def test_preprocess_input_with_valid_input(self):
# Should obtain same result using grouping vector or data frame.
exp = (3, 2, np.array([0, 1, 0]),
(np.array([0, 0, 1]), np.array([1, 2, 2])),
np.array([1., 2., 3.]))
obs = _preprocess_input(self.dm, self.grouping, None)
npt.assert_equal(obs, exp)
obs = _preprocess_input(self.dm, self.df, 'Group')
npt.assert_equal(obs, exp)
def test_preprocess_input_with_valid_input(self):
# Should obtain same result using grouping vector or data frame.
exp = (3, 2, np.array([0, 1, 0]), (np.array([0, 0,
1]), np.array([1, 2, 2])),
np.array([1., 2., 3.]))
obs = _preprocess_input(self.dm, self.grouping, None)
npt.assert_equal(obs, exp)
obs = _preprocess_input(self.dm, self.df, 'Group')
npt.assert_equal(obs, exp)
def test_preprocess_input_raises_error(self):
# Requires a DistanceMatrix.
with self.assertRaises(TypeError):
_preprocess_input(
DissimilarityMatrix([[0, 2], [3, 0]], ['a', 'b']),
[1, 2], None)
# Requires column if DataFrame.
with self.assertRaises(ValueError):
_preprocess_input(self.dm, self.df, None)
# Cannot provide column if not data frame.
with self.assertRaises(ValueError):
_preprocess_input(self.dm, self.grouping, 'Group')
# Column must exist in data frame.
with self.assertRaises(ValueError):
_preprocess_input(self.dm, self.df, 'foo')
# All distance matrix IDs must be in data frame.
with self.assertRaises(ValueError):
_preprocess_input(self.dm, self.df_missing_id, 'Group')
# Grouping vector length must match number of objects in dm.
with self.assertRaises(ValueError):
_preprocess_input(self.dm, [1, 2], None)
# Grouping vector cannot have only unique values.
with self.assertRaises(ValueError):
_preprocess_input(self.dm, [1, 2, 3], None)
# Grouping vector cannot have only a single group.
with self.assertRaises(ValueError):
_preprocess_input(self.dm, [1, 1, 1], None)
def permdisp(distance_matrix,
grouping,
column=None,
test='centroid',
permutations=999,
paired=False,
subjects=None):
"""Test for Homogeneity of Multivariate Groups Disperisons using Marti
Anderson's PERMDISP2 procedure.
PERMDISP is a multivariate analogue of Levene's test for homogeneity of
multivariate variances. Distances are handled by reducing the
original distances to principal coordinates. PERMDISP calculates an
F-statistic to assess whether the dispersions between groups is significant
Parameters
----------
distance_matrix : DistanceMatrix
Distance matrix containing distances between objects (e.g., distances
between samples of microbial communities).
grouping : 1-D array_like or pandas.DataFrame
Vector indicating the assignment of objects to groups. For example,
these could be strings or integers denoting which group an object
belongs to. If `grouping` is 1-D ``array_like``, it must be the same
length and in the same order as the objects in `distance_matrix`. If
`grouping` is a ``DataFrame``, the column specified by `column` will be
used as the grouping vector. The ``DataFrame`` must be indexed by the
IDs in `distance_matrix` (i.e., the row labels must be distance matrix
IDs), but the order of IDs between `distance_matrix` and the
``DataFrame`` need not be the same. All IDs in the distance matrix must
be present in the ``DataFrame``. Extra IDs in the ``DataFrame`` are
allowed (they are ignored in the calculations).
column : str, optional
Column name to use as the grouping vector if `grouping` is a
``DataFrame``. Must be provided if `grouping` is a ``DataFrame``.
Cannot be provided if `grouping` is 1-D ``array_like``.
test : {'centroid', 'median'}
determines whether the analysis is done using centroid or spatial
median.
permutations : int, optional
Number of permutations to use when assessing statistical
significance. Must be greater than or equal to zero. If zero,
statistical significance calculations will be skipped and the p-value
will be ``np.nan``.
paired : bool, optional
If True: limit the type of permutations, such that permutations happen
only over groups, not over samples.
