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fitglme

Fit generalized linear mixed-effects model

Syntax

glme = fitglme(tbl,formula)
glme = fitglme(tbl,formula,Name,Value)

Description

example

glme = fitglme(tbl,formula) returns a generalized linear mixed-effects model, glme. The model is specified by formula and fitted to the predictor variables in the table or dataset array, tbl.

glme = fitglme(tbl,formula,Name,Value) returns a generalized linear mixed-effects model using additional options specified by one or more Name,Value pair arguments. For example, you can specify the distribution of the response, the link function, or the covariance pattern of the random-effects terms.

Examples

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Load the sample data.

load mfr

This simulated data is from a manufacturing company that operates 50 factories across the world, with each factory running a batch process to create a finished product. The company wants to decrease the number of defects in each batch, so it developed a new manufacturing process. To test the effectiveness of the new process, the company selected 20 of its factories at random to participate in an experiment: Ten factories implemented the new process, while the other ten continued to run the old process. In each of the 20 factories, the company ran five batches (for a total of 100 batches) and recorded the following data:

  • Flag to indicate whether the batch used the new process (newprocess)

  • Processing time for each batch, in hours (time)

  • Temperature of the batch, in degrees Celsius (temp)

  • Categorical variable indicating the supplier of the chemical used in the batch (supplier)

  • Number of defects in the batch (defects)

The data also includes time_dev and temp_dev, which represent the absolute deviation of time and temperature, respectively, from the process standard of 3 hours at 20 degrees Celsius.

Fit a generalized linear mixed-effects model using newprocess, time_dev, temp_dev, and supplier as fixed-effects predictors. Include a random-effects term for intercept grouped by factory, to account for quality differences that might exist due to factory-specific variations. The response variable defects has a Poisson distribution, and the appropriate link function for this model is log. Use the Laplace fit method to estimate the coefficients. Specify the dummy variable encoding as 'effects', so the dummy variable coefficients sum to 0.

The number of defects can be modeled using a Poisson distribution

defectsijPoisson(μij).

This corresponds to the generalized linear mixed-effects model

log(μij)=β0+β1newprocessij+β2time_devij+β3temp_devij+β4supplier_Cij+β5supplier_Bij+bi,

where

  • defectsij is the number of defects observed in the batch produced by factory i during batch j.

  • μij is the mean number of defects corresponding to factory i (where i=1,2,...,20) during batch j (where j=1,2,...,5).

  • newprocessij, time_devij, and temp_devij are the measurements for each variable that correspond to factory i during batch j. For example, newprocessij indicates whether the batch produced by factory i during batch j used the new process.

  • supplier_Cij and supplier_Bij are dummy variables that use effects (sum-to-zero) coding to indicate whether company C or B, respectively, supplied the process chemicals for the batch produced by factory i during batch j.

  • biN(0,σb2) is a random-effects intercept for each factory i that accounts for factory-specific variation in quality.

glme = fitglme(mfr,'defects ~ 1 + newprocess + time_dev + temp_dev + supplier + (1|factory)', ...
    'Distribution','Poisson','Link','log','FitMethod','Laplace', ...
    'DummyVarCoding','effects');

Display the model.

disp(glme)
Generalized linear mixed-effects model fit by ML

Model information:
    Number of observations             100
    Fixed effects coefficients           6
    Random effects coefficients         20
    Covariance parameters                1
    Distribution                    Poisson
    Link                            Log   
    FitMethod                       Laplace

Formula:
    defects ~ 1 + newprocess + time_dev + temp_dev + supplier + (1 | factory)

Model fit statistics:
    AIC       BIC       LogLikelihood    Deviance
    416.35    434.58    -201.17          402.35  

Fixed effects coefficients (95% CIs):
    Name                 Estimate     SE          tStat       DF    pValue    
    '(Intercept)'           1.4689     0.15988      9.1875    94    9.8194e-15
    'newprocess'          -0.36766     0.17755     -2.0708    94      0.041122
    'time_dev'           -0.094521     0.82849    -0.11409    94       0.90941
    'temp_dev'            -0.28317      0.9617    -0.29444    94       0.76907
    'supplier_C'         -0.071868    0.078024     -0.9211    94       0.35936
    'supplier_B'          0.071072     0.07739     0.91836    94       0.36078


    Lower        Upper    
       1.1515       1.7864
     -0.72019    -0.015134
      -1.7395       1.5505
      -2.1926       1.6263
     -0.22679     0.083051
    -0.082588      0.22473

Random effects covariance parameters:
Group: factory (20 Levels)
    Name1                Name2                Type         Estimate
    '(Intercept)'        '(Intercept)'        'std'        0.31381 

Group: Error
    Name                      Estimate
    'sqrt(Dispersion)'        1       

The Model information table displays the total number of observations in the sample data (100), the number of fixed- and random-effects coefficients (6 and 20, respectively), and the number of covariance parameters (1). It also indicates that the response variable has a Poisson distribution, the link function is Log, and the fit method is Laplace.

