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Plot YLL or YLD Associated vs Attributable per Hospital

Source: R/prep_daly_plots.R
plot_burden_by_hospital.Rd

Produces a horizontal grouped bar chart comparing the associated and attributable burden (YLL or YLD) per 1 000 patients across hospitals. Bars are sorted by the associated value (largest at top by default). Each bar is labelled with its rounded value.

Usage

plot_burden_by_hospital(
  data,
  metric = c("YLL", "YLD"),
  center_col = "center_name",
  assoc_col = NULL,
  attr_col = NULL,
  syndrome_col = NULL,
  syndrome_name = NULL,
  sort_by = c("associated", "attributable", "none"),
  label_digits = 1,
  colours = NULL,
  base_size = 14,
  title = NULL,
  subtitle = NULL
)

Arguments

data

Data frame. One row per hospital (or one row per hospital x syndrome). Must contain the columns named by center_col, assoc_col, and attr_col.

metric

Character. "YLL" or "YLD". Controls which default column names and axis labels are used. Ignored when assoc_col and attr_col are supplied explicitly. Default "YLL".

center_col

Character. Column containing hospital / centre names. Default "center_name".

assoc_col

Character or NULL. Column for the associated per-1 000 value. If NULL (default), auto-set to "YLL_assoc_per_1000" or "YLD_assoc_per_1000" based on metric.

attr_col

Character or NULL. Column for the attributable per-1 000 value. If NULL (default), auto-set to "YLL_attr_per_1000" or "YLD_attr_per_1000" based on metric.

syndrome_col

Character or NULL. Column name containing syndrome 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. "Bloodstream infection"). Requires syndrome_col to be set. If NULL (default), all rows are used.

sort_by

Character. "associated" (default), "attributable", or "none". Controls hospital ordering on the y-axis.

label_digits

Integer. Decimal places in bar value labels. Default 1.

colours

Named character vector with exactly two elements: "associated" and "attributable". If NULL (default), a colour pair is chosen automatically based on metric (red tones for YLL, blue tones for YLD).

base_size

Numeric. Base font size. Default 14.

title

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

subtitle

Character. Custom subtitle. Auto-generated if NULL.

Value

A ggplot object.

Details

The input data should be a hospital-level summary data frame (e.g. the output of compute_hospital_daly()) that already contains the per-1 000 columns. If the summary was computed across multiple syndromes, use syndrome_col and syndrome_name to restrict the plot to one syndrome before pivoting.