update documented examples

Leo-Simpson · Dec 11, 2020 · 8129b48 · 8129b48
1 parent 9944de1
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diff --git a/classo/solve_R1.py b/classo/solve_R1.py
@@ -155,7 +155,7 @@ def Classo_R1(pb, lam):
 
 
 def pathlasso_R1(pb, path, n_active = False, return_sp_path = False):
-    n = pb.dim[0]
+    n, d, k = pb.dim
     BETA, tol = [], pb.tol
     if pb.type == "Path-Alg":
         beta, sp_path = solve_path(pb.matrix, path[-1], n_active, 0, "R1")
@@ -181,7 +181,7 @@ def pathlasso_R1(pb, path, n_active = False, return_sp_path = False):
     if type(n_active) == int and n_active > 0:
         n_act = n_active
     else:
-        n_act = n
+        n_act = d
     for lam in path:
         X = Classo_R1(pb, lam)
         beta, init = X[0], X[1]

diff --git a/classo/solve_R2.py b/classo/solve_R2.py
@@ -70,6 +70,8 @@ def Classo_R2(pb, lam, compute = True):
 
     tol = pb.tol * LA.norm(y) / LA.norm(A, "fro")  # tolerance rescaled
 
+
+    """
     # cvx
     # call to the cvx function of minimization
     if pb_type == "cvx":
@@ -85,6 +87,7 @@ def Classo_R2(pb, lam, compute = True):
         if regpath:
             return (x.value, True)
         return x.value
+    """
 
     if compute:
         pb.compute_param()
@@ -176,7 +179,7 @@ def Classo_R2(pb, lam, compute = True):
 
 
 def pathlasso_R2(pb, path, n_active = False):
-    n = pb.dim[0]
+    n, d, k = pb.dim
     BETA, tol = [], pb.tol
     if pb.type == "Path-Alg":
         (A, C, y) = pb.matrix
@@ -194,7 +197,7 @@ def pathlasso_R2(pb, path, n_active = False):
     if type(n_active) == int and n_active > 0:
         n_act = n_active
     else:
-        n_act = n
+        n_act = d
     for lam in path:
         X = Classo_R2(pb, lam, compute = False)
         BETA.append(X[0])

diff --git a/classo/solve_R3.py b/classo/solve_R3.py
@@ -152,7 +152,7 @@ def pathlasso_R3(pb, path, n_active = False):
     if type(n_active) == int and n_active > 0:
         n_act = n_active
     else:
-        n_act = n
+        n_act = d
 
     for lam in path:
         X = Classo_R3(pb, lam)

diff --git a/classo/solve_R4.py b/classo/solve_R4.py
@@ -131,7 +131,7 @@ def Classo_R4(pb, lam):
 
 
 def pathlasso_R4(pb, path, n_active = False):
-    n = pb.dim[0]
+    n, d, k = pb.dim
     BETA, SIGMA, tol = [], [], pb.tol
     pb.type = "DR"
     save_init = pb.init
@@ -140,7 +140,7 @@ def pathlasso_R4(pb, path, n_active = False):
     if type(n_active) == int and n_active > 0:
         n_act = n_active
     else:
-        n_act = n
+        n_act = d
 
     for lam in path:
         X = Classo_R4(pb, lam)

diff --git a/docs/source/auto_examples/auto_examples_jupyter.zip b/docs/source/auto_examples/auto_examples_jupyter.zip
diff --git a/docs/source/auto_examples/auto_examples_python.zip b/docs/source/auto_examples/auto_examples_python.zip
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_advanced_example_001.png b/docs/source/auto_examples/images/sphx_glr_plot_advanced_example_001.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_advanced_example_002.png b/docs/source/auto_examples/images/sphx_glr_plot_advanced_example_002.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_advanced_example_003.png b/docs/source/auto_examples/images/sphx_glr_plot_advanced_example_003.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_advanced_example_004.png b/docs/source/auto_examples/images/sphx_glr_plot_advanced_example_004.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_advanced_example_005.png b/docs/source/auto_examples/images/sphx_glr_plot_advanced_example_005.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_advanced_example_006.png b/docs/source/auto_examples/images/sphx_glr_plot_advanced_example_006.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_combo_example_001.png b/docs/source/auto_examples/images/sphx_glr_plot_combo_example_001.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_combo_example_002.png b/docs/source/auto_examples/images/sphx_glr_plot_combo_example_002.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_combo_example_003.png b/docs/source/auto_examples/images/sphx_glr_plot_combo_example_003.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_combo_example_004.png b/docs/source/auto_examples/images/sphx_glr_plot_combo_example_004.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_combo_example_005.png b/docs/source/auto_examples/images/sphx_glr_plot_combo_example_005.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_combo_example_006.png b/docs/source/auto_examples/images/sphx_glr_plot_combo_example_006.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_001.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_001.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_002.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_002.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_003.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_003.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_004.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_004.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_005.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_005.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_006.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_006.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_007.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_007.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_008.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_008.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_009.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_009.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_010.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_010.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_011.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_011.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_012.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_012.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_013.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_013.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_014.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_014.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_015.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_015.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_016.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_016.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_017.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_017.png
diff --git a/docs/source/auto_examples/images/sphx_glr_plot_pH_example_018.png b/docs/source/auto_examples/images/sphx_glr_plot_pH_example_018.png
diff --git a/docs/source/auto_examples/images/thumb/sphx_glr_plot_COMBO_example_thumb.png b/docs/source/auto_examples/images/thumb/sphx_glr_plot_COMBO_example_thumb.png
diff --git a/docs/source/auto_examples/images/thumb/sphx_glr_plot_advanced_example_thumb.png b/docs/source/auto_examples/images/thumb/sphx_glr_plot_advanced_example_thumb.png
diff --git a/docs/source/auto_examples/images/thumb/sphx_glr_plot_pH_example_thumb.png b/docs/source/auto_examples/images/thumb/sphx_glr_plot_pH_example_thumb.png
diff --git a/docs/source/auto_examples/index.rst b/docs/source/auto_examples/index.rst
@@ -14,7 +14,7 @@ Bellow is a gallery of examples.
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="Let&#x27;s present what classo does when using its default parameters on synthetic data">
+    <div class="sphx-glr-thumbcontainer" tooltip="Let&#x27;s present what classo does when using its default parameters on synthetic data.">
 