[Sep 27, 2019: CORRECT IMPLEMENTATION? Only operates on allowed permutations.]
:subjects: 1-D array_like with indices for subjects for use in paired permanova.
If None: array (0...ni) will be generated for each group (same size!).
Returns
-------
pandas.Series
Results of the statistical test, including ``test statistic`` and
``p-value``.
Raises
------
TypeError
If, when using the spatial median test, the pcoa ordination is not of
type np.float32 or np.float64, the spatial median function will fail
and the centroid test should be used instead
ValueError
If the test is not centroid or median.
TypeError
If the distance matrix is not an instance of a
``skbio.DistanceMatrix``.
ValueError
If there is only one group
ValueError
If a list and a column name are both provided
ValueError
If a list is provided for `grouping` and it's length does not match
the number of ids in distance_matrix
ValueError
If all of the values in the grouping vector are unique
KeyError
If there are ids in grouping that are not in distance_matrix
See Also
--------
permanova
Notes
-----
The significance of the results from this function will be the same as the
results found in vegan's betadisper, however due to floating point
variability the F-statistic results may vary slightly.
See [1]_ for the original method reference, as well as
``vegan::betadisper``, available in R's vegan package [2]_.
References
----------
.. [1] Anderson, Marti J. "Distance-Based Tests for Homogeneity of
Multivariate Dispersions." Biometrics 62 (2006):245-253
.. [2] http://cran.r-project.org/web/packages/vegan/index.html
.. [3] M. J. Anderson, “Permutational Multivariate Analysis of Variance (PERMANOVA),”
Wiley StatsRef: Statistics Reference Online. pp. 1–15, 15-Nov-2017.
Examples
--------
Load a 6x6 distance matrix and grouping vector denoting 2 groups of
objects:
>>> from skbio import DistanceMatrix
>>> dm = DistanceMatrix([[0, 0.5, 0.75, 1, 0.66, 0.33],
... [0.5, 0, 0.25, 0.33, 0.77, 0.61],
... [0.75, 0.25, 0, 0.1, 0.44, 0.55],
... [1, 0.33, 0.1, 0, 0.75, 0.88],
... [0.66, 0.77, 0.44, 0.75, 0, 0.77],
... [0.33, 0.61, 0.55, 0.88, 0.77, 0]],
... ['s1', 's2', 's3', 's4', 's5', 's6'])
>>> grouping = ['G1', 'G1', 'G1', 'G2', 'G2', 'G2']
Run PERMDISP using 99 permutations to caluculate the p-value:
>>> from permanova_paired import permdisp
>>> import numpy as np
>>> #make output deterministic, should not be included during normal use
>>> np.random.seed(0)
>>> permdisp(dm, grouping, permutations=99)
method name PERMDISP
test statistic name F-value
sample size 6
number of groups 2
test statistic 1.03296
p-value 0.35
number of permutations 99
Name: PERMDISP results, dtype: object
The return value is a ``pandas.Series`` object containing the results of
the statistical test.
To suppress calculation of the p-value and only obtain the F statistic,
specify zero permutations:
>>> permdisp(dm, grouping, permutations=0)
method name PERMDISP
test statistic name F-value
sample size 6
number of groups 2
test statistic 1.03296
p-value NaN
number of permutations 0
Name: PERMDISP results, dtype: object
PERMDISP computes variances based on two types of tests, using either
centroids or spatial medians, also commonly referred to as a geometric
median. The spatial median is thought to yield a more robust test
statistic, and this test is used by default. Spatial medians are computed
using an iterative algorithm to find the optimally minimum point from all
other points in a group while centroids are computed using a deterministic
formula. As such the two different tests yeild slightly different F
statistics.