Formula indicates the model specification using Wilkinson’s notation.

The Model fit statistics table displays statistics used to assess the goodness of fit of the model. This includes the Akaike information criterion (AIC), Bayesian information criterion (BIC) values, log likelihood (LogLikelihood), and deviance (Deviance) values.

The Fixed effects coefficients table indicates that fitglme returned 95% confidence intervals. It contains one row for each fixed-effects predictor, and each column contains statistics corresponding to that predictor. Column 1 (Name) contains the name of each fixed-effects coefficient, column 2 (Estimate) contains its estimated value, and column 3 (SE) contains the standard error of the coefficient. Column 4 (tStat) contains the t-statistic for a hypothesis test that the coefficient is equal to 0. Column 5 (DF) and column 6 (pValue) contain the degrees of freedom and p-value that correspond to the t-statistic, respectively. The last two columns (Lower and Upper) display the lower and upper limits, respectively, of the 95% confidence interval for each fixed-effects coefficient.

Random effects covariance parameters displays a table for each grouping variable (here, only factory), including its total number of levels (20), and the type and estimate of the covariance parameter. Here, std indicates that fitglme returns the standard deviation of the random effect associated with the factory predictor, which has an estimated value of 0.31381. It also displays a table containing the error parameter type (here, the square root of the dispersion parameter), and its estimated value of 1.

The standard display generated by fitglme does not provide confidence intervals for the random-effects parameters. To compute and display these values, use covarianceParameters.

Input Arguments

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Input data, which includes the response variable, predictor variables, and grouping variables, specified as a table or dataset array. The predictor variables can be continuous or grouping variables (see Grouping Variables). You must specify the model for the variables using formula.

Formula for model specification, specified as a character vector or string scalar of the form 'y ~ fixed + (random1|grouping1) + ... + (randomR|groupingR)'. The formula is case sensitive. For a full description, see Formula.

Example: 'y ~ treatment + (1|block)'

Name-Value Pair Arguments

Specify optional comma-separated pairs of Name,Value arguments. Name is the argument name and Value is the corresponding value. Name must appear inside quotes. You can specify several name and value pair arguments in any order as Name1,Value1,...,NameN,ValueN.

Example: 'Distribution','Poisson','Link','log','FitMethod','Laplace','DummyVarCoding','effects' specifies the response variable distribution as Poisson, the link function as log, the fit method as Laplace, and dummy variable coding where the coefficients sum to 0.

Number of trials for binomial distribution, that is the sample size, specified as the comma-separated pair consisting of a scalar value, a vector of the same length as the response, or the name of a variable in the input table. If you specify the name of a variable, then the variable must be of the same length as the response. BinomialSize applies only when the Distribution parameter is 'binomial'.

If BinomialSize is a scalar value, that means all observations have the same number of trials.

Data Types: single | double

Indicator to check the positive definiteness of the Hessian of the objective function with respect to unconstrained parameters at convergence, specified as the comma-separated pair consisting of 'CheckHessian' and either false or true. Default is false.

Specify 'CheckHessian' as true to verify optimality of the solution or to determine if the model is overparameterized in the number of covariance parameters.

If you specify 'FitMethod' as 'MPL' or 'REMPL', then the covariance of the fixed effects and the covariance parameters is based on the fitted linear mixed-effects model from the final pseudo likelihood iteration.

Example: 'CheckHessian',true

Method to compute covariance of estimated parameters, specified as the comma-separated pair consisting of 'CovarianceMethod' and either 'conditional' or 'JointHessian'. If you specify 'conditional', then fitglme computes a fast approximation to the covariance of fixed effects given the estimated covariance parameters. It does not compute the covariance of covariance parameters. If you specify 'JointHessian', then fitglme computes the joint covariance of fixed effects and covariance parameters via the observed information matrix using the Laplacian loglikelihood.

If you specify 'FitMethod' as 'MPL' or 'REMPL', then the covariance of the fixed effects and the covariance parameters is based on the fitted linear mixed-effects model from the final pseudo likelihood iteration.

