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Ridge / Density Plot of Length of Stay (LOS)

Source: R/prep_eda_plots.R
plot_los_ridge.Rd

Visualises the distribution of length of stay (LOS) on a log10 x-axis using either a stacked ridge plot (mode = "all") or a single-centre density curve (mode = "single").

Usage

plot_los_ridge(
  data,
  mode = c("all", "single"),
  center = NULL,
  patient_col = "patient_id",
  center_col = "center_name",
  admission_col = "admission_date",
  discharge_col = "final_outcome_date",
  filter_outcome = NULL,
  outcome_col = "final_outcome",
  min_los = 1,
  max_los = 365,
  colours = NULL,
  scale = 1.2,
  alpha = 0.7,
  base_size = 14,
  title = NULL,
  syndrome_col = NULL,
  syndrome_name = NULL
)

Arguments

data

A data frame.

mode

Character. One of "all" (ridge plot, all centres stacked on y-axis, ordered by median LOS ascending) or "single" (density curve for one centre specified by center).

center

Character. Centre name required when mode = "single".

patient_col

Character. Column of patient identifiers.

center_col

Character. Column of centre identifiers.

admission_col

Character. Column containing admission date/datetime. Default "admission_date".

discharge_col

Character. Column containing discharge / final outcome date. Default "final_outcome_date".

filter_outcome

Character or NULL. If not NULL, only rows whose outcome column (outcome_col) equals this value are used (e.g. "Discharged"). Set NULL to include all outcomes. Default NULL.

outcome_col

Character. Column of patient outcomes, used only when filter_outcome is not NULL. Default "final_outcome".

min_los

Numeric. Minimum LOS (days) to include. Rows below this are removed (prevents log(0) issues). Default 1.

max_los

Numeric. Maximum LOS (days) to include. Default 365.

colours

Named character vector of colours for centres. If NULL (default), the RColorBrewer "Set2" palette is used.

scale

Numeric. scale argument passed to ggridges::geom_density_ridges(). Controls overlap between ridges. Default 1.2.

alpha

Numeric. Fill transparency (0-1). Default 0.7.

base_size

Numeric. Base font size. Default 14.

title

Character or NULL. Plot title. Auto-generated if NULL.

syndrome_col

Character or NULL. Column of syndrome labels for pre-filtering. Default NULL.

syndrome_name

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

Value

A ggplot object.

Details

LOS is computed as difftime(discharge_col, admission_col, units = "days"). One row per unique patient x centre x admission_date x discharge_date is retained before plotting. Rows with LOS < min_los or LOS > max_los are dropped.