summary method for class coxphMixture. Provides a detailed summary
of the fitted model, including coefficients, hazard ratios, standard errors,
z-statistics, and p-values for both the outcome model and the mismatch model.
Usage
# S3 method for class 'coxphMixture'
summary(object, conf.int = 0.95, scale = 1, ...)Value
An object of class summary.coxphMixture containing:
- call
The function call.
- n
Total number of observations.
- nevent
Number of events.
- coefficients
Matrix of coefficients for the outcome model.
- m.coefficients
Matrix of coefficients for the mismatch model.
- conf.int
Matrix of confidence intervals for the hazard ratios.
- logtest
Log-likelihood information (Outcome Model).
- avgcmr
The average posterior probability of a correct match.
Examples
library(survival)
set.seed(201)
# Simulate survival data (N = 200)
n <- 200
x1 <- rnorm(n)
x2 <- rbinom(n, 1, 0.5)
true_time <- rexp(n, rate = exp(0.5 * x1 - 0.5 * x2))
cens_time <- rexp(n, rate = 0.5)
# Simulate auxiliary match scores and linkage errors
# Lower match scores correspond to a higher probability of mismatch
match_score <- runif(n, 0.5, 1.0)
is_mismatch <- rbinom(n, 1, prob = 1 - match_score)
# Induce linkage errors by shuffling covariates of mismatched records
linked_x1 <- x1
linked_x2 <- x2
mis_idx <- which(is_mismatch == 1)
shuffled_idx <- sample(mis_idx)
linked_x1[mis_idx] <- x1[shuffled_idx]
linked_x2[mis_idx] <- x2[shuffled_idx]
linked_data <- data.frame(
time = pmin(true_time, cens_time),
status = as.numeric(true_time <= cens_time),
x1 = linked_x1, x2 = linked_x2,
match_score = match_score
)
# Fit the Cox PH Mixture Model (Slawski et al., 2023)
adj <- adjMixture(linked.data = linked_data, m.formula = ~ match_score)
fit <- plcoxph(Surv(time, status) ~ x1 + x2, adjustment = adj,
control = list(max.iter = 15))
# Print detailed statistical summary
sum_fit <- summary(fit)
print(sum_fit)
#>
#> Call:
#> plcoxph(formula = Surv(time, status) ~ x1 + x2, adjustment = adj,
#> control = list(max.iter = 15))
#>
#> --- Outcome Model (Cox PH) ---
#> coef exp(coef) se(coef) z Pr(>|z|)
#> x1 1.1366 3.1160 0.2375 4.785 1.71e-06 ***
#> x2 -1.3127 0.2691 0.4236 -3.099 0.00194 **
#> ---
#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
#>
#> --- Hazard Ratios & Confidence Intervals ---
#> exp(coef) exp(-coef) lower .95 upper .95
#> x1 3.1160 0.3209 1.9562 4.9635
#> x2 0.2691 3.7161 0.1173 0.6173
#>
#> --- Mismatch Indicator Model ---
#> Estimate Std. Error z value Pr(>|z|)
#> (Intercept) -5.687 2.337 -2.434 0.0149 *
#> match_score 7.128 2.977 2.395 0.0166 *
#> ---
#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
#>
#> Average Estimated Correct Match Rate: 0.4527
#> Events: 113 / Total: 200
#> Iterations: 15
#>