up TMLE and get rid of windows

.github/workflows/CI.yml

@@ -19,7 +19,6 @@ jobs:
  os:
  - ubuntu-latest
  - macOS-latest
- - windows-latest
  arch:
  - 'x64'
  steps:

Project.toml

@@ -55,7 +55,7 @@ MLJModels = "0.16"
 MLJXGBoostInterface = "0.3.4"
 MultipleTesting = "0.6.0"
 Optim = "1.7"
-TMLE = "0.13.1"
+TMLE = "0.14.0"
 Tables = "1.10.1"
 YAML = "0.4.9"
 julia = "1.7, 1"

src/cli.jl

@@ -23,8 +23,8 @@ function cli_settings()
 
  "--estimands"
  arg_type = String
- help = "A string (`generateATEs`) or a serialized TMLE.Configuration (accepted formats: .json | .yaml | .jls)"
- default = "generateATEs"
+ help = "A string (`factorialATE`) or a serialized TMLE.Configuration (accepted formats: .json | .yaml | .jls)"
+ default = "factorialATE"
 
  "--estimators"
  arg_type = String

src/runner.jl

@@ -8,7 +8,7 @@ mutable struct Runner
  verbosity::Int
  failed_nuisance::Set
  function Runner(dataset; 
- estimands="generateATEs", 
+ estimands="factorialATE", 
  estimators="glmnet",
  verbosity=0, 
  outputs=Outputs(), 
@@ -120,7 +120,7 @@ end
 
 """
  tmle(dataset; 
- estimands="generateATEs", 
+ estimands="factorialATE", 
  estimators="glmnet"; 
  verbosity=0, 
  outputs=Outputs(),
@@ -138,7 +138,7 @@ TMLE CLI.
 
 # Options
 
-- `--estimands`: A string ("generateATEs") or a serialized TMLE.Configuration (accepted formats: .json | .yaml | .jls)
+- `--estimands`: A string ("factorialATE") or a serialized TMLE.Configuration (accepted formats: .json | .yaml | .jls)
 - `--estimators`: A julia file containing the estimators to use.
 - `-v, --verbosity`: Verbosity level.
 - `-o, --outputs`: Ouputs to be generated.
@@ -151,7 +151,7 @@ TMLE CLI.
 - `-s, --sort_estimands`: Sort estimands to minimize cache usage (A brute force approach will be used, resulting in exponentially long sorting time).
 """
 function tmle(dataset::String;
- estimands::String="generateATEs", 
+ estimands::String="factorialATE", 
  estimators::String="glmnet",
  verbosity::Int=0, 
  outputs::Outputs=Outputs(),

src/utils.jl

@@ -81,19 +81,19 @@ This explicitely requires that the following columns belong to the dataset:
 
 All ATE parameters are generated.
 """
-function TMLE.generateATEs(dataset)
+function TMLE.factorialATE(dataset)
  colnames = names(dataset)
  "T" ∈ colnames || throw(ArgumentError("No column 'T' found in the dataset for the treatment variable."))
  "Y" ∈ colnames || throw(ArgumentError("No column 'Y' found in the dataset for the outcome variable."))
  confounding_variables = Tuple(name for name in colnames if occursin(r"^W", name))
  length(confounding_variables) > 0 || throw(ArgumentError("Could not find any confounding variable (starting with 'W') in the dataset."))
 
- return [generateATEs(dataset, (:T, ), :Y; confounders=confounding_variables)]
+ return [factorialATE(dataset, (:T, ), :Y; confounders=confounding_variables)]
 end
 
 function build_estimands_list(estimands_pattern, dataset)
- estimands = if estimands_pattern == "generateATEs"
- generateATEs(dataset)
+ estimands = if estimands_pattern == "factorialATE"
+ factorialATE(dataset)
  else
  proofread_estimands(estimands_pattern, dataset)
  end

test/utils.jl

@@ -75,18 +75,17 @@ end
  rm(filename)
 end
 
-@testset "Test generateATEs" begin
+@testset "Test factorialATE" begin
  dataset = DataFrame(C=[1, 2, 3, 4],)
- @test_throws ArgumentError TargetedEstimation.build_estimands_list("generateATEs", dataset)
+ @test_throws ArgumentError TargetedEstimation.build_estimands_list("factorialATE", dataset)
  dataset.T = [0, 1, missing, 2]
- @test_throws ArgumentError TargetedEstimation.build_estimands_list("generateATEs", dataset)
+ @test_throws ArgumentError TargetedEstimation.build_estimands_list("factorialATE", dataset)
  dataset.Y = [0, 1, 2, 2]
  dataset.W1 = [1, 1, 1, 1]
  dataset.W_2 = [1, 1, 1, 1]
- composedATE = TargetedEstimation.build_estimands_list("generateATEs", dataset)[1]
+ composedATE = TargetedEstimation.build_estimands_list("factorialATE", dataset)[1]
  @test composedATE.args == (
  TMLE.StatisticalATE(:Y, (T = (case = 1, control = 0),), (T = (:W1, :W_2),), ()),
- TMLE.StatisticalATE(:Y, (T = (case = 2, control = 0),), (T = (:W1, :W_2),), ()),
  TMLE.StatisticalATE(:Y, (T = (case = 2, control = 1),), (T = (:W1, :W_2),), ())
  )
 end