lme.lmList {nlme} | R Documentation

## LME fit from lmList Object

### Description

If the random effects names defined in `random` are a subset of the `lmList` object coefficient names, initial estimates for the covariance matrix of the random effects are obtained (overwriting any values given in `random`). `formula(fixed)` and the `data` argument in the calling sequence used to obtain `fixed` are passed as the `fixed` and `data` arguments to `lme.formula`, together with any other additional arguments in the function call. See the documentation on `lme.formula` for a description of that function.

### Usage

    ## S3 method for class 'lmList':
    lme(fixed, data, random, correlation, weights, subset, method,
        na.action, control, contrasts)

### Arguments

`fixed` | an object inheriting from class `lmList`, representing a list of `lm` fits with a common model.
`data` | this argument is included for consistency with the generic function. It is ignored in this method function.
`random` | an optional one-sided linear formula with no conditioning expression, or a `pdMat` object with a `formula` attribute. Multiple levels of grouping are not allowed with this method function. Defaults to a formula consisting of the right hand side of `formula(fixed)`.
`correlation` | an optional `corStruct` object describing the within-group correlation structure. See the documentation of `corClasses` for a description of the available `corStruct` classes. Defaults to `NULL`, corresponding to no within-group correlations.
`weights` | an optional `varFunc` object or one-sided formula describing the within-group heteroscedasticity structure. If given as a formula, it is used as the argument to `varFixed`, corresponding to fixed variance weights. See the documentation on `varClasses` for a description of the available `varFunc` classes. Defaults to `NULL`, corresponding to homocesdatic within-group errors.
`subset` | an optional expression indicating the subset of the rows of `data` that should be used in the fit. This can be a logical vector, or a numeric vector indicating which observation numbers are to be included, or a character vector of the row names to be included. All observations are included by default.
`method` | a character string. If `"REML"` the model is fit by maximizing the restricted log-likelihood. If `"ML"` the log-likelihood is maximized. Defaults to `"REML"`.
`na.action` | a function that indicates what should happen when the data contain `NA`s. The default action (`na.fail`) causes `lme` to print an error message and terminate if there are any incomplete observations.
`control` | a list of control values for the estimation algorithm to replace the default values returned by the function `lmeControl`. Defaults to an empty list.
`contrasts` | an optional list. See the `contrasts.arg` of `model.matrix.default`.

### Value

an object of class `lme` representing the linear mixed-effects model fit. Generic functions such as `print`, `plot` and `summary` have methods to show the results of the fit. See `lmeObject` for the components of the fit. The functions `resid`, `coef`, `fitted`, `fixed.effects`, and `random.effects` can be used to extract some of its components.

### Author(s)

Jose Pinheiro Jose.Pinheiro@pharma.novartis.com and Douglas Bates bates@stat.wisc.edu

### References

The computational methods are described in Bates, D.M. and Pinheiro (1998) and follow on the general framework of Lindstrom, M.J. and Bates, D.M. (1988). The model formulation is described in Laird, N.M. and Ware, J.H. (1982). The variance-covariance parametrizations are described in <Pinheiro, J.C. and Bates., D.M. (1996). The different correlation structures available for the `correlation` argument are described in Box, G.E.P., Jenkins, G.M., and Reinsel G.C. (1994), Littel, R.C., Milliken, G.A., Stroup, W.W., and Wolfinger, R.D. (1996), and Venables, W.N. and Ripley, B.D. (1997). The use of variance functions for linear and nonlinear mixed effects models is presented in detail in Davidian, M. and Giltinan, D.M. (1995).

Bates, D.M. and Pinheiro, J.C. (1998) "Computational methods for multilevel models" available in PostScript or PDF formats at http://franz.stat.wisc.edu/pub/NLME/

Box, G.E.P., Jenkins, G.M., and Reinsel G.C. (1994) "Time Series Analysis: Forecasting and Control", 3rd Edition, Holden-Day.

Davidian, M. and Giltinan, D.M. (1995) "Nonlinear Mixed Effects Models for Repeated Measurement Data", Chapman and Hall.

Laird, N.M. and Ware, J.H. (1982) "Random-Effects Models for Longitudinal Data", Biometrics, 38, 963-974.

Lindstrom, M.J. and Bates, D.M. (1988) "Newton-Raphson and EM Algorithms for Linear Mixed-Effects Models for Repeated-Measures Data", Journal of the American Statistical Association, 83, 1014-1022.

Littel, R.C., Milliken, G.A., Stroup, W.W., and Wolfinger, R.D. (1996) "SAS Systems for Mixed Models", SAS Institute.

Pinheiro, J.C. and Bates., D.M. (1996) "Unconstrained Parametrizations for Variance-Covariance Matrices", Statistics and Computing, 6, 289-296.

Venables, W.N. and Ripley, B.D. (1997) "Modern Applied Statistics with S-plus", 2nd Edition, Springer-Verlag.

### See Also

`lme`, `lmList`, `lmeObject`

### Examples

    data(Orthodont)
    fm1 <- lmList(Orthodont)
    fm2 <- lme(fm1)
    summary(fm1)
    summary(fm2)

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