tests/testthat/test-LF_targeted.R

In jeremyrcoyle/tmle3: The Extensible TMLE Framework

context("Basic interventions: TSM for single static intervention.")

library(sl3)
# library(tmle3)
library(uuid)
library(assertthat)
library(data.table)
library(future)
# setup data for test
# tmle3_Fit$debug(".tmle_fit")

data(cpp)
data <- as.data.table(cpp)
data$parity01 <- as.numeric(data$parity > 0)
data$parity01_fac <- factor(data$parity01)
data$haz01 <- as.numeric(data$haz > 0)
data[is.na(data)] <- 0
node_list <- list(
  W = c(
    "apgar1", "apgar5", "gagebrth", "mage",
    "meducyrs", "sexn"
  ),
  A = "parity01",
  Y = "haz01"
)

qlib <- make_learner_stack(
  "Lrnr_mean",
  "Lrnr_glm_fast"
)

glib <- make_learner_stack(
  "Lrnr_mean",
  "Lrnr_glm_fast"
)

logit_metalearner <- make_learner(
  Lrnr_solnp, metalearner_logistic_binomial,
  loss_loglik_binomial
)
Q_learner <- make_learner(Lrnr_sl, qlib, logit_metalearner)
g_learner <- make_learner(Lrnr_sl, glib, logit_metalearner)
learner_list <- list(Y = Q_learner, A = g_learner)
tmle_spec <- tmle_TSM_all()

# define data
tmle_task <- tmle_spec$make_tmle_task(data, node_list)

# define likelihood
initial_likelihood <- tmle_spec$make_initial_likelihood(tmle_task, learner_list)

# define update method (submodel + loss function)
# disable cvtmle for this test to compare with tmle package
updater <- tmle3_Update$new(cvtmle = FALSE)

targeted_likelihood <- Targeted_Likelihood$new(initial_likelihood, updater)
tl_preds <- targeted_likelihood$get_likelihood(tmle_task, "Y", "validation")
lf_targ <- LF_targeted$new("Y", targeted_likelihood)
lf_preds <- lf_targ$get_likelihood(tmle_task, "validation")
test_that("LF_targeted returns the correct likelihood values", expect_equal(tl_preds, lf_preds))