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Boxplot of Length of Stay by Age Group

Source: R/prep_eda_plots.R
plot_los_by_agebin.Rd

Displays the distribution of LOS (y-axis, log10 scale) across patient age groups (x-axis) using boxplots. Supports "faceted" (one panel per centre), "overall" (all centres pooled), and "single" (one centre) modes.

Usage

plot_los_by_agebin(
  data,
  mode = c("faceted", "overall", "single"),
  center = NULL,
  patient_col = "PatientInformation_id",
  agebin_col = "Age_bin",
  age_col = "age_years",
  age_breaks = NULL,
  age_labels = NULL,
  center_col = "center_name",
  admission_col = "admission_date",
  discharge_col = "final_outcome_date",
  min_los = 1,
  max_los = 365,
  age_levels = NULL,
  fill_colour = "#2C7FB8",
  fill_alpha = 0.7,
  outlier_alpha = 0.25,
  box_width = 0.6,
  ncol = 3,
  base_size = 14,
  title = NULL,
  subtitle = NULL,
  syndrome_col = NULL,
  syndrome_name = NULL
)

Arguments

data

A data frame.

mode

Character. One of "faceted", "overall", or "single".

center

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

patient_col

Character. Column of patient identifiers.

agebin_col

Character. Pre-existing age group column. Used when age_breaks is NULL. Default "Age_bin".

age_col

Character. Continuous age column used when age_breaks is provided. Default "age_years".

age_breaks

Numeric vector or NULL. Breakpoints for deriving custom bins from age_col (e.g. c(0, 5, 15, 30, 50, 70, Inf)). NULL = use agebin_col directly.

age_labels

Character vector or NULL. Labels for each bin created by age_breaks. Must have length length(age_breaks) - 1. NULL = auto-generate from breaks.

center_col

Character. Column of centre identifiers.

admission_col

Character. Admission date column. Default "admission_date".

discharge_col

Character. Discharge / final outcome date column. Default "final_outcome_date".

min_los

Numeric. Minimum LOS (days) to include. Default 1.

max_los

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

age_levels

Character vector or NULL. Custom bin order when using agebin_col. NULL = auto-sort.

fill_colour

Character. Box fill colour. Default "#2C7FB8".

fill_alpha

Numeric. Box fill transparency (0-1). Default 0.7.

outlier_alpha

Numeric. Outlier point transparency (0-1). Default 0.25.

box_width

Numeric. Width of each box. Default 0.6.

ncol

Integer. Number of facet columns (mode = "faceted" only). Default 3.

base_size

Numeric. Base font size. Default 14.

title

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

subtitle

Character or NULL. Plot subtitle. NULL = none.

syndrome_col

Character or NULL. Syndrome column 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 x discharge is retained. Rows with LOS < min_los or LOS > max_los are dropped.

Two ways to supply age groups:

  1. Pre-existing column (default) – set agebin_col to an existing categorical column (e.g. "Age_bin"). Bins are sorted automatically (<1, 1-5, ..., 85+); override order with age_levels.

  2. Custom breaks from continuous age – set age_breaks to a numeric vector (e.g. c(0, 5, 15, 30, 50, 70, Inf)) and age_col to the continuous age column (default "age_years"). Bins are derived via cut() and labelled automatically. agebin_col is ignored when age_breaks is provided.