Example: 'CovarianceMethod','JointHessian'

Pattern of the covariance matrix of the random effects, specified as the comma-separated pair consisting of 'CovariancePattern' and 'FullCholesky', 'Isotropic', 'Full', 'Diagonal', 'CompSymm', a square symmetric logical matrix, a string array, or a cell array containing character vectors or logical matrices.

If there are R random-effects terms, then the value of 'CovariancePattern' must be a string array or cell array of length R, where each element r of the array specifies the pattern of the covariance matrix of the random-effects vector associated with the rth random-effects term. The options for each element follow.

ValueDescription
'FullCholesky'Full covariance matrix using the Cholesky parameterization. fitglme estimates all elements of the covariance matrix.
'Isotropic'

Diagonal covariance matrix with equal variances. That is, off-diagonal elements of the covariance matrix are constrained to be 0, and the diagonal elements are constrained to be equal. For example, if there are three random-effects terms with an isotropic covariance structure, this covariance matrix looks like

(σb2000σb2000σb2)

where σ21 is the common variance of the random-effects terms.

'Full'Full covariance matrix, using the log-Cholesky parameterization. fitlme estimates all elements of the covariance matrix.
'Diagonal'

Diagonal covariance matrix. That is, off-diagonal elements of the covariance matrix are constrained to be 0.

(σb12000σb22000σb32)

'CompSymm'

Compound symmetry structure. That is, common variance along diagonals and equal correlation between all random effects. For example, if there are three random-effects terms with a covariance matrix having a compound symmetry structure, this covariance matrix looks like

(σb12σb1,b2σb1,b2σb1,b2σb12σb1,b2σb1,b2σb1,b2σb12)

where σ2b1 is the common variance of the random-effects terms and σb1,b2 is the common covariance between any two random-effects term .

PATSquare symmetric logical matrix. If 'CovariancePattern' is defined by the matrix PAT, and if PAT(a,b) = false, then the (a,b) element of the corresponding covariance matrix is constrained to be 0.

For scalar random-effects terms, the default is 'Isotropic'. Otherwise, the default is 'FullCholesky'.

Example: 'CovariancePattern','Diagonal'

Example: 'CovariancePattern',{'Full','Diagonal'}

Data Types: char | string | logical | cell

Indicator to compute dispersion parameter for 'binomial' and 'poisson' distributions, specified as the comma-separated pair consisting of 'DispersionFlag' and one of the following.

ValueDescription
trueEstimate a dispersion parameter when computing standard errors
falseUse the theoretical value of 1.0 when computing standard errors

'DispersionFlag' only applies if 'FitMethod' is 'MPL' or 'REMPL'.

The fitting function always estimates the dispersion for other distributions.

Example: 'DispersionFlag',true

Distribution of the response variable, specified as the comma-separated pair consisting of 'Distribution' and one of the following.

ValueDescription
'Normal'Normal distribution
'Binomial'Binomial distribution
'Poisson'Poisson distribution
'Gamma'Gamma distribution
'InverseGaussian'Inverse Gaussian distribution

Example: 'Distribution','Binomial'

Coding to use for dummy variables created from the categorical variables, specified as the comma-separated pair consisting of 'DummyVarCoding' and one of the following.

ValueDescription
'reference'Default. Coefficient for first category set to 0.
'effects'Coefficients sum to 0.
'full'One dummy variable for each category.

Example: 'DummyVarCoding','effects'

Method used to approximate empirical Bayes estimates of random effects, specified as the comma-separated pair consisting of 'EBMethod' and one of the following.

  • 'Auto'

  • 'LineSearchNewton'

  • 'TrustRegion2D'

  • 'fsolve'

'Auto' is similar to 'LineSearchNewton' but uses a different convergence criterion and does not display iterative progress. 'Auto' and 'LineSearchNewton' may fail for non-canonical link functions. For non-canonical link functions, 'TrustRegion2D' or 'fsolve' are recommended. You must have Optimization Toolbox™ to use 'fsolve'.

Example: 'EBMethod','LineSearchNewton'

Options for empirical Bayes optimization, specified as the comma-separated pair consisting of 'EBOptions' and a structure containing the following.

ValueDescription
'TolFun'Relative tolerance on the gradient norm. Default is 1e-6.
'TolX'Absolute tolerance on the step size. Default is 1e-8.
'MaxIter'Maximum number of iterations. Default is 100.
'Display''off', 'iter', or 'final'. Default is 'off'.

If EBMethod is 'Auto' and 'FitMethod' is 'Laplace', TolFun is the relative tolerance on the linear predictor of the model, and the 'Display' option does not apply.

