R: assess model calibration of a trtsel object

calibrate.trtsel {TreatmentSelection}

R Documentation

assess model calibration of a trtsel object

Description

Assess calibration of fitted models for risk and treatment effect given marker. Plots are used to compare observed vs. fitted risks and treatment effects and Hosmer-Lemeshow goodness-of-fit tests are reported. An object of class "trtsel" must first be created using the function "trtsel" by supplying a data.frame containing marker, treatment, and event status information.

Usage

## S3 method for class 'trtsel'
calibrate(x, ..., groups = 10, plot.type = "calibration",
  trt.names = c("Treatment", "No Treatment"), line.color = "black",
  point.color = "grey10", ci = 0.95, main = NULL, ylim = NULL,
  xlim = NULL, ylab = NULL, xlab = NULL)

Arguments

`x`	An object of class "trtsel", created by using the function "trtsel."
`...`	ignored.
`groups`	Number of groups; observations are split into groups based on quantiles of predicted risk or treatment effect, depending on plot.type. For plot.type = "treatment effect", observations are split into groups based on quantile of predicted treatment effect; for plot.type= "calibration", "risk.t0", or "risk.t1", and for the Hosmer-Lemshow test statistic, observations on each treatment are split into groups based on quantile of predicted risk. The default value is 10.
`plot.type`	Which type of plot to produce. Options are "calibration" (default), which plots average predicted vs. observed risks on a log scale; "risk.t1" and "risk.t0" which overlays observed risks on fitted risk curves for T = 1 and T = 0 subjects, respectively; and "treatment effect" which overlays observed treatment effects on the fitted treatment effect curve.
`trt.names`	A vector of length 2 indicating the names for the two treatment options, T= 1 and T = 0, respectively, for the plot legend. This option is only used when plot.type="calibration". The default value is c("Treatment", "No Treatment").
`line.color`	color for lines in calibration plots.
`point.color`	color for points in calibration plots.
`ci`	numeric value (default 0.95) specifying the level for confidence intervals.
`main`	The main title for the plot. Only applies if plot.type is specified.
`ylim`	The limits for the y-axis of the plot, in the form c(lower,upper). Only applies if plot.type is specified.
`xlim`	The limits for the x-axisof the plot, in the form c(lower,upper). Only applies if plot.type is specified.
`ylab`	A label for the y-axis. Default values depend on plot.type. Only applies if plot.type is specified.
`xlab`	A label for the x-axis. Default values depend on plot.type. Only applies if plot.type is specified.

Value

A list with the following components:

`HL.TestStat`	Hosmer-Lemeshow test statistic for assessing fit of the risk models for the T = 0 and T = 1 groups.
`p.value`	P-values for the Hosmer-Lemeshow tests in each treatment group.
`Df`	Degrees of freedom for the chi-square distribution used to generate a p-value for the Hosmer-Lemeshow chi-square test. This equals "groups" - 2.
`plot`	If plot output was created, the ggplot plotting object.

Examples


data(tsdata)

###########################
## Create trtsel objects 
###########################
trtsel.Y1 <- trtsel(event ~ Y1*trt, 
                   treatment.name = "trt", 
                   data = tsdata, 
                   study.design = "RCT",
                   default.trt = "trt all")

trtsel.Y1

##############################
## Assess model calibration
##############################

 
cali.Y1 <- calibrate(trtsel.Y1, plot.type = "calibration")
cali.Y1

# A "treatment effect" plot 
calibrate(trtsel.Y1, line.color = "coral", plot.type = "treatment effect")