Estimate Transportable Specificity in the Target Population

Estimates the specificity (true negative rate) of a binary classifier at one or more thresholds in a target population using data transported from a source population. Supports both counterfactual (under hypothetical intervention) and factual (observational) prediction model transportability.

Usage

tr_specificity(
  predictions,
  outcomes,
  treatment = NULL,
  source,
  covariates,
  threshold = 0.5,
  treatment_level = NULL,
  analysis = c("transport", "joint"),
  estimator = c("dr", "om", "ipw", "naive"),
  selection_model = NULL,
  propensity_model = NULL,
  outcome_model = NULL,
  se_method = c("none", "bootstrap", "influence"),
  n_boot = 200,
  conf_level = 0.95,
  stratified_boot = TRUE,
  cross_fit = FALSE,
  n_folds = 5,
  ps_trim = NULL,
  parallel = FALSE,
  ncores = NULL,
  ...
)

tr_tnr(
  predictions,
  outcomes,
  treatment = NULL,
  source,
  covariates,
  threshold = 0.5,
  treatment_level = NULL,
  analysis = c("transport", "joint"),
  estimator = c("dr", "om", "ipw", "naive"),
  selection_model = NULL,
  propensity_model = NULL,
  outcome_model = NULL,
  se_method = c("none", "bootstrap", "influence"),
  n_boot = 200,
  conf_level = 0.95,
  stratified_boot = TRUE,
  cross_fit = FALSE,
  n_folds = 5,
  ps_trim = NULL,
  parallel = FALSE,
  ncores = NULL,
  ...
)

Arguments

predictions

Numeric vector of model predictions.

outcomes

Numeric vector of observed outcomes.

treatment

Numeric vector of treatment indicators (0/1), or NULL for factual prediction model transportability (no treatment/intervention). When NULL, only the selection model is used for weighting.

source

Numeric vector of population indicators (1=source/RCT, 0=target).

covariates

A matrix or data frame of baseline covariates.

threshold

Numeric vector of classification thresholds. Predictions above this value are classified as positive. Can be a single value or a vector for computing sensitivity at multiple thresholds simultaneously. Default is 0.5.

treatment_level

The treatment level of interest (default: NULL). Required when treatment is provided; should be NULL when treatment is NULL (factual mode).

analysis

Character string specifying the type of analysis:

"transport": Use source outcomes for target estimation (default)
"joint": Pool source and target data

estimator

Character string specifying the estimator:

"naive": Naive estimator (biased)
"om": Outcome model estimator
"ipw": Inverse probability weighting estimator
"dr": Doubly robust estimator (default)

selection_model

Optional fitted selection model for P(S=0|X). If NULL, a logistic regression model is fit using the covariates.

propensity_model

Optional fitted propensity score model for P(A=1|X,S=1). If NULL, a logistic regression model is fit using source data.

outcome_model

Optional fitted outcome model for E[L(Y,g)|X,A,S]. If NULL, a regression model is fit using the relevant data. For binary outcomes, this should be a model for E[Y|X,A] (binomial family). For continuous outcomes, this should be a model for E[L|X,A] (gaussian family).

se_method

Method for standard error estimation:

"bootstrap": Bootstrap standard errors (default)
"influence": Influence function-based standard errors
"none": No standard error estimation

n_boot

Number of bootstrap replications (default: 500).

conf_level

Confidence level for intervals (default: 0.95).

stratified_boot

Logical indicating whether to use stratified bootstrap that preserves the source/target ratio (default: TRUE). Recommended for transportability analysis.

cross_fit

Logical indicating whether to use cross-fitting for nuisance model estimation (default: FALSE).

n_folds

Number of folds for cross-fitting (default: 5).

ps_trim

Propensity score trimming specification. Controls how extreme propensity scores are handled. Can be:

NULL (default): Uses absolute bounds c(0.01, 0.99)
"none": No trimming applied
"quantile": Quantile-based trimming with default c(0.01, 0.99)
"absolute": Explicit absolute bounds with default c(0.01, 0.99)
A numeric vector of length 2: c(lower, upper) absolute bounds
A single numeric: Symmetric bounds c(x, 1-x)
A list with method ("absolute"/"quantile"/"none") and bounds

parallel

Logical indicating whether to use parallel processing for bootstrap (default: FALSE).

ncores

Number of cores for parallel processing (default: NULL, which uses all available cores minus one).

...

Additional arguments passed to internal functions.

Value

An object of class c("tr_specificity", "tr_performance") containing:

estimate: Point estimate(s) of transportable specificity
se: Standard error(s) (if computed)
ci_lower: Lower confidence interval bound(s)
ci_upper: Upper confidence interval bound(s)
threshold: Threshold value(s) used
estimator: Estimator used
analysis: Analysis type
naive_estimate: Naive specificity for comparison
n_target: Number of target observations
n_source: Number of source observations
treatment_level: Treatment level (NULL for factual mode)

Details

Specificity (also known as true negative rate) is defined as: $$Specificity(c) = P(\hat{Y} \le c | Y = 0)$$

See tr_sensitivity() for details on counterfactual vs factual modes and the available estimators. The estimators for specificity mirror those for sensitivity.

References

Steingrimsson, J. A., et al. (2023). "Transporting a Prediction Model for Use in a New Target Population." American Journal of Epidemiology, 192(2), 296-304. doi:10.1093/aje/kwac128

Steingrimsson, J. A., Wen, L., Voter, S., & Dahabreh, I. J. (2024). "Interpretable meta-analysis of model or marker performance." arXiv preprint arXiv:2409.13458.

Examples

# Generate example data
set.seed(123)
n <- 1000
x <- rnorm(n)
s <- rbinom(n, 1, plogis(0.5 - 0.3 * x))
a <- ifelse(s == 1, rbinom(n, 1, 0.5), rbinom(n, 1, plogis(-0.5 + 0.5 * x)))
y <- rbinom(n, 1, plogis(-1 + x - 0.5 * a))
pred <- plogis(-1 + 0.8 * x)

# Estimate transportable specificity
result <- tr_specificity(
  predictions = pred,
  outcomes = y,
  treatment = a,
  source = s,
  covariates = data.frame(x = x),
  treatment_level = 0,
  estimator = "dr",
  se_method = "none"
)
print(result)
#> 
#> Transportable Specificity Estimate
#> ===================================
#> 
#> Estimator: DR 
#> Analysis: transport 
#> Treatment level: 0 
#> N (source): 624 
#> N (target): 376 
#> 
#> Threshold: 0.5 
#> Estimate: 0.9196 
#> Naive estimate: 0.9397