If 'EBMethod' is 'fsolve', then 'EBOptions' must be specified as an object created by optimoptions('fsolve').

Data Types: struct

Indices for rows to exclude from the generalized linear mixed-effects model in the data, specified as the comma-separated pair consisting of 'Exclude' and a vector of integer or logical values.

For example, you can exclude the 13th and 67th rows from the fit as follows.

Example: 'Exclude',[13,67]

Data Types: single | double | logical

Method for estimating model parameters, specified as the comma-separated pair consisting of 'FitMethod' and one of the following.

  • 'MPL' — Maximum pseudo likelihood

  • 'REMPL' — Restricted maximum pseudo likelihood

  • 'Laplace' — Maximum likelihood using Laplace approximation

  • 'ApproximateLaplace' — Maximum likelihood using approximate Laplace approximation with fixed effects profiled out

Example: 'FitMethod','REMPL'

Initial number of pseudo likelihood iterations used to initialize parameters for ApproximateLaplace and Laplace fit methods, specified as the comma-separated pair consisting of 'InitPLIterations' and an integer value greater than or equal to 1.

Data Types: single | double

Starting value for conditional mean, specified as the comma-separated pair consisting of 'MuStart' and a scalar value. Valid values are as follows.

Response DistributionValid Values
'Normal'(-Inf,Inf)
'Binomial'(0,1)
'Poisson'(0,Inf)
'Gamma'(0,Inf)
'InverseGaussian'(0,Inf)

Data Types: single | double

Offset, specified as the comma-separated pair consisting of 'Offset' and an n-by-1 vector of scalar values, where n is the length of the response vector. You can also specify the variable name of an n-by-1 vector of scalar values. 'Offset' is used as an additional predictor that has a coefficient value fixed at 1.0.

Data Types: single | double

Optimization algorithm, specified as the comma-separated pair consisting of 'Optimizer' and either of the following.

ValueDescription
'quasinewton'Uses a trust region based quasi-Newton optimizer. You can change the options of the algorithm using statset('fitglme'). If you do not specify the options, then fitglme uses the default options of statset('fitglme').
'fminsearch'Uses a derivative-free Nelder-Mead method. You can change the options of the algorithm using optimset('fminsearch'). If you do not specify the options, then fitglme uses the default options of optimset('fminsearch').
'fminunc'Uses a line search-based quasi-Newton method. You must have Optimization Toolbox to specify this option. You can change the options of the algorithm using optimoptions('fminunc'). If you do not specify the options, then fitglme uses the default options of optimoptions('fminunc') with 'Algorithm' set to 'quasi-newton'.

Example: 'Optimizer','fminsearch'

Options for the optimization algorithm, specified as the comma-separated pair consisting of 'OptimizerOptions' and a structure returned by statset('fitglme'), a structure created by optimset('fminsearch'), or an object returned by optimoptions('fminunc').

  • If 'Optimizer' is 'fminsearch', then use optimset('fminsearch') to change the options of the algorithm. If 'Optimizer' is 'fminsearch' and you do not supply 'OptimizerOptions', then the defaults used in fitglme are the default options created by optimset('fminsearch').

  • If 'Optimizer' is 'fminunc', then use optimoptions('fminunc') to change the options of the optimization algorithm. See optimoptions for the options 'fminunc' uses. If 'Optimizer' is 'fminunc' and you do not supply 'OptimizerOptions', then the defaults used in fitglme are the default options created by optimoptions('fminunc') with 'Algorithm' set to 'quasi-newton'.

  • If 'Optimizer' is 'quasinewton', then use statset('fitglme') to change the optimization parameters. If 'Optimizer' is 'quasinewton' and you do not change the optimization parameters using statset, then fitglme uses the default options created by statset('fitglme').

The 'quasinewton' optimizer uses the following fields in the structure created by statset('fitglme').

Relative tolerance on the gradient of the objective function, specified as a positive scalar value.

Absolute tolerance on the step size, specified as a positive scalar value.

Maximum number of iterations allowed, specified as a positive scalar value.

Level of display, specified as one of 'off', 'iter', or 'final'.

Maximum number of pseudo likelihood (PL) iterations, specified as the comma-separated pair consisting of 'PLIterations' and a positive integer value. PL is used for fitting the model if 'FitMethod' is 'MPL' or 'REMPL'. For other 'FitMethod' values, PL iterations are used to initialize parameters for subsequent optimization.

Example: 'PLIterations',200

Data Types: single | double

Relative tolerance factor for pseudo likelihood iterations, specified as the comma-separated pair consisting of 'PLTolerance' and a positive scalar value.

