plot.calib_msm {calibmsm}

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)