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Plot Final Outcome Proportions by Age Bin

Source: R/prep_eda_plots.R
plot_outcome_by_agebin.Rd

Produces a horizontal 100% stacked bar chart showing how final outcomes (Death, Discharged, LAMA, Referred) are distributed across age groups. Each bar represents one age bin and sums to 100%. An n= label above each bar shows the total patients in that age group.

Usage

plot_outcome_by_agebin(
  data,
  mode = c("faceted", "overall", "single"),
  center = NULL,
  patient_col = "PatientInformation_id",
  agebin_col = "Age_bin",
  outcome_col = "final_outcome",
  center_col = "center_name",
  merge_referred = TRUE,
  age_levels = NULL,
  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".

agebin_col

Character. Age bin column. Default "Age_bin".

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.

age_levels

Character vector or NULL. Custom ordering of age bin labels. If NULL (default), bins are sorted automatically (<1 first, numeric ranges in order, open-ended bins last).

palette

Named character vector. Outcome -> fill colour mapping. Unmatched outcomes receive grey. Default uses red/green/grey/blue preset.

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

Value

A ggplot object.

Details

Deduplication: one record per patient per centre – first recorded outcome and age bin per patient per centre. Each patient contributes exactly one bar segment per centre.

Age bin ordering: bins are ordered numerically (<1, 1-5, 5-10, ..., 85+) automatically. Supply age_levels to override with a custom order.

Supports three display modes:

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

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

  • "single" – one specific centre.