULL,
  patient_col = "PatientInformation_id",
  outcome_col = "final_outcome",
  center_col = "center_name",
  merge_referred = TRUE,
  palette = c(Death = "#E74C3C", Died = "#E74C3C", Discharged = "#2ECC71", LAMA =
    "#95A5A6", Referred = "#3498DB", `Transferred to other hospital` = "#3498DB"),
  ncol = 2,
  base_size = 14,
  title = NULL,
  syndrome_col = NULL,
  syndrome_name = NULL
)

Arguments

data

Data frame. Long-format AMR dataset.

mode

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

center

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

patient_col

Character. Patient ID column. Default "PatientInformation_id".

outcome_col

Character. Final outcome column. Default "final_outcome".

center_col

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

merge_referred

Logical. Recode "Transferred to other hospital" to "Referred". Default TRUE.

palette

Named character vector mapping outcome values to colours. Any outcome not in the vector gets a default ggplot colour. Default uses a preset palette for common outcome categories.

ncol

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

base_size

Numeric. Base font size. Default 14.

title

Character. Custom plot 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 to be set. If NULL (default), all syndromes are included.

Value

A ggplot object.

Details

Deduplication: a patient may appear multiple times in a long-format dataset (one row per isolate or antibiotic). This function takes the first recorded outcome per patient per centre so each patient is counted once.

Referred merging: by default, "Transferred to other hospital" is recoded to "Referred" since they represent the same clinical event across different centres. Set merge_referred = FALSE to keep them separate.

Supports three display modes:

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

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

  • "single" – one specific centre; pass the name via center.