Merge pull request #8 from rsyi/master

FIx documentation (mocking skopt, updating counting functions).

docs/conf.py

@@ -20,7 +20,7 @@
 
 # Add mock modules.
 import mock
-MOCK_MODULES = ['matplotlib', 'matplotlib.pylab', 'matplotlib.pyplot', 'numpy', 'pandas', 'scipy', 'scipy.stats', 'sklearn', 'sklearn.ensemble', 'sklearn.metrics', 'sklearn.model_selection', 'xgboost']
+MOCK_MODULES = ['matplotlib', 'matplotlib.pylab', 'matplotlib.pyplot', 'numpy', 'pandas', 'scipy', 'scipy.stats', 'sklearn', 'sklearn.ensemble', 'sklearn.metrics', 'sklearn.model_selection', 'xgboost', 'skopt', 'skopt.space']
 for mod_name in MOCK_MODULES:
    sys.modules[mod_name] = mock.Mock()
 

docs/source/pylift.explore.rst

@@ -1,22 +1,22 @@
-pylift.explore package
-======================
+pylift\.explore package
+=======================
 
 Submodules
 ----------
 
-pylift.explore.base module
---------------------------
+pylift\.explore\.base module
+----------------------------
 
 .. automodule:: pylift.explore.base
-   :members:
-   :undoc-members:
-   :show-inheritance:
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
 
 Module contents
 ---------------
 
 .. automodule:: pylift.explore
-   :members:
-   :undoc-members:
-   :show-inheritance:
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/pylift.methods.rst

@@ -1,30 +1,30 @@
-pylift.methods package
-======================
+pylift\.methods package
+=======================
 
 Submodules
 ----------
 
-pylift.methods.base module
---------------------------
+pylift\.methods\.base module
+----------------------------
 
 .. automodule:: pylift.methods.base
-   :members:
-   :undoc-members:
-   :show-inheritance:
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
-pylift.methods.derivatives module
----------------------------------
+pylift\.methods\.derivatives module
+-----------------------------------
 
 .. automodule:: pylift.methods.derivatives
-   :members:
-   :undoc-members:
-   :show-inheritance:
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
 
 Module contents
 ---------------
 
 .. automodule:: pylift.methods
-   :members:
-   :undoc-members:
-   :show-inheritance:
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/pylift.rst

@@ -6,41 +6,41 @@ Subpackages
 
 .. toctree::
 
-   pylift.explore
-   pylift.methods
+    pylift.explore
+    pylift.methods
 
 Submodules
 ----------
 
-pylift.eval module
-------------------
+pylift\.eval module
+-------------------
 
 .. automodule:: pylift.eval
-   :members:
-   :undoc-members:
-   :show-inheritance:
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
-pylift.generate\_data module
-----------------------------
+pylift\.generate\_data module
+-----------------------------
 
 .. automodule:: pylift.generate_data
-   :members:
-   :undoc-members:
-   :show-inheritance:
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
-pylift.style module
--------------------
+pylift\.style module
+--------------------
 
 .. automodule:: pylift.style
-   :members:
-   :undoc-members:
-   :show-inheritance:
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
 
 Module contents
 ---------------
 
 .. automodule:: pylift
-   :members:
-   :undoc-members:
-   :show-inheritance:
+    :members:
+    :undoc-members:
+    :show-inheritance:

pylift/eval.py

@@ -32,9 +32,9 @@ def _ensure_array(arraylike):
 def _get_counts(treatment, outcome, p):
     """Extract (treatment,outcome) pair counts from treatment and outcome vectors.
 
-    Calculate counts of outcome/treatment combinations. Variables are named
-    nt#o#, where the # corresponds to a binary value for test and outcome,
-    respectively.
+    Calculate effective counts of outcome/treatment combinations (rescaled by
+    propensity). Variables are named nt#o#, where the # corresponds to a binary
+    value for test and outcome, respectively.
 
     Parameters
     ----------
@@ -48,13 +48,13 @@ def _get_counts(treatment, outcome, p):
     Returns
     -------
     Nt1o1 : int
-        Number of entries where (treatment, outcome) == (1,1).
+        Effective number of entries where (treatment, outcome) == (1,1).
     Nt0o1 : int
-        Number of entries where (treatment, outcome) == (0,1).
+        Effective number of entries where (treatment, outcome) == (0,1).
     Nt1o0 : int
-        Number of entries where (treatment, outcome) == (1,0).
+        Effective number of entries where (treatment, outcome) == (1,0).
     Nt0o0 : int
-        Number of entries where (treatment, outcome) == (0,0).
+        Effective number of entries where (treatment, outcome) == (0,0).
 
     """
     Nt1o1 = 0.5*np.sum(1/p[(treatment == 1) & (outcome > 0)])
@@ -64,27 +64,28 @@ def _get_counts(treatment, outcome, p):
     return Nt1o1, Nt0o1, Nt1o0, Nt0o0
 
 def _get_tc_counts(Nt1o1, Nt0o1, Nt1o0, Nt0o0):
-    """Get treatment and control group sizes from `_get_counts` output.
+    """Get effective (scaled by propensity) treatment and control group sizes
+    from `_get_counts` output.
 
     Parameters
     ----------
     Nt1o1 : int
-        Number of entries where (treatment, outcome) == (1,1).
+        Effective number of entries where (treatment, outcome) == (1,1).
     Nt0o1 : int
-        Number of entries where (treatment, outcome) == (0,1).
+        Effective number of entries where (treatment, outcome) == (0,1).
     Nt1o0 : int
-        Number of entries where (treatment, outcome) == (1,0).
+        Effective number of entries where (treatment, outcome) == (1,0).
     Nt0o0 : int
-        Number of entries where (treatment, outcome) == (0,0).
+        Effective number of entries where (treatment, outcome) == (0,0).
 
     Returns
     -------
     Nt1 : int
-        Size of treatment group.
+        Effective size of treatment group.
     Nt0 : int
-        Size of control group.
+        Effective size of control group.
     N : int
-        Size of full group.
+        Effective size of full group.
 
     """
     Nt1 = Nt1o0 + Nt1o1