.. currentmodule:: statsmodels.regression.mixed_linear_model

.. _mixedlmmod:

Linear Mixed Effects Models
===========================

Linear Mixed Effects models are used for regression analyses involving
dependent data.  Such data arise when working with longitudinal and
other study designs in which multiple observations are made on each
subject.  Some specific linear mixed effects models are

* *Random intercepts models*, where all responses in a group are
  additively shifted by a value that is specific to the group.

* *Random slopes models*, where the responses in a group follow a
  (conditional) mean trajectory that is linear in the observed
  covariates, with the slopes (and possibly intercepts) varying by
  group.

* *Variance components models*, where the levels of one or more
  categorical covariates are associated with draws from distributions.
  These random terms additively determine the conditional mean of each
  observation based on its covariate values.

The statsmodels implementation of LME is primarily group-based,
meaning that random effects must be independently-realized for
responses in different groups.  There are two types of random effects
in our implementation of mixed models: (i) random coefficients
(possibly vectors) that have an unknown covariance matrix, and (ii)
random coefficients that are independent draws from a common
univariate distribution.  For both (i) and (ii), the random effects
influence the conditional mean of a group through their matrix/vector
product with a group-specific design matrix.

A simple example of random coefficients, as in (i) above, is:

.. math::

   Y_{ij} = \beta_0 + \beta_1X_{ij} + \gamma_{0i} + \gamma_{1i}X_{ij} + \epsilon_{ij}

Here, :math:`Y_{ij}` is the :math:`j^\rm{th}` measured response for subject
:math:`i`, and :math:`X_{ij}` is a covariate for this response.  The
"fixed effects parameters" :math:`\beta_0` and :math:`\beta_1` are
shared by all subjects, and the errors :math:`\epsilon_{ij}` are
independent of everything else, and identically distributed (with mean
zero).  The "random effects parameters" :math:`\gamma_{0i}` and
:math:`\gamma_{1i}` follow a bivariate distribution with mean zero,
described by three parameters: :math:`{\rm var}(\gamma_{0i})`,
:math:`{\rm var}(\gamma_{1i})`, and :math:`{\rm cov}(\gamma_{0i},
\gamma_{1i})`.  There is also a parameter for :math:`{\rm
var}(\epsilon_{ij})`.

A simple example of variance components, as in (ii) above, is:

.. math::

   Y_{ijk} = \beta_0 + \eta_{1i} + \eta_{2j} + \epsilon_{ijk}

Here, :math:`Y_{ijk}` is the :math:`k^\rm{th}` measured response under
conditions :math:`i, j`.  The only "mean structure parameter" is
:math:`\beta_0`.  The :math:`\eta_{1i}` are independent and
identically distributed with zero mean, and variance :math:`\tau_1^2`,
and the :math:`\eta_{2j}` are independent and identically distributed
with zero mean, and variance :math:`\tau_2^2`.

statsmodels MixedLM handles most non-crossed random effects models,
and some crossed models.  To include crossed random effects in a
model, it is necessary to treat the entire dataset as a single group.
The variance components arguments to the model can then be used to
define models with various combinations of crossed and non-crossed
random effects.

The statsmodels LME framework currently supports post-estimation
inference via Wald tests and confidence intervals on the coefficients,
profile likelihood analysis, likelihood ratio testing, and AIC.

Examples
--------

.. ipython:: python

  import statsmodels.api as sm
  import statsmodels.formula.api as smf

  data = sm.datasets.get_rdataset("dietox", "geepack", cache=True).data

  md = smf.mixedlm("Weight ~ Time", data, groups=data["Pig"])
  mdf = md.fit()
  print(mdf.summary())

Detailed examples can be found here

* `Mixed LM <examples/notebooks/generated/mixed_lm_example.ipynb>`_

There are some notebook examples on the Wiki:
`Wiki notebooks for MixedLM <https://github.com/statsmodels/statsmodels/wiki/Examples#linear-mixed-models>`_



Technical Documentation
-----------------------

The data are partitioned into disjoint groups.
The probability model for group :math:`i` is:

.. math::

    Y = X\beta + Z\gamma + Q_1\eta_1 + \cdots + Q_k\eta_k + \epsilon

where

* :math:`n_i` is the number of observations in group :math:`i`
* :math:`Y` is a :math:`n_i` dimensional response vector
* :math:`X` is a :math:`n_i * k_{fe}` dimensional matrix of fixed effects
  coefficients
* :math:`\beta` is a :math:`k_{fe}`-dimensional vector of fixed effects slopes
* :math:`Z` is a :math:`n_i * k_{re}` dimensional matrix of random effects
  coefficients
* :math:`\gamma` is a :math:`k_{re}`-dimensional random vector with mean 0
  and covariance matrix :math:`\Psi`; note that each group
  gets its own independent realization of gamma.
* :math:`Q_j` is a :math:`n_i \times q_j` dimensional design matrix for the
  :math:`j^\rm{th}` variance component.
* :math:`\eta_j` is a :math:`q_j`-dimensional random vector containing independent
  and identically distributed values with variance :math:`\tau_j^2`.
* :math:`\epsilon` is a :math:`n_i` dimensional vector of i.i.d normal
  errors with mean 0 and variance :math:`\sigma^2`; the :math:`\epsilon`
  values are independent both within and between groups

:math:`Y, X, \{Q_j\}` and :math:`Z` must be entirely observed.  :math:`\beta`,
:math:`\Psi`, and :math:`\sigma^2` are estimated using ML or REML estimation,
and :math:`\gamma`, :math:`\{\eta_j\}` and :math:`\epsilon` are
random so define the probability model.

The marginal mean structure is :math:`E[Y|X,Z] = X*\beta`.  If only
the marginal mean structure is of interest, GEE is a good alternative
to mixed models.

Notation:

* :math:`cov_{re}` is the random effects covariance matrix (referred
  to above as :math:`\Psi`) and :math:`scale` is the (scalar) error
  variance.  There is also a single estimated variance parameter
  :math:`\tau_j^2` for each variance component.  For a single group,
  the marginal covariance matrix of endog given exog is
  :math:`scale*I + Z * cov_{re} * Z`, where :math:`Z` is the design
  matrix for the random effects in one group.

References
^^^^^^^^^^

The primary reference for the implementation details is:

*   MJ Lindstrom, DM Bates (1988).  *Newton Raphson and EM algorithms for
    linear mixed effects models for repeated measures data*.  Journal of
    the American Statistical Association. Volume 83, Issue 404, pages 1014-1022.

See also this more recent document:

* http://econ.ucsb.edu/~doug/245a/Papers/Mixed%20Effects%20Implement.pdf

All the likelihood, gradient, and Hessian calculations closely follow
Lindstrom and Bates.

The following two documents are written more from the perspective of
users:

* https://r-forge.r-project.org/scm/viewvc.php/*checkout*/www/lMMwR/lrgprt.pdf?revision=949&root=lme4&pathrev=1781

* http://lme4.r-forge.r-project.org/slides/2009-07-07-Rennes/3Longitudinal-4.pdf

.. Class hierarchy: TODO

   General references for this class of models are

Module Reference
----------------

.. module:: statsmodels.regression.mixed_linear_model
   :synopsis: Mixed Linear Models


The model class is:

.. autosummary::
   :toctree: generated/

   MixedLM

The result class is:

.. autosummary::
   :toctree: generated/

   MixedLMResults
