plot.calib_msm: Plots calibration curves estimated using 'calib_msm'.

In calibmsm: Calibration Plots for the Transition Probabilities from Multistate Models

Plots calibration curves estimated using calib_msm.

Description

Plots calibration curves for the transition probabilities of a multistate model estimated using BLR-IPCW and pseudo-value approaches.

Usage

## S3 method for class 'calib_msm'
plot(
  x,
  ...,
  combine = TRUE,
  ncol = NULL,
  nrow = NULL,
  size.line = 0.5,
  size.text = 12,
  marg.density = FALSE,
  marg.density.size = 5,
  marg.density.type = "density",
  marg.rug = FALSE,
  marg.rug.transparency = 0.1,
  titles.include = TRUE,
  titles = NULL,
  axis.titles.x = NULL,
  axis.titles.text.x = "Predicted risk",
  axis.titles.y = NULL,
  axis.titles.text.y = "Observed risk",
  legend.include = TRUE,
  legend.seperate = FALSE,
  legend.title = NULL,
  legend.position = "bottom"
)

Arguments

x	Object of class 'calib_msm' generated from calib_msm.
...	Other
combine	Whether to combine into one plot using ggarrange, or return as a list of individual plots
ncol	Number of columns for combined calibration plot
nrow	Number of rows for combined calibration plot
size.line	Size of line plots
size.text	Size of text in plot
marg.density	Whether to produce marginal density plots TRUE/FALSE
marg.density.size	Size of the main plot relative to the density plots (see ggMarginal)
marg.density.type	What type of marginal plot to show (see ggMarginal)
marg.rug	Whether to produce marginal rug plots TRUE/FALSE
marg.rug.transparency	Degree of transparency for the density rug plot along each axis
titles.include	Whether to include titles for each individual calibration plots
titles	Vector of titles for the calibration plots. Defaults to "State k" for each plot.
axis.titles.x	Position of plots for which to include title on x-axis
axis.titles.text.x	x-axis title
axis.titles.y	Position of plots for which to include title on y-axis
axis.titles.text.y	y-axis title
legend.include	Whether to produce a legend
legend.seperate	= Whether to include legend in plot (FALSE) or as a seperate object (TRUE)
legend.title	Title of legend
legend.position	Position of legend

Value

If combine = TRUE, returns an object of classes gg, ggplot, and ggarrange, as all ggplots have been combined into one object. If combine = FALSE, returns an object of class list, each element containing an object of class gg and ggplot.

Examples

# Estimate and plot BLR-IPCW calibration curves for the predicted transition
# probabilities at time t = 1826, when predictions were made at time
# s = 0 in state j = 1. These predicted transition probabilities are stored in tps0.

# Extract the predicted transition probabilities out of state j = 1
tp.pred <- dplyr::select(dplyr::filter(tps0, j == 1), any_of(paste("pstate", 1:6, sep = "")))

# Now estimate the observed event probabilities for each possible transition.
dat.calib <-
calib_msm(data.ms = msebmtcal,
 data.raw = ebmtcal,
 j=1,
 s=0,
 t = 1826,
 tp.pred = tp.pred,
 w.covs = c("year", "agecl", "proph", "match"))

 # These are then plotted
 plot(dat.calib, combine = TRUE, nrow = 2, ncol = 3)

calibmsm documentation built on June 22, 2024, 9:33 a.m.