skbio.stats.composition.dirmult_lme#

skbio.stats.composition.dirmult_lme(table, metadata, formula, grouping=None, pseudocount=0.5, draws=128, p_adjust='holm', seed=None, re_formula=None, vc_formula=None, model_kwargs={}, fit_method=None, fit_warnings=False, fit_kwargs={})[source]#

Fit a Dirichlet-multinomial linear mixed effects model.

The Dirichlet-multinomial distribution is a compound distribution that combines a Dirichlet distribution over the probabilities of a multinomial distribution. This distribution is used to model the distribution of species abundances in a community.

To fit the linear mixed effect model we first fit a Dirichlet-multinomial distribution for each sample, and then we compute the fold change and p-value for each feature. The fold change is computed as the slopes from the resulting model. Statistical tests are then performed on the posterior samples, drawn from each Dirichlet-multinomial distribution. The log-fold changes as well as their credible intervals, the p-values and the multiple comparison corrected p-values are reported.

This function uses the MixedLM class from statsmodels.

Parameters:

tablearray-like: The data for the model. If data is a pd.DataFrame, it must contain the dependent variables in data.columns. If data is not a pd.DataFrame, it must contain the dependent variable in indices of data. data can be a a numpy structured array, or a numpy recarray, or a dictionary. It must not contain duplicate indices.
metadata: array-like: The metadata for the model. If metadata is a pd.DataFrame, it must contain the covariates in metadata.columns. If metadata is not a pd.DataFrame, it must contain the covariates in indices of metadata. metadata can be a numpy structured array, or a numpy recarray, or a dictionary. It must not contain duplicate indices.
formulastr or generic Formula object: The formula specifying the model.
groupingstr: The column name in data that identifies the grouping variable.
pseudocountfloat, optional: A non-zero value added to the input counts to ensure that all of the estimated abundances are strictly greater than zero. Default is 0.5.
drawsint, optional: The number of draws from the Dirichilet-multinomial posterior distribution. Default is 128.
p_adjuststr or None, optional: Method to correct p-values for multiple comparisons. Options are Holm- Boniferroni (“holm” or “holm-bonferroni”) (default), Benjamini- Hochberg (“bh”, “fdr_bh” or “benjamini-hochberg”), or any method supported by statsmodels’ multipletests function. Case-insensitive. If None, no correction will be performed.
seedint, Generator or RandomState, optional: A user-provided random seed or random generator instance for drawing from the Dirichlet distribution. See details.
re_formulastr, optional: Random coefficient formula. See MixedLM.from_formula.
vc_formulastr, optional: Variance component formula. See MixedLM.from_formula.
model_kwargsdict, optional: Additional keyword arguments to pass to MixedLM.from_formula
fit_methodstr or list of str, optional: Optimization method for model fitting. Can be a single method name, or a list of method names to be tried sequentially. See statsmodels.optimization for available methods. If None, a default list of methods will be tried.
fit_warningsbool, optional: Issue warnings if any during the model fitting process. Default is False. Warnings are usually issued when the optimization methods do not converge, which is common in the analysis.
fit_kwargsdict, optional: Additional keyword arguments to pass to MixedLM.fit.

Returns:

pd.DataFrame

A table of features, their log-fold changes and other relevant statistics.

FeatureID is the feature identifier, ie: dependent variables

Covariate is the covariate name, ie: independent variables

Log2(FC) is the expected log2-fold change. The reported Log2(FC) is the average of all of the log2-fold changes computed from each of the posterior draws.

CI(2.5) is the 2.5% quantile of the log2-fold change. The reported CI(2.5) is the average of the 2.5% quantile of all of the log2-fold changes computed from each of the posterior draws.

CI(97.5) is the 97.5% quantile of the log2-fold change. The reported CI(97.5) is the average of the 97.5% quantile of all of the log2-fold changes computed from each of the posterior draws.

pvalue is the p-value of the linear mixed effects model. The reported values are the average of all of the p-values computed from the linear mixed effects models calculated across all of the posterior draws.

qvalue is the corrected p-value of the linear mixed effects model for multiple comparisons. The reported values are the average of all of the q-values computed from the linear mixed effects models calculated across all of the posterior draws.

See also

dirmult_ttest
statsmodels.formula.api.mixedlm
statsmodels.regression.mixed_linear_model.MixedLM

Examples

>>> import pandas as pd
>>> from skbio.stats.composition import dirmult_lme
>>> table = pd.DataFrame(
...     [[1.00000053, 6.09924644],
...      [0.99999843, 7.0000045],
...      [1.09999884, 8.08474053],
...      [1.09999758, 1.10000349],
...      [0.99999902, 2.00000027],
...      [1.09999862, 2.99998318],
...      [1.00000084, 2.10001257],
...      [0.9999991, 3.09998418],
...      [0.99999899, 3.9999742],
...      [1.10000124, 5.0001796],
...      [1.00000053, 6.09924644],
...      [1.10000173, 6.99693644]],
...     index=['u1', 'u2', 'u3', 'x1', 'x2', 'x3', 'y1', 'y2', 'y3', 'z1',
...            'z2', 'z3'],
...     columns=['Y1', 'Y2'])
>>> metadata = pd.DataFrame(
...     {'patient': [1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4],
...      'treatment': [1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2],
...      'time': [1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3],},
...     index=['x1', 'x2', 'x3', 'y1', 'y2', 'y3', 'z1', 'z2', 'z3', 'u1',
...            'u2', 'u3'])
>>> result = dirmult_lme(table, metadata, formula='time + treatment',
...                      grouping='patient', seed=0, p_adjust='sidak')
>>> result
  FeatureID  Covariate  Log2(FC)   CI(2.5)  CI(97.5)    pvalue    qvalue
0        Y1       time -0.210769 -1.571095  1.144057  0.411140  0.879760
1        Y1  treatment -0.164704 -3.456697  3.384563  0.593769  0.972767
2        Y2       time  0.210769 -1.144057  1.571095  0.411140  0.879760
3        Y2  treatment  0.164704 -3.384563  3.456697  0.593769  0.972767