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Plot Mono vs Polymicrobial Infections by Facility

Source: R/prep_eda_plots.R
plot_mono_poly_by_facility.Rd

Produces a dodged bar chart comparing the number of unique patients with Monomicrobial vs Polymicrobial infections at each centre. Hospitals appear on the x-axis; the two bars per hospital are coloured by infection type. Count labels are printed above each bar.

Usage

plot_mono_poly_by_facility(
  data,
  patient_col = "PatientInformation_id",
  poly_col = "is_polymicrobial",
  center_col = "center_name",
  mono_label = "Monomicrobial",
  poly_label = "Polymicrobial",
  colours = NULL,
  bar_width = 0.68,
  base_size = 14,
  title = NULL,
  syndrome_col = NULL,
  syndrome_name = NULL
)

Arguments

data

Data frame. Long-format AMR dataset.

patient_col

Character. Patient ID column. Default "PatientInformation_id".

poly_col

Character. Column with binary infection type (0 = mono, 1 = poly). Default "is_polymicrobial".

center_col

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

mono_label

Character. Label for monomicrobial bars. Default "Monomicrobial".

poly_label

Character. Label for polymicrobial bars. Default "Polymicrobial".

colours

Named character vector. Fill colours keyed by mono_label and poly_label. Default blue/red.

bar_width

Numeric. Width of each individual bar. Default 0.68.

base_size

Numeric. Base font size. Default 14.

title

Character. Custom title. Auto-generated if 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: distinct(patient, centre, infection type) – each unique patient-centre-infection type combination is counted once. A patient who has both mono and polymicrobial episodes at the same centre contributes to both bars, matching the original EDA script.

Infection type: the poly_col column is expected to contain binary values (0 = Monomicrobial, 1 = Polymicrobial). The labels shown in the legend and plot are controlled by mono_label and poly_label.