cate: Conditional Average Treatment Effect estimation

Description

Conditional Average Treatment Effect estimation with cross-fitting.

Usage

cate(
  response.model,
  treatment.model,
  cate.model = ~1,
  calibration.model = NULL,
  missing.model = NULL,
  data,
  contrast,
  nfolds = 1,
  rep = 1,
  id = NULL,
  silent = FALSE,
  stratify = FALSE,
  mc.cores = NULL,
  var.type = "IC",
  second.order = TRUE,
  response_model = deprecated,
  cate_model = deprecated,
  propensity_model = deprecated,
  propensity.model = deprecated,
  treatment = deprecated,
  ...
)

Value

cate.targeted object

Arguments

response.model: formula or learner object (formula => learner_glm)
treatment.model: formula or learner object (formula => learner_glm)
cate.model: formula specifying regression design for conditional average treatment effects
calibration.model: linear calibration model. Specify covariates in addition to predicted potential outcomes to include in the calibration.
missing.model: formula or learner object (formula => learner_glm(family = binomial); default NULL. Model for the missingness mechanism $P(R=1 \mid X, A)$. Required when the outcome in response.model contains NAs. If the formula LHS is omitted, the observation indicator is used automatically. When stratify = TRUE the missing model is fit separately per treatment arm. When supplied, the AIPW score is inverse-probability-of-observation weighted and (if second.order = TRUE) an additional second-order term is added to the influence function.
data: data.frame
contrast: treatment contrast (default 1 vs 0)
nfolds: number of folds (positive integer), or a pre-specified list of fold indices where each element is an integer vector of observation indices forming a partition of 1:nrow(data).
rep: number of replications of cross-fitting procedure by averaging estimates and influence functions from each replication
id: (integer or character) optional subject id vector of length nrow(data). The id can also be specified as part of the cate.model argument with a formula syntax: ~ 1 + cluster(id).
silent: suppress all messages and progressbars
stratify: if TRUE the response.model and missing.model (if provided) will be stratified by treatment
mc.cores: (optional) number of cores. parallel::mcmapply used instead of future
var.type: when equal to "IC" the asymptotic variance is derived from the influence function. Otherwise, based on expressions in Bannick et al. (2025) valid under different covariate-adaptive randomization schemes (only available for ATE and when calibration.model is also specified)
second.order: add seconder order term to IF to handle misspecification of outcome models
response_model: Deprecated. Use response.model instead.
cate_model: Deprecated. Use cate.model instead.
propensity_model: Deprecated. Use treatment.model instead.
propensity.model: Deprecated. Use treatment.model instead.
treatment: Deprecated. Use cate.model instead.
...: additional arguments to future.apply::future_mapply

Author

Klaus Kähler Holst, Andreas Nordland

Details

We have observed data $(Y,A,W)$ where $Y$ is the response variable, $A$ the binary treatment, and $W$ covariates. We further let $V$ be a subset of the covariates. Define the conditional potential mean outcome $$\psi_{a}(P)(V) = E_{P}[E_{P}(Y\mid A=a, W)|V]$$ and let $m(V; \beta)$ denote a parametric working model, then the target parameter is the mean-squared error $$\beta(P) = \operatorname{argmin}_{\beta} E_{P}[\{\Psi_{1}(P)(V)-\Psi_{0}(P)(V)\} - m(V; \beta)]^{2}$$

Missing data is handled under a Missing At Random assumption (MAR). Let $R$ denote the indicator for data not being missing, $R\perp Y|W,A$. The nuisance models are $Q(w,a) = E(Y|W=w, A=a)$, $g_a(w) = P(A=a|W=w)$, and $\rho(w, a) = P(R=1|W=w, A=a)$. For the expected potential outcome $E[Y(a)]$, the AIPW estimator then takes the form $$\frac{1}{n}\sum_{i=1}^n R_i I(A_i=a) / \{g_a(W_i) \rho(W_i, a)\} (Y_i - Q(W_i,a)) + Q(W_i, a)$$.

References

Mark J. van der Laan (2006) Statistical Inference for Variable Importance, The International Journal of Biostatistics.

Bannick, Shao & Liu et al. (2025) A General Form of Covariate Adjustment in Clinical Trials under Covariate-Adaptive Randomization, Biometrika.

Examples

Run this code

sim1 <- function(n=1000, ...) {
  w1 <- rnorm(n)
  w2 <- rnorm(n)
  a <- rbinom(n, 1, plogis(-1 + w1))
  y <- cos(w1) + w2*a + 0.2*w2^2 + a + rnorm(n)
  data.frame(y, a, w1, w2)
}

d <- sim1(5000)
## ATE
cate(cate.model=~1,
     response.model=y~a*(w1+w2),
     treatment.model=a~w1+w2,
     data=d)
## CATE
cate(cate.model=~1+w2,
     response.model=y~a*(w1+w2),
     treatment.model=a~w1+w2,
     data=d)

if (FALSE) {
# superlearner
mod1 <- list(
   glm = learner_glm(y~w1+w2),
   gam = learner_gam(y~s(w1) + s(w2))
)
s1 <- learner_sl(mod1, nfolds=5)
cate(cate.model=~1,
     response.model=s1,
     treatment.model=learner_glm(a~w1+w2, family=binomial),
     data=d,
     stratify=TRUE)
}

## Missing data
sim_missing_cate <- function(n = 5000, seed = 1) {
  set.seed(seed)
  w1 <- rnorm(n)
  w2 <- rnorm(n)
  a  <- rbinom(n, 1, 0.5) # randomized trial
  y_full <- 1 + a + w1 + 0.5 * w2 + rnorm(n)
  pR <- plogis(0.5 - 1 * w2 * a + 0.5 * a)
  R  <- rbinom(n, 1, pR)
  y  <- ifelse(R == 1, y_full, NA_real_)
  data.frame(y0 = y_full, y = y, a = a, w1 = w1, w2 = w2)
}
d <- sim_missing_cate()

# ignoring missing data (complete-case analysis)
cate(cate.model = ~1,
     response.model = y ~ a * w2, # wrong outcome model
     treatment.model = a ~ 1,
     data = na.omit(d), nfolds = 1L)
# MAR analysis
fit <- cate(cate.model = ~1,
            response.model = y ~ a * w2,
            treatment.model = a ~ 1,
            missing.model  = ~ a * (w1 + w2),
            data = d, nfolds = 1L)
fit

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