intxmean: Estimate the CATE model using specified scoring methods

In precmed: Precision Medicine

Estimate the CATE model using specified scoring methods

Description

Coefficients of the CATE estimated with boosting, linear regression, two regression, contrast regression, random forest, generalized additive model

Usage

intxmean(
  y,
  trt,
  x.cate,
  x.init,
  x.ps,
  score.method = c("boosting", "gaussian", "twoReg", "contrastReg", "gam",
    "randomForest"),
  ps.method = "glm",
  minPS = 0.01,
  maxPS = 0.99,
  initial.predictor.method = "boosting",
  xvar.smooth.init,
  xvar.smooth.score,
  tree.depth = 2,
  n.trees.rf = 1000,
  n.trees.boosting = 200,
  B = 1,
  Kfold = 2,
  plot.gbmperf = TRUE,
  ...
)

Arguments

y	Observed outcome; vector of size n (observations)
trt	Treatment received; vector of size n units with treatment coded as 0/1
x.cate	Matrix of p.cate baseline covariates; dimension n by p.cate (covariates in the outcome model)
x.init	Matrix of p.init baseline covariates; dimension n by p.init It must be specified when score.method = contrastReg or twoReg.
x.ps	Matrix of p.ps baseline covariates (plus a leading column of 1 for the intercept); dimension n by p.ps + 1 (covariates in the propensity score model plus intercept)
score.method	A vector of one or multiple methods to estimate the CATE score. Allowed values are: 'boosting', 'gaussian', 'twoReg', 'contrastReg', 'randomForest', 'gam'. Default specifies all 6 methods.
ps.method	A character value for the method to estimate the propensity score. Allowed values include one of: 'glm' for logistic regression with main effects only (default), or 'lasso' for a logistic regression with main effects and LASSO penalization on two-way interactions (added to the model if interactions are not specified in ps.model). Relevant only when ps.model has more than one variable.
minPS	A numerical value (in '[0, 1]') below which estimated propensity scores should be truncated. Default is 0.01.
maxPS	A number above which estimated propensity scores should be trimmed; scalar
initial.predictor.method	A character vector for the method used to get initial outcome predictions conditional on the covariates in cate.model in score.method = 'twoReg' and 'contrastReg'. Allowed values include one of 'gaussian' (fastest), 'boosting' (default) and 'gam'.
xvar.smooth.init	A vector of characters indicating the name of the variables used as the smooth terms if initial.predictor.method = 'gam'. The variables must be selected from the variables listed in init.model. Default is NULL, which uses all variables in init.model.
xvar.smooth.score	A vector of characters indicating the name of the variables used as the smooth terms if score.method = 'gam'. The variables must be selected from the variables listed in cate.model. Default is NULL, which uses all variables in cate.model.
tree.depth	A positive integer specifying the depth of individual trees in boosting (usually 2-3). Used only if score.method = 'boosting' or if score.method = 'twoReg' or 'contrastReg' and initial.predictor.method = 'boosting'. Default is 2.
n.trees.rf	A positive integer specifying the number of trees. Used only if score.method = 'randomForest'. Default is 1000.
n.trees.boosting	A positive integer specifying the maximum number of trees in boosting (usually 100-1000). Used only if score.method = 'boosting' or if score.method = 'twoReg' or 'contrastReg' and initial.predictor.method = 'boosting'. Default is 200.
B	A positive integer specifying the number of time cross-fitting is repeated in score.method = 'twoReg' and 'contrastReg'. Default is 3.
Kfold	A positive integer specifying the number of folds (parts) used in cross-fitting to partition the data in score.method = 'twoReg' and 'contrastReg'. Default is 6.
plot.gbmperf	A logical value indicating whether to plot the performance measures in boosting. Used only if score.method = 'boosting' or if score.method = 'twoReg' or 'contrastReg' and initial.predictor.method = 'boosting'. Default is TRUE.
...	Additional arguments for gbm()

Value

Depending on what score.method is, the outputs is a combination of the following: result.boosting: Results of boosting fit and best iteration, for trt = 0 and trt = 1 separately result.gaussian: Linear regression estimator (beta1 - beta0); vector of length p.cate + 1 result.twoReg: Two regression estimator (beta1 - beta0); vector of length p.cate + 1 result.contrastReg: A list of the contrast regression results with 3 elements: $delta.contrastReg: Contrast regression DR estimator; vector of length p.cate + 1 $sigma.contrastReg: Variance covariance matrix for delta.contrastReg; matrix of size p.cate + 1 by p.cate + 1 result.randomForest: Results of random forest fit and best iteration, for trt = 0 and trt = 1 separately result.gam: Results of generalized additive model fit and best iteration, for trt = 0 and trt = 1 separately best.iter: Largest best iterations for boosting (if used) fgam: Formula applied in GAM when initial.predictor.method = 'gam' warn.fit: Warnings occurred when fitting score.method err.fit:: Errors occurred when fitting score.method

precmed documentation built on Oct. 6, 2024, 1:07 a.m.