appe.glm {APPEstimation}  R Documentation 
C
statistics adjusted for predictor distributions
Calculates adjusted C
statistics by predictor distributions for
a generalized linear model with binary outcome.
appe.glm(mdl, dat.train, dat.test, method = "uLSIF", sigma = NULL,
lambda = NULL, kernel_num = NULL, fold = 5, stabilize = TRUE,
qstb = 0.025, reps = 2000, conf.level = 0.95)
mdl 
a 
dat.train 
a dataframe used to construct a prediction model (specified in

dat.test 
a dataframe corresponding to a validation (testing) data. Need to include outcome and all predictors. 
method 
uLSIF or KLIEP.
Same as the argument in 
sigma 
a positive numeric vector corresponding to candidate values of a
bandwidth for Gaussian kernel.
Same as the argument in 
lambda 
a positive numeric vector corresponding to candidate values of a
regularization parameter.
Same as the argument in 
kernel_num 
a positive integer corresponding to number of kernels.
Same as the argument in 
fold 
a positive integer corresponding to a number of the folds of
crossvalidation in the KLIEP method.
Same as the argument in 
stabilize 
a logical value as to whether tail weight stabilization is performed
or not.
If TRUE, both tails of the estimated density ratio distribution are
replaced by the constant value which is specified at 
qstb 
a positive numerical value less than 1 to control the degree of weight stabilization. Default value is 0.025, indicating estimated density ratio values less than the 2.5 percentile and more than the 97.5 percentile are set to 2.5 percentile and 97.5 percentile, respectively. 
reps 
a positive integer to specify bootstrap repetitions. If 0, bootstrap calculations are not performed. 
conf.level 
a numerical value indicating a confidence level of interval. 
Adjusted and nonadjusted estimates of C
statistics are provided
as matrix form.
"Cstat" indicates nonadjusted version, "C adjusted by score"
indicates adjusted version by linear predictors distribution, and
"C adjusted by predictors" indicates adjusted version by
predictor distributions (multidimensionally).
For confidence intervals, "Percentile" indicates a confidence interval
by percentile method and "Approx" indicates approximated versions
by Normal distribution.
set.seed(100)
# generating learning data
n0 = 100
Z = cbind(rbeta(n0, 5, 5), rbeta(n0, 5, 5))
Y = apply(Z, 1, function (xx) {
rbinom(1, 1, (1/(1+exp((sum(c(2,2,2) * c(1,xx)))))))})
dat = data.frame(Y=Y, Za=Z[,1], Zb=Z[,2])
# the model to be evaluated
mdl = glm(Y~., binomial, data=dat)
# validation dataset, with different centers on predictors
n1 = 100
Z1 = cbind(rbeta(n1, 6, 4), rbeta(n1, 6, 4))
Y1 = apply(Z1, 1, function (xx) {
rbinom(1, 1, (1/(1+exp((sum(c(2,2,2) * c(1,xx)))))))})
dat1 = data.frame(Y=Y1, Za=Z1[,1], Zb=Z1[,2])
# calculation of L1 and L2 for this model
appe.glm(mdl, dat, dat1, reps=0)