R/summarize_subgroups.R
summarize.subgroups.RdSummarizes covariate values within the estimated subgroups
summarize.subgroups(x, ...)
# S3 method for default
summarize.subgroups(x, subgroup, ...)
# S3 method for subgroup_fitted
summarize.subgroups(x, ...)a fitted object from fit.subgroup() or a matrix of covariate values
optional arguments to summarize.subgroups methods
vector of indicators of same length as the number of rows in x if x is a matrix.
A value of 1 in the ith position of subgroup indicates patient i is in the subgroup
of patients recommended the treatment and a value of 0 in the ith position of subgroup indicates patient i is in the subgroup
of patients recommended the control.
If x is a fitted object returned by fit.subgroup(), subgroup is not needed.
The p-values shown are raw p-values and are not adjusted for multiple comparisons.
fit.subgroup for function which fits subgroup identification models and
print.subgroup_summary for arguments for printing options for summarize.subgroups().
library(personalized)
set.seed(123)
n.obs <- 1000
n.vars <- 50
x <- matrix(rnorm(n.obs * n.vars, sd = 3), n.obs, n.vars)
# simulate non-randomized treatment
xbetat <- 0.5 + 0.5 * x[,21] - 0.5 * x[,41]
trt.prob <- exp(xbetat) / (1 + exp(xbetat))
trt01 <- rbinom(n.obs, 1, prob = trt.prob)
trt <- 2 * trt01 - 1
# simulate response
delta <- 2 * (0.5 + x[,2] - x[,3] - x[,11] + x[,1] * x[,12])
xbeta <- x[,1] + x[,11] - 2 * x[,12]^2 + x[,13]
xbeta <- xbeta + delta * trt
# continuous outcomes
y <- drop(xbeta) + rnorm(n.obs, sd = 2)
# create function for fitting propensity score model
prop.func <- function(x, trt)
{
# fit propensity score model
propens.model <- cv.glmnet(y = trt,
x = x, family = "binomial")
pi.x <- predict(propens.model, s = "lambda.min",
newx = x, type = "response")[,1]
pi.x
}
subgrp.model <- fit.subgroup(x = x, y = y,
trt = trt01,
propensity.func = prop.func,
loss = "sq_loss_lasso",
nfolds = 5) # option for cv.glmnet
comp <- summarize.subgroups(subgrp.model)
print(comp, p.value = 0.01)
#> Avg (recom 0) Avg (recom 1) 0 - 1 SE (recom 0) SE (recom 1)
#> V2 -1.3890 1.9147 -3.3037 0.1124 0.1146
#> V3 1.4399 -1.8286 3.2686 0.1067 0.1118
#> V13 -0.5653 0.2542 -0.8195 0.1282 0.1405
# or we can simply supply the matrix x and the subgroups
comp2 <- summarize.subgroups(x, subgroup = 1 * (subgrp.model$benefit.scores > 0))
print(comp2, p.value = 0.01)
#> Avg (recom 0) Avg (recom 1) 0 - 1 SE (recom 0) SE (recom 1)
#> V2 -1.3890 1.9147 -3.3037 0.1124 0.1146
#> V3 1.4399 -1.8286 3.2686 0.1067 0.1118
#> V13 -0.5653 0.2542 -0.8195 0.1282 0.1405