 .. only:: html
 
@@ -53,6 +53,48 @@ Bellow is a gallery of examples.
    :hidden:
 
    /auto_examples/plot_advanced_example
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="The next microbiome example considers the  `Central Park Soil dataset &lt;https://github.com/Leo-S...">
+
+.. only:: html
+
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_pH_example_thumb.png
+     :alt: pH prediction using the Central Park soil dataset
+
+     :ref:`sphx_glr_auto_examples_plot_pH_example.py`
+
+.. raw:: html
+
+    </div>
+
+
+.. toctree::
+   :hidden:
+
+   /auto_examples/plot_pH_example
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="We first consider the `COMBO data set &lt;https://github.com/Leo-Simpson/c-lasso/tree/master/examp...">
+
+.. only:: html
+
+ .. figure:: /auto_examples/images/thumb/sphx_glr_plot_combo_example_thumb.png
+     :alt: BMI prediction using the COMBO dataset
+
+     :ref:`sphx_glr_auto_examples_plot_combo_example.py`
+
+.. raw:: html
+
+    </div>
+
+
+.. toctree::
+   :hidden:
+
+   /auto_examples/plot_combo_example
 .. raw:: html
 
     <div class="sphx-glr-clear"></div>

diff --git a/docs/source/auto_examples/plot_COMBO_example.ipynb b/docs/source/auto_examples/plot_COMBO_example.ipynb
@@ -0,0 +1,198 @@
+{
+  "cells": [
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "%matplotlib inline"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "\n# BMI prediction using the COMBO dataset \n\nWe first consider the `COMBO data set <https://github.com/Leo-Simpson/c-lasso/tree/master/examples/COMBO_data>`_\nand show how to predict Body Mass Index (BMI) from microbial genus abundances and two non-compositional covariates  using \"filtered_data\".\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "from classo import csv_to_np, classo_problem, clr\nimport numpy as np"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Load microbiome and covariate data X\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "X0  = csv_to_np('COMBO_data/complete_data/GeneraCounts.csv', begin = 0).astype(float)\nX_C = csv_to_np('COMBO_data/CaloriData.csv', begin = 0).astype(float)\nX_F = csv_to_np('COMBO_data/FatData.csv', begin = 0).astype(float)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Load BMI measurements y\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "y   = csv_to_np('COMBO_data/BMI.csv', begin = 0).astype(float)[:, 0]\nlabels = csv_to_np('COMBO_data/complete_data/GeneraPhylo.csv').astype(str)[:, -1]"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Normalize/transform data\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "y   = y - np.mean(y) #BMI data (n = 96)\nX_C = X_C - np.mean(X_C, axis = 0)  #Covariate data (Calorie)\nX_F = X_F - np.mean(X_F, axis = 0)  #Covariate data (Fat)\nX0 = clr(X0, 1 / 2).T"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Set up design matrix and zero-sum constraints for 45 genera\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "X     = np.concatenate((X0, X_C, X_F, np.ones((len(X0), 1))), axis = 1) # Joint microbiome and covariate data and offset\nlabel = np.concatenate([labels, np.array(['Calorie', 'Fat', 'Bias'])])\nC = np.ones((1, len(X[0])))\nC[0, -1], C[0, -2], C[0, -3] = 0., 0., 0."
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Set up c-lassso problem\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "problem = classo_problem(X, y, C)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Use stability selection with theoretical lambda [Combettes & M\u00fcller, 2020b]\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "problem.model_selection.StabSelparameters.method      = 'lam'\nproblem.model_selection.StabSelparameters.threshold_label = 0.5"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Use formulation R3\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "problem.formulation.concomitant = True\n\nproblem.solve()\nprint(problem)\nprint(problem.solution)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Use formulation R4\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "problem.formulation.huber = True\nproblem.formulation.concomitant = True\n\nproblem.solve()\nprint(problem)\nprint(problem.solution)"
+      ]
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "language": "python",
+      "name": "python3"
+    },
+    "language_info": {
+      "codemirror_mode": {
+        "name": "ipython",
+        "version": 3
+      },
+      "file_extension": ".py",
+      "mimetype": "text/x-python",
+      "name": "python",
+      "nbconvert_exporter": "python",
+      "pygments_lexer": "ipython3",
+      "version": "3.9.0"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 0
+}