lmer.h File Reference

#include "Mutils.h"
#include "triplet_to_col.h"
#include "dgBCMatrix.h"
#include "bCrosstab.h"
#include <R_ext/Lapack.h>
#include <R_ext/Constants.h>

Go to the source code of this file.

Functions
SEXP	lmer_validate (SEXP x)
SEXP	lmer_update_mm (SEXP x, SEXP mmats)
SEXP	lmer_create (SEXP flist, SEXP mmats)
SEXP	lmer_inflate (SEXP x)
SEXP	lmer_initial (SEXP x)
SEXP	lmer_factor (SEXP x)
SEXP	lmer_invert (SEXP x)
SEXP	lmer_sigma (SEXP x, SEXP REML)
SEXP	lmer_coef (SEXP x, SEXP Unc)
SEXP	lmer_coefGets (SEXP x, SEXP coef, SEXP Unc)
SEXP	lmer_fixef (SEXP x)
SEXP	lmer_ranef (SEXP x)
SEXP	lmer_ECMEsteps (SEXP x, SEXP nsteps, SEXP REMLp, SEXP Verbp)
SEXP	lmer_gradient (SEXP x, SEXP REMLp, SEXP Uncp)
SEXP	lmer_variances (SEXP x)
SEXP	lmer_Crosstab (SEXP flist)
SEXP	lmer_firstDer (SEXP x, SEXP val)

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Function Documentation

SEXP lmer_coef (  SEXP  x, SEXP  Unc )

Extract the upper triangles of the Omega matrices. These aren't "coefficients" but the extractor is called coef for historical reasons. Within each group these values are in the order of the diagonal entries first then the strict upper triangle in row order. Parameters: x  pointer to an lme object Unc  pointer to a logical scalar indicating if the parameters are in the unconstrained form. Returns: numeric vector of the values in the upper triangles of the Omega matrices

SEXP lmer_coefGets (  SEXP  x, SEXP  coef, SEXP  Unc )

Assign the upper triangles of the Omega matrices. (Called coef for historical reasons.) Parameters: x  pointer to an lme object coef  pointer to an numeric vector of appropriate length Unc  pointer to a logical scalar indicating if the parameters are in the unconstrained form. Returns: R_NilValue

SEXP lmer_create (  SEXP  flist, SEXP  mmats )

Create an lmer object from a list of grouping factors and a list of model matrices. There is one more model matrix than grouping factor. The last model matrix is the fixed effects and the response. Parameters: facs  pointer to a list of grouping factors ncv  pointer to a list of model matrices Returns: pointer to an lmer object

SEXP lmer_Crosstab (  SEXP  flist  )

SEXP lmer_ECMEsteps (  SEXP  x, SEXP  nsteps, SEXP  REMLp, SEXP  Verbp )

Perform ECME steps for the REML or ML criterion. Parameters: x  pointer to an ssclme object nsteps  pointer to an integer scalar - the number of ECME steps to perform REMLp  pointer to a logical scalar indicating if REML is to be used verb  pointer to a logical scalar indicating verbose output Returns: R_NilValue if verb == FALSE, otherwise a list of iteration numbers, deviances, parameters, and gradients.

SEXP lmer_factor (  SEXP  x  )

If status[["factored"]] is FALSE, create and factor Z'Z+Omega. Also create RZX and RXX, the deviance components, and the value of the deviance for both ML and REML. Parameters: x  pointer to an lmer object Returns: NULL

SEXP lmer_firstDer (  SEXP  x, SEXP  val )

Fill in four symmetric matrices for each level, providing the information to generate the gradient or the ECME step. The four matrices are 1) -m_i^{-1} 2) 3) [{}(+)] 4) The term added to 3) to get [{}] Parameters: x  pointer to an lme object val  pointer to a list of matrices of the correct sizes Returns: val

SEXP lmer_fixef (  SEXP  x  )

Extract the conditional estimates of the fixed effects Parameters: x  Pointer to an lme object Returns: a numeric vector containing the conditional estimates of the fixed effects

SEXP lmer_gradient (  SEXP  x, SEXP  REMLp, SEXP  Uncp )

SEXP lmer_inflate (  SEXP  x  )

Copy ZtZ to ZZpO and L. Inflate diagonal blocks of ZZpO by Omega. Update devComp[1]. Parameters: x  pointer to an lmer object

SEXP lmer_initial (  SEXP  x  )

Create and insert initial values for Omega. Parameters: x  pointer to an lmer object Returns: NULL

SEXP lmer_invert (  SEXP  x  )

If necessary, factor Z'Z+Omega, ZtX, and XtX then, if necessary, replace the RZX and RXX slots by the corresponding parts of the inverse of the Cholesky factor. Replace the elements of the D slot by the blockwise inverses and evaluate bVar. Parameters: x  pointer to an lmer object Returns: NULL (x is updated in place)

SEXP lmer_ranef (  SEXP  x  )

Extract the conditional modes of the random effects. Parameters: x  Pointer to an lme object Returns: a vector containing the conditional modes of the random effects

SEXP lmer_sigma (  SEXP  x, SEXP  REML )

Extract the ML or REML conditional estimate of sigma Parameters: x  pointer to an lme object REML  logical scalar - TRUE if REML estimates are requested Returns: pointer to a numeric scalar

SEXP lmer_update_mm (  SEXP  x, SEXP  mmats )

Update the arrays ZtZ, ZtX, and XtX in an lme object according to a list of model matrices. Parameters: x  pointer to an lmer object mmats  pointer to a list of model matrices Returns: NULL

SEXP lmer_validate (  SEXP  x  )

Check validity of an lmer object. Parameters: x  Pointer to an lmer object Returns: TRUE if the object is a valid lmer object, else a string describing the nature of the violation.

SEXP lmer_variances (  SEXP  x  )

Return the unscaled variances Parameters: x  pointer to an lmer object Returns: a list similar to the Omega list with the unscaled variances

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