>>> np.random.seed(0)
>>> permdisp(dm, grouping, test='centroid', permutations=6)
method name PERMDISP
test statistic name F-value
sample size 6
number of groups 2
test statistic 3.67082
p-value 0.428571
number of permutations 6
Name: PERMDISP results, dtype: object
You can also provide a ``pandas.DataFrame`` and a column denoting the
grouping instead of a grouping vector. The following DataFrame's
Grouping column specifies the same grouping as the vector we used in the
previous examples.:
>>> import pandas as pd
>>> df = pd.DataFrame.from_dict(
... {'Grouping': {'s1': 'G1', 's2': 'G1', 's3': 'G1', 's4': 'G2',
... 's5': 'G2', 's6': 'G2'}})
>>> permdisp(dm, df, 'Grouping', permutations=6, test='centroid')
method name PERMDISP
test statistic name F-value
sample size 6
number of groups 2
test statistic 3.67082
p-value 0.428571
number of permutations 6
Name: PERMDISP results, dtype: object
Note that when providing a ``DataFrame``, the ordering of rows and/or
columns does not affect the grouping vector that is extracted. The
``DataFrame`` must be indexed by the distance matrix IDs (i.e., the row
labels must be distance matrix IDs).
If IDs (rows) are present in the ``DataFrame`` but not in the distance
matrix, they are ignored. The previous example's ``s7`` ID illustrates this
behavior: note that even though the ``DataFrame`` had 7 objects, only 6
were used in the test (see the "Sample size" row in the results above to
confirm this). Thus, the ``DataFrame`` can be a superset of the distance
matrix IDs. Note that the reverse is not true: IDs in the distance matrix
*must* be present in the ``DataFrame`` or an error will be raised.
PERMDISP should be used to determine whether the dispersions between the
groups in your distance matrix are significantly separated.
A non-significant test result indicates that group dispersions are similar
to each other. PERMANOVA or ANOSIM should then be used in conjunction to
determine whether clustering within groups is significant.
"""
if test not in ['centroid', 'median']:
raise ValueError('Test must be centroid or median')
ordination = pcoa(distance_matrix)
samples = ordination.samples
sample_size, num_groups, grouping, tri_idxs, distances = _preprocess_input(
distance_matrix, grouping, column)
# Create subjects indexing array:
subjects = _create_subjects_index_arr(subjects=subjects, grouping=grouping)
test_stat_function = partial(_compute_groups, samples, test)
stat, p_value, effect_sizes = _run_monte_carlo_stats(
test_stat_function, grouping, subjects, permutations, paired)
results = _build_results('PERMDISP', paired, 'F-value', sample_size,
num_groups, stat, p_value, effect_sizes,
permutations)
return results
def permanova(distance_matrix,
grouping,
column=None,
permutations=999,
paired=False,
subjects=None):
"""Test for significant differences between groups using PERMANOVA.
Permutational Multivariate Analysis of Variance (PERMANOVA) is a
non-parametric method that tests whether two or more groups of objects
(e.g., samples) are significantly different based on a categorical factor.
It is conceptually similar to ANOVA except that it operates on a distance
matrix, which allows for multivariate analysis. PERMANOVA computes a
pseudo-F2 statistic.
Statistical significance is assessed via a permutation test. The assignment
of objects to groups (`grouping`) is randomly permuted a number of times
(controlled via `permutations`). A pseudo-F2 statistic is computed for each
permutation and the p-value is the proportion of permuted pseudo-F2
statisics that are equal to or greater than the original (unpermuted)
pseudo-F2 statistic.
Parameters
----------
distance_matrix : DistanceMatrix
Distance matrix containing distances between objects (e.g., distances
between samples of microbial communities).
grouping : 1-D array_like or pandas.DataFrame
Vector indicating the assignment of objects to groups. For example,
these could be strings or integers denoting which group an object
belongs to. If `grouping` is 1-D ``array_like``, it must be the same
length and in the same order as the objects in `distance_matrix`. If
`grouping` is a ``DataFrame``, the column specified by `column` will be
used as the grouping vector. The ``DataFrame`` must be indexed by the
IDs in `distance_matrix` (i.e., the row labels must be distance matrix
IDs), but the order of IDs between `distance_matrix` and the
``DataFrame`` need not be the same. All IDs in the distance matrix must
be present in the ``DataFrame``. Extra IDs in the ``DataFrame`` are
allowed (they are ignored in the calculations).
column : str, optional
Column name to use as the grouping vector if `grouping` is a
``DataFrame``. Must be provided if `grouping` is a ``DataFrame``.
