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Plot Distribution of Final Outcomes by Year

Source: R/prep_eda_plots.R
plot_outcome_by_year.Rd

Produces a stacked bar chart where the x-axis shows the year derived from date_col, the y-axis shows the number of unique patients, and bars are filled by final outcome category. Each bar segment is labelled with count and percentage; a total n= label sits above each bar.

Usage

plot_outcome_by_year(
  data,
  mode = c("faceted", "overall", "single"),
  center = NULL,
  patient_col = "PatientInformation_id",
  outcome_col = "final_outcome",
  date_col = "final_outcome_date",
  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".

date_col

Character. Date column used to extract the year (must be a Date or POSIXct column). Default "final_outcome_date".

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. Unmatched outcomes get a default ggplot colour.

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. Syndrome filter column. Default NULL.

syndrome_name

Character or NULL. Syndrome value to retain. Requires syndrome_col. Default NULL.

Value

A ggplot object.

Details

One outcome is taken per patient per centre (the first recorded value) to avoid double-counting long-format rows.

Supports three display modes:

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

  • "overall" – all centres pooled into a single chart.

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