Merge pull request #29 from Zsailer/ridge

Add Ridge model.
harmslab · Apr 10, 2018 · 2e52c50 · 2e52c50
2 parents 038afd9 + b2890ff
commit 2e52c50
Show file tree

Hide file tree

Showing 29 changed files with 627 additions and 306 deletions.
diff --git a/docs/api/epistasis.mapping.rst b/docs/api/epistasis.mapping.rst
@@ -0,0 +1,7 @@
+epistasis\.mapping module
+-------------------------
+
+.. automodule:: epistasis.mapping
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/epistasis.matrix.rst b/docs/api/epistasis.matrix.rst
@@ -0,0 +1,7 @@
+epistasis\.matrix module
+------------------------
+
+.. automodule:: epistasis.matrix
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/epistasis.models.linear.rst b/docs/api/epistasis.models.linear.rst
@@ -0,0 +1,26 @@
+epistasis\.models\.linear package
+=================================
+
+epistasis\.models\.linear\.lasso module
+---------------------------------------
+
+.. automodule:: epistasis.models.linear.lasso
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+epistasis\.models\.linear\.ordinary module
+------------------------------------------
+
+.. automodule:: epistasis.models.linear.ordinary
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+epistasis\.models\.linear\.ridge module
+---------------------------------------
+
+.. automodule:: epistasis.models.linear.ridge
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/epistasis.models.nonlinear.rst b/docs/api/epistasis.models.nonlinear.rst
@@ -0,0 +1,27 @@
+epistasis\.models\.nonlinear package
+====================================
+
+epistasis\.models\.nonlinear\.ordinary module
+---------------------------------------------
+
+.. automodule:: epistasis.models.nonlinear.ordinary
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+epistasis\.models\.nonlinear\.power module
+------------------------------------------
+
+.. automodule:: epistasis.models.nonlinear.power
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: epistasis.models.nonlinear
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/epistasis.models.rst b/docs/api/epistasis.models.rst
@@ -1,7 +1,12 @@
 epistasis\.models package
 =========================
 
-.. automodule:: epistasis.models.__init__
+See subpackages for specific models.
+
+.. toctree::
+
+    epistasis.models.linear
+    epistasis.models.nonlinear
 
 epistasis\.models\.base module
 ------------------------------
@@ -19,18 +24,10 @@ epistasis\.models\.classifiers module
     :undoc-members:
     :show-inheritance:
 
-epistasis\.models\.linear module
---------------------------------
-
-.. automodule:: epistasis.models.linear
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-epistasis\.models\.nonlinear module
------------------------------------
+epistasis\.models\.ensemble module
+----------------------------------
 
-.. automodule:: epistasis.models.nonlinear
+.. automodule:: epistasis.models.ensemble
     :members:
     :undoc-members:
     :show-inheritance:
@@ -43,18 +40,19 @@ epistasis\.models\.pipeline module
     :undoc-members:
     :show-inheritance:
 
-epistasis\.models\.power module
+epistasis\.models\.utils module
 -------------------------------
 
-.. automodule:: epistasis.models.power
+.. automodule:: epistasis.models.utils
     :members:
     :undoc-members:
     :show-inheritance:
 
-epistasis\.models\.utils module
--------------------------------
 
-.. automodule:: epistasis.models.utils
+Module contents
+---------------
+
+.. automodule:: epistasis.models
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/epistasis.pyplot.rst b/docs/api/epistasis.pyplot.rst
@@ -1,8 +1,5 @@
 epistasis\.pyplot package
-=======================
-
-.. automodule:: epistasis.pyplot.__init__
-
+=========================
 
 epistasis\.pyplot\.coefs module
 -------------------------------

diff --git a/docs/api/epistasis.sampling.rst b/docs/api/epistasis.sampling.rst
@@ -1,8 +1,6 @@
 epistasis\.sampling package
 ===========================
 
-.. automodule:: epistasis.sampling.__init__
-
 epistasis\.sampling\.bayesian module
 ------------------------------------
 

diff --git a/docs/api/epistasis.simulate.rst b/docs/api/epistasis.simulate.rst
@@ -1,7 +1,6 @@
 epistasis\.simulate package
 ===========================
 
-.. automodule:: epistasis.simulate.__init__
 
 epistasis\.simulate\.base module
 --------------------------------
@@ -18,3 +17,11 @@ epistasis\.simulate\.linear module
     :members:
     :undoc-members:
     :show-inheritance:
+
+epistasis\.simulate\.power module
+---------------------------------
+
+.. automodule:: epistasis.simulate.power
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/epistasis.stats.rst b/docs/api/epistasis.stats.rst
@@ -0,0 +1,7 @@
+epistasis\.stats module
+-----------------------
+
+.. automodule:: epistasis.stats
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/main.rst b/docs/api/main.rst
@@ -5,9 +5,12 @@ This page lists all modules in the epitasis library. If you find missing documen
 feel free to open an issue or (better yet) submit a pull request!
 