Cannot be provided if `grouping` is 1-D ``array_like``.
permutations : int, optional
Number of permutations to use when assessing statistical
significance. Must be greater than or equal to zero. If zero,
statistical significance calculations will be skipped and the p-value
will be ``np.nan``.
paired : bool, optional
If True: limit the type of permutations, such that permutations happen
only over groups, not over samples. SSwithin is then estimated and
subtracted from the SS between when estimating F_pseudo.
:subjects: 1-D array_like with indices for subjects for use in paired permanova.
If None: array (0...ni) will be generated for each group (same size!).
Returns
-------
pandas.Series
Results of the statistical test, including ``test statistic`` and
``p-value``.
Notes
-----
See [1]_ for the original method reference, as well as ``vegan::adonis``,
available in R's vegan package [2]_.
The p-value will be ``np.nan`` if `permutations` is zero.
Is based on and uses the skbio package (install manually: pip install skbio).
Based on code for permanova and permdisp, but extended for repeated measures or paired data.
Uses pseudo-F2 (instead of more biased pseudo-F1 in original code)
References
----------
.. [1] Anderson, Marti J. "A new method for non-parametric multivariate
analysis of variance." Austral Ecology 26.1 (2001): 32-46.
.. [2] http://cran.r-project.org/web/packages/vegan/index.html
.. [3] M. J. Anderson, “Permutational Multivariate Analysis of Variance (PERMANOVA),”
Wiley StatsRef: Statistics Reference Online. pp. 1–15, 15-Nov-2017.
Examples
--------
See :mod:`skbio.stats.distance.anosim` for usage examples (both functions
provide similar interfaces).
"""
sample_size, num_groups, grouping, tri_idxs, distances = _preprocess_input(
distance_matrix, grouping, column)
# Create subjects indexing array:
subjects = _create_subjects_index_arr(subjects=subjects, grouping=grouping)
# Calculate number of objects in each group.
group_sizes = np.bincount(grouping)
s_T = (distances**2).sum() / sample_size
test_stat_function = partial(_compute_f_stat, sample_size, num_groups,
tri_idxs, distances, group_sizes, s_T)
stat, p_value, effect_sizes = _run_monte_carlo_stats(
test_stat_function, grouping, subjects, permutations, paired)
results = _build_results('PERMANOVA', paired, 'pseudo-F2', sample_size,
num_groups, stat, p_value, effect_sizes,
permutations)
#stats_dict = {'method': 'PERMANOVA', 'paired': paired, 'statistic name':'pseudo-F','sample_size':sample_size,'num_groups':num_groups,'statistic value':stat,'p-value':p_value, 'effect_sizes':effect_sizes, 'permutations':permutations,'result string': results}
return results
def test_preprocess_input_raises_error(self):
# Requires a DistanceMatrix.
with self.assertRaises(TypeError):
_preprocess_input(
DissimilarityMatrix([[0, 2], [3, 0]], ['a', 'b']), [1, 2],
None)
# Requires column if DataFrame.
with self.assertRaises(ValueError):
_preprocess_input(self.dm, self.df, None)
# Cannot provide column if not data frame.
with self.assertRaises(ValueError):
_preprocess_input(self.dm, self.grouping, 'Group')
# Column must exist in data frame.
with self.assertRaises(ValueError):
_preprocess_input(self.dm, self.df, 'foo')
# All distance matrix IDs must be in data frame.
with self.assertRaises(ValueError):
_preprocess_input(self.dm, self.df_missing_id, 'Group')
# Grouping vector length must match number of objects in dm.
with self.assertRaises(ValueError):
_preprocess_input(self.dm, [1, 2], None)
# Grouping vector cannot have only unique values.
with self.assertRaises(ValueError):
_preprocess_input(self.dm, [1, 2, 3], None)
# Grouping vector cannot have only a single group.
with self.assertRaises(ValueError):
_preprocess_input(self.dm, [1, 1, 1], None)
