calibrate.trtsel: assess model calibration of a trtsel object

In TreatmentSelection: Evaluate Treatment Selection Biomarkers

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.

See Also

trtsel for creating trtsel objects, plot.trtsel for plotting risk curves and more, evaluate.trtsel for evaluating marker performance, and compare.trtsel to compare two trtsel 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")

TreatmentSelection documentation built on May 1, 2019, 6:32 p.m.