Develop global refactoring

.github/workflows/code-cov.yaml

@@ -39,6 +39,8 @@ jobs:
         dependencies: 'NA'
         install-pandoc: false
         packages: |
+          [email protected]
+          [email protected]
           grf
           causalweight
           mediation
@@ -53,6 +55,7 @@ jobs:
 
     - name: Run tests with coverage
       run: |
+        export LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH}
         pytest --cov=med_bench --cov-report=xml
 
     - name: Upload coverage to Codecov

.github/workflows/tests-with-R.yaml

@@ -39,6 +39,8 @@ jobs:
         dependencies: 'NA'
         install-pandoc: false
         packages: |
+          [email protected]
+          [email protected]
           grf
           causalweight
           mediation
@@ -53,4 +55,5 @@ jobs:
 
     - name: Run tests
       run: |
-        pytest
+        export LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH}
+        pytest

.gitignore

@@ -131,3 +131,13 @@ dmypy.json
 # DS_STORE files
 src/.DS_Store
 .DS_Store
+
+# Mac
+.idea/
+
+# Ignore PDFs
+*.pdf
+
+# Ignore local scripts
+
+scripts/

README.md

@@ -21,26 +21,6 @@ pip install git+git://github.com/judithabk6/med_bench.git
 
 Installation time is a few minutes on a standard personal computer.
 
-Some estimators rely on their R implementation which requires the installation of the corresponding R packages. This can be done using `rpy2`
-
-````python
-import rpy2
-import rpy2.robjects.packages as rpackages
-utils = rpackages.importr('utils')
-utils.chooseCRANmirror(ind=33)
-
-utils.install_packages('grf')
-
-utils.install_packages('causalweight')
-
-utils.install_packages('mediation')
-
-
-utils.install_packages('devtools')
-devtools = rpackages.importr('devtools')
-devtools.install_github('ohines/plmed')
-plmed = rpackages.importr('plmed')
-````
 
 ## Content
 The `src` folder contains the main module with the implementation of the different estimators, the `script` folder contains the function used to simulate data and run the experiments, and the `results` folder contains all available results and code to reproduce the figures.

docs/conf.py

@@ -2,19 +2,24 @@
 import sys
 
 import med_bench
-import med_bench.get_estimation
 import med_bench.get_simulated_data
-import med_bench.mediation
+import med_bench.estimation
+from med_bench.estimation.mediation_coefficient_product import CoefficientProduct
+from med_bench.estimation.mediation_dml import DoubleMachineLearning
+from med_bench.estimation.mediation_g_computation import GComputation
+from med_bench.estimation.mediation_ipw import InversePropensityWeighting
+from med_bench.estimation.mediation_mr import MultiplyRobust
+from med_bench.estimation.mediation_tmle import TMLE
 import med_bench.utils
 import med_bench.utils.utils
-import med_bench.utils.nuisances
 
 
 sys.path.insert(0, os.path.abspath('../'))
 
 project = 'med_bench'
-copyright = '2024, Judith Abecassis, Houssam Zenati, Bertrand Thirion, Hadrien Mariaccia, Mouad Zbakh'
-author = 'Judith Abecassis, Houssam Zenati, Bertrand Thirion, Hadrien Mariaccia, Mouad Zbakh'
+copyright = '2025, Judith Abecassis, Houssam Zenati, Bertrand Thirion, Hadrien Mariaccia, Mouad Zbakh, Sami Boumaïza, Julie Josse'
+author = 'Judith Abecassis, Houssam Zenati, Bertrand Thirion, Hadrien Mariaccia, Mouad Zbakh, Sami Boumaïza, Julie Josse'
+
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/modules.rst

@@ -1,57 +1,68 @@
 .. toctree::
    :maxdepth: 4
-   :caption: Contents:
+   :caption: API:
 
 
-med_bench
-=================
-.. automodule:: med_bench
-   :members:
-   :undoc-members:
-   :show-inheritance:
 
 
-get_estimation
---------
 
-.. automodule:: med_bench.get_estimation
+
+Estimation
+==========
+.. automodule:: med_bench.estimation
     :members:
     :undoc-members:
     :show-inheritance:
 
 
-get_simulated_data
---------
+.. automodule:: med_bench.estimation.mediation_coefficient_product
+    :members:
+    :undoc-members:
 
-.. automodule:: med_bench.get_simulated_data
+
+.. automodule:: med_bench.estimation.mediation_g_computation
     :members:
     :undoc-members:
-    :show-inheritance:
 
+.. automodule:: med_bench.estimation.mediation_ipw
+    :members:
+    :undoc-members:
 
-mediation
---------
 
-.. automodule:: med_bench.mediation
+.. automodule:: med_bench.estimation.mediation_mr
     :members:
     :undoc-members:
-    :show-inheritance:
 
 
-utils
---------
+.. automodule:: med_bench.estimation.mediation_dml
+    :members:
+    :undoc-members:
 
-.. automodule:: med_bench.utils.utils
+
+
+.. automodule:: med_bench.estimation.mediation_tmle
+    :members:
+    :undoc-members:
+
+
+
+get_simulated_data
+==========
+
+.. automodule:: med_bench.get_simulated_data
     :members:
     :undoc-members:
     :show-inheritance:
 
 
-nuisances
---------
+utils
+==========
 
-.. automodule:: med_bench.utils.nuisances
+.. automodule:: med_bench.utils.utils
     :members:
     :undoc-members:
     :show-inheritance:
 
+
+
+

setup.py

@@ -20,7 +20,6 @@
         'pandas>=1.2.1',
         'scikit-learn>=0.22.1',
         'numpy>=1.19.2',
-        'rpy2>=2.9.4',
         'scipy>=1.5.2',
         'seaborn>=0.11.1',
         'matplotlib>=3.3.2',