rmsMD (version 1.0.1)

ggrmsMD: Create plots for RCS variables from an rms model

Description

The ggrmsMD function processes the output from models fitted using the rms package and produces one or more ggplot2 objects visualising restricted cubic splines (RCS). The function detects RCS terms in the model and plots them all, with a suitable y-axis selected based on the model type. This outputs a list of plots, or a multi-panel figure using the combined argument. As outputs are ggplot objects they can easily be further customised by the user.

Usage

ggrmsMD(
  modelfit,
  data,
  noeffline = TRUE,
  shade_inferior = "none",
  combined = TRUE,
  ylab = NULL,
  xlabs = NULL,
  titles = NULL,
  ylim = NULL,
  log_y = FALSE,
  log_y_breaks = NULL,
  xlims = NULL,
  log_x_vars = NULL,
  log_x_breaks = NULL,
  lrm_prob = FALSE,
  var = NULL,
  np = 400,
  ...
)

Value

A ggplot object (if one variable is plotted), a list of ggplot objects (if multiple variables), or a single combined cowplot plot if combined = TRUE.

Arguments

modelfit

A model object from ols, lrm, or cph (from the rms package).

data

The dataset used to fit the model.

noeffline

Logical. If TRUE (default), adds a horizontal dashed line at 1 for odds/hazard ratio plots.

shade_inferior

Character. Options are "none" (default), "higher", or "lower". Applies red/green shading above or below 1 on the y-axis to indicate worse/better outcomes.

combined

Logical. If TRUE, returns a single multi-panel plot using cowplot::plot_grid().

ylab

Optional character. Override the default y-axis label.

xlabs

A named list of x-axis labels for each variable. E.g., list(age = "Age (years)", bmi = "BMI (kg/m²")).

titles

A named list of plot titles for each variable.

ylim

Numeric vector (length 2). y-axis limits applied to all plots. E.g., c(0.5, 2).

log_y

Logical. If TRUE, y-axis is log10-transformed.

log_y_breaks

Optional numeric vector specifying y-axis tick marks when log_y = TRUE. E.g., c(0.25, 0.5, 1, 2, 4).

xlims

A named list of x-axis limits per variable. E.g., list(age = c(20, 80)).

log_x_vars

Character vector. Names of variables for which x-axis should be log10-transformed.

log_x_breaks

A named list specifying x-axis tick marks for variables with log10-transformed x-axis.

lrm_prob

Logical. If TRUE and model is lrm, plots predicted probabilities instead of odds ratios.

var

Character vector. Optional. Variables to plot. If NULL (default), all RCS variables in the model will be plotted.

np

Integer. Number of points used to predict spline curves. Default is 400. Consider increasing when using log-transformed x-axes.

...

Additional arguments passed to cowplot::plot_grid() when combined = TRUE.

Examples

# For details examples and plots please see the provided vignettes