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Plot YLL or YLD Associated vs Attributable by Organism

Source: R/prep_daly_plots.R
plot_burden_by_organism.Rd

Produces a horizontal grouped bar chart showing the top n organisms ranked by their associated burden (YLL or YLD), with a paired attributable bar alongside each. Organisms are ranked by the associated value so the highest-burden pathogen appears at the top.

Usage

plot_burden_by_organism(
  data,
  metric = c("YLL", "YLD"),
  n = 10,
  organism_col = NULL,
  assoc_col = NULL,
  attr_col = NULL,
  n_admissions = NULL,
  syndrome_col = NULL,
  syndrome_name = NULL,
  label_digits = 1,
  colours = NULL,
  base_size = 14,
  title = NULL,
  subtitle = NULL
)

Arguments

data

Data frame. One row per organism. Must contain the columns named by organism_col, assoc_col, and attr_col.

metric

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

n

Integer. Number of top organisms to display. Default 10.

organism_col

Character or NULL. Column containing organism / pathogen names. If NULL (default), auto-set to "organism_name" for YLL (matching daly_calc_yll_* examples) and "pathogen" for YLD (matching daly_calc_yld_* defaults).

assoc_col

Character or NULL. Column for the associated burden value. If NULL (default), auto-set to "YLL_associated_k" (YLL) or "YLD_associated" (YLD) – matching the output column names of compute_yll_associated() and compute_yld_associated() respectively.

attr_col

Character or NULL. Column for the attributable burden value. If NULL (default), auto-set to "YLL_attributable_k" (YLL) or "YLD_attributable" (YLD) – matching the output column names of compute_yll_attributable() and compute_yld_attributable() respectively.

n_admissions

Numeric or NULL. When supplied, the associated and attributable values are divided by n_admissions and multiplied by 1 000 before plotting. Default NULL (no normalisation; values are plotted in thousands as returned by the YLL/YLD functions).

syndrome_col

Character or NULL. Column name containing syndrome labels. If NULL (default), no filtering is applied.

syndrome_name

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

label_digits

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

colours

Named character vector with elements "associated" and "attributable". If NULL (default), auto-chosen based on metric.

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 pathogen-level summary data frame with one row per organism, already containing both the associated and attributable burden columns. For YLD this is typically the output of compute_yld_associated() left-joined with compute_yld_attributable(). For YLL it is the by_pathogen slot of compute_yll_associated() left-joined with the equivalent slot from compute_yll_attributable().