 .. toctree::
-   :maxdepth: 2
+    :maxdepth: 2
 
-   epistasis.models
-   epistasis.pyplot
-   epistasis.sampling
-   epistasis.simulate
+    epistasis.models
+    epistasis.pyplot
+    epistasis.sampling
+    epistasis.simulate
+    epistasis.mapping
+    epistasis.matrix
+    epistasis.stats
diff --git a/docs/gallery/gallery_jupyter.zip b/docs/gallery/gallery_jupyter.zip
diff --git a/docs/gallery/gallery_python.zip b/docs/gallery/gallery_python.zip
diff --git a/docs/pages/models.rst b/docs/pages/models.rst
@@ -4,6 +4,7 @@ Detailed list of models
 This page lists all models included in the Epistasis Package.
 
 * EpistasisLinearRegression_: estimate epistatic coefficents in a linear genotype-phenotype map.
+* EpistasisRidge_: estimate *sparse* epistatic coefficients in a linear genotype-phenotype map
 * EpistasisLasso_: estimate *sparse* epistatic coefficients in a linear genotype-phenotype map
 * EpistasisNonlinearRegression_: estimates high-order epistatic coefficients in a nonlinear genotype-phenotype map.
 * EpistasisNonlinearLasso_: estimate *sparse* epistatic coefficients in a nonlinear genotype-phenotype map.
@@ -13,6 +14,7 @@ This page lists all models included in the Epistasis Package.
 * EpistasisEnsembleRegression_: use a statistical ensemble of "states" to decompose variation in a genotype-phenotype map.
 
 .. _EpistasisLinearRegression: models.html#epistasislinearregression
+.. _EpistasisRidge: models.html#epistasisridge
 .. _EpistasisLasso: models.html#epistasislasso
 .. _EpistasisNonlinearRegression: models.html#epistasisnonlinearregression
 .. _EpistasisNonlinearLasso: models.html#epistasisnonlinearlasso
@@ -51,6 +53,35 @@ genotype-phenotype map. Simple define the order of the model.
   # Fit the model.
   model.fit()
 
+EpistasisRidge
+--------------
+
+A L2-norm epistasis model for estimating sparse epistatic coefficients. The
+optimization function imposes a penalty on the number of coefficients and finds
+the model that maximally explains the data while using the fewest coefficients.
+
+.. code-block:: python
+
+  from gpmap import GenotypePhenotypeMap
+  from epistasis.models import EpistasisRidge
+
+  wildtype = 'AA'
+  genotypes = ['AA', 'AT', 'TA', 'TT']
+  phenotypes = [0.1, 0.2, 0.7, 1.2]
+
+  # Read genotype-phenotype map.
+  gpm = GenotypePhenotypeMap(wildtype, genotypes, phenotypes)
+
+  # Initialize the data.
+  model = EpistasisRidge(order=2)
+
+  # Add Genotype-phenotype map data.
+  model.add_gpm(gpm)
+
+  # Fit the model.
+  model.fit()
+
+
 EpistasisLasso
 --------------
 
@@ -61,7 +92,7 @@ the model that maximally explains the data while using the fewest coefficients.
 .. code-block:: python
 
   from gpmap import GenotypePhenotypeMap
-  from epistasis.models import EpistasisLinearRegression
+  from epistasis.models import EpistasisLasso
 
   wildtype = 'AA'
   genotypes = ['AA', 'AT', 'TA', 'TT']

diff --git a/epistasis/models/__init__.py b/epistasis/models/__init__.py
@@ -2,11 +2,8 @@
 A library of models to decompose high-order epistasis in genotype-phenotype
 maps.
 """
-from .linear import EpistasisLinearRegression, EpistasisLasso
-from .power import EpistasisPowerTransform, EpistasisPowerTransformLasso
+from .linear import EpistasisLinearRegression, EpistasisLasso, EpistasisRidge
 from .nonlinear import (EpistasisNonlinearRegression,
-                         EpistasisNonlinearLasso,
-                         Parameter,
-                         Parameters)
+                        EpistasisPowerTransform)
 from .classifiers import EpistasisLogisticRegression
 from .pipeline import EpistasisPipeline
diff --git a/epistasis/models/linear/__init__.py b/epistasis/models/linear/__init__.py
@@ -0,0 +1,3 @@
+from .ordinary import EpistasisLinearRegression
+from .lasso import EpistasisLasso
+from .ridge import EpistasisRidge