tests/testthat/test-cv_likelihood.R

In jeremyrcoyle/tmle3: The Extensible TMLE Framework

context("CV-Likelihood: fold-specific Likelihood estimates")

set.seed(1234)
library(sl3)
# library(tmle3)
library(uuid)
library(assertthat)
library(data.table)
library(future)
# setup data for test
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"
)

metalearner <- make_learner(Lrnr_nnls)
Q_learner <- make_learner(Lrnr_sl, qlib, metalearner)
g_learner <- make_learner(Lrnr_sl, glib, 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)

# todo: verify that likelihoods come from expected folds, etc