Example: 'PLTolerance',1e-06

Data Types: single | double

Method to start iterative optimization, specified as the comma-separated pair consisting of 'StartMethod' and either of the following.

ValueDescription
'default'An internally defined default value
'random'A random initial value

Example: 'StartMethod','random'

, specified as the comma-separated pair consisting of 'UseSequentialFitting' and either false or true. If 'UseSequentialFitting' is false, all maximum likelihood methods are initialized using one or more pseudo likelihood iterations. If 'UseSequentialFitting' is true, the initial values from pseudo likelihood iterations are refined using 'ApproximateLaplace' for 'Laplace' fitting.

Example: 'UseSequentialFitting',true

Indicator to display the optimization process on screen, specified as the comma-separated pair consisting of 'Verbose' and 0, 1, or 2. If 'Verbose' is specified as 1 or 2, then fitglme displays the progress of the iterative model-fitting process. Specifying 'Verbose' as 2 displays iterative optimization information from the individual pseudo likelihood iterations. Specifying 'Verbose' as 1 omits this display.

The setting for 'Verbose' overrides the field 'Display' in 'OptimizerOptions'.

Example: 'Verbose',1

Observation weights, specified as the comma-separated pair consisting of 'Weights' and an n-by-1 vector of nonnegative scalar values, where n is the number of observations. If the response distribution is binomial or Poisson, then 'Weights' must be a vector of positive integers.

Data Types: single | double

Output Arguments

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Generalized linear mixed-effects model, specified as a GeneralizedLinearMixedModel object. For properties and methods of this object, see GeneralizedLinearMixedModel.

More About

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Formula

In general, a formula for model specification is a character vector or string scalar of the form 'y ~ terms'. For the generalized linear mixed-effects models, this formula is in the form 'y ~ fixed + (random1|grouping1) + ... + (randomR|groupingR)', where fixed and random contain the fixed-effects and the random-effects terms.

Suppose a table tbl contains the following:

  • A response variable, y

  • Predictor variables, Xj, which can be continuous or grouping variables

  • Grouping variables, g1, g2, ..., gR,

where the grouping variables in Xj and gr can be categorical, logical, character arrays, string arrays, or cell arrays of character vectors.

Then, in a formula of the form, 'y ~ fixed + (random1|g1) + ... + (randomR|gR)', the term fixed corresponds to a specification of the fixed-effects design matrix X, random1 is a specification of the random-effects design matrix Z1 corresponding to grouping variable g1, and similarly randomR is a specification of the random-effects design matrix ZR corresponding to grouping variable gR. You can express the fixed and random terms using Wilkinson notation.

Wilkinson notation describes the factors present in models. The notation relates to factors present in models, not to the multipliers (coefficients) of those factors.

Wilkinson NotationFactors in Standard Notation
1Constant (intercept) term
X^k, where k is a positive integerX, X2, ..., Xk
X1 + X2X1, X2
X1*X2X1, X2, X1.*X2 (elementwise multiplication of X1 and X2)
X1:X2X1.*X2 only
- X2Do not include X2
X1*X2 + X3X1, X2, X3, X1*X2
X1 + X2 + X3 + X1:X2X1, X2, X3, X1*X2
X1*X2*X3 - X1:X2:X3X1, X2, X3, X1*X2, X1*X3, X2*X3
X1*(X2 + X3)X1, X2, X3, X1*X2, X1*X3

Statistics and Machine Learning Toolbox™ notation always includes a constant term unless you explicitly remove the term using -1. Here are some examples for generalized linear mixed-effects model specification.

Examples:

FormulaDescription
'y ~ X1 + X2'Fixed effects for the intercept, X1 and X2. This is equivalent to 'y ~ 1 + X1 + X2'.
'y ~ -1 + X1 + X2'No intercept and fixed effects for X1 and X2. The implicit intercept term is suppressed by including -1.
'y ~ 1 + (1 | g1)'Fixed effects for the intercept plus random effect for the intercept for each level of the grouping variable g1.
'y ~ X1 + (1 | g1)'Random intercept model with a fixed slope.
'y ~ X1 + (X1 | g1)'Random intercept and slope, with possible correlation between them. This is equivalent to 'y ~ 1 + X1 + (1 + X1|g1)'.
'y ~ X1 + (1 | g1) + (-1 + X1 | g1)' Independent random effects terms for intercept and slope.
'y ~ 1 + (1 | g1) + (1 | g2) + (1 | g1:g2)'Random intercept model with independent main effects for g1 and g2, plus an independent interaction effect.

Introduced in R2014b