Merge pull request scikit-bio#1370 from mortonjt/patch_1002

DOC: Adding clarification for eigenvalues for RDA
gregcaporaso · Jun 6, 2016 · f627315 · f627315
2 parents de10810 + f136625
commit f627315
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/skbio/stats/ordination/_redundancy_analysis.py b/skbio/stats/ordination/_redundancy_analysis.py
@@ -72,6 +72,10 @@ def rda(y, x, scale_Y=False, scaling=1):
     -----
     The algorithm is based on [1]_, \S 11.1, and is expected to
     give the same results as ``rda(y, x)`` in R's package vegan.
+    The eigenvalues reported in vegan are re-normalized to
+    :math:`\sqrt{\frac{s}{n-1}}` `n` is the number of samples,
+    and `s` is the original eigenvalues. Here we will only return
+    the original eigenvalues, as recommended in [1]_.
 
     See Also
     --------

diff --git a/skbio/stats/ordination/tests/test_redundancy_analysis.py b/skbio/stats/ordination/tests/test_redundancy_analysis.py
@@ -81,13 +81,12 @@ def test_scaling1(self):
                                      index=self.env_ids,
                                      columns=cropped_pc_ids)
 
-        # These are wrong. See issue #1002
         proportion_explained = pd.Series([0.44275783, 0.25614586,
                                           0.15280354, 0.10497021,
                                           0.02873375, 0.00987052,
                                           0.00471828],
                                          index=self.pc_ids)
-        # These are wrong. See issue #1002
+
         eigvals = pd.Series([25.897954, 14.982578, 8.937841, 6.139956,
                              1.680705, 0.577350, 0.275984],
                             index=self.pc_ids)
@@ -143,13 +142,12 @@ def test_scaling2(self):
                                      index=self.env_ids,
                                      columns=cropped_pc_ids)
 
-        # These are wrong. See issue #1002
         proportion_explained = pd.Series([0.44275783, 0.25614586,
                                           0.15280354, 0.10497021,
                                           0.02873375, 0.00987052,
                                           0.00471828],
                                          index=self.pc_ids)
-        # These are wrong. See issue #1002
+
         eigvals = pd.Series([25.897954, 14.982578, 8.937841, 6.139956,
                              1.680705, 0.577350, 0.275984],
                             index=self.pc_ids)