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Plot Patient Distribution by Location Type Across Facilities

Source: R/prep_eda_plots.R
plot_location_by_facility.Rd

Produces a dodged bar chart showing the number of unique patients in each location type (ICU, Ward, Other) per facility. Raw location strings are normalised automatically via case-insensitive pattern matching, so centre-specific ICU names (e.g. "Respiratory ICU (RICU)") all map to "ICU".

Usage

plot_location_by_facility(
  data,
  patient_col = "PatientInformation_id",
  location_col = "location",
  center_col = "center_name",
  icu_pattern = "icu",
  ward_pattern = "ward",
  icu_label = "ICU",
  ward_label = "Ward",
  other_label = "Other",
  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".

location_col

Character. Location/unit column. Default "location".

center_col

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

icu_pattern

Character. Case-insensitive regex pattern that identifies ICU values. Default "icu".

ward_pattern

Character. Case-insensitive regex pattern that identifies Ward values. Default "ward".

icu_label

Character. Display label for ICU bars. Default "ICU".

ward_label

Character. Display label for Ward bars. Default "Ward".

other_label

Character. Display label for all other locations. Default "Other".

colours

Named character vector. Fill colours keyed by icu_label, ward_label, and other_label. Default pink/green/grey.

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. NULL = no filter.

syndrome_name

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

Value

A ggplot object.

Details

Normalisation: a location value is classified as:

  • ICU – if the lower-cased string contains icu_pattern (default "icu")

  • Ward – else if it contains ward_pattern (default "ward")

  • Other – everything else

Deduplication: distinct(patient, centre, location type) – each unique patient-centre-location combination is counted once.