lme4: lmer.h File Reference

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Functions
SEXP	mer_create_L (SEXP CmP)
	Create and initialize L.
SEXP	mer_MCMCsamp (SEXP x, SEXP fm)
	Generate a Markov-chain Monte Carlo sample from an mer object.
SEXP	mer_optimize (SEXP x, SEXP verb)
	Optimize the profiled deviance of an lmer object or the Laplace approximation to the deviance of a nlmer or glmer object.
SEXP	mer_postVar (SEXP x)
	Extract the conditional variances of the random effects in an mer object.
SEXP	mer_ST_chol (SEXP x)
	Return a list of (upper) Cholesky factors from the ST list.
SEXP	mer_ST_getPars (SEXP x)
	Extract the parameters from the ST slot of an mer object.
SEXP	mer_ST_initialize (SEXP ST, SEXP Gp, SEXP Zt)
	Evaluate starting estimates for the elements of ST.
SEXP	mer_ST_setPars (SEXP x, SEXP pars)
	Update the ST slot of an mer object from a REAL vector of parameters and update the sparse model matrix A.
SEXP	mer_update_dev (SEXP x)
	Evaluate the discrepancy and log of the penalized discrepancy.
SEXP	mer_update_L (SEXP x)
	Externally callable update_L.
SEXP	mer_update_mu (SEXP x)
	Externally callable update_mu.
SEXP	mer_update_projection (SEXP x)
	Externally callable lmm_update_projection.
SEXP	mer_update_ranef (SEXP x)
	Externally callable update_ranef.
SEXP	mer_update_RX (SEXP x)
	Externally callable update_RX.
SEXP	mer_update_u (SEXP x, SEXP verbP)
	Externally callable update_u.
SEXP	mer_validate (SEXP x)
	Check validity of an mer object.
SEXP	merMCMC_validate (SEXP x)
	Check validity of an merMCMC object.
SEXP	merMCMC_VarCorr (SEXP x, SEXP typ)
SEXP	spR_optimize (SEXP x, SEXP verbP)
	Optimize the log-likelihood for the sparse representation of a Rasch model.
SEXP	spR_update_mu (SEXP x)
	Update the eta, mu, resid and var slots in a sparseRasch object from the current values of the model parameters in the beta slot.

Function Documentation

SEXP mer_create_L ( SEXP CmP )

Create and initialize L.

Parameters:

CmP

pointer to the model matrix for the orthogonal random effects (transposed)

Returns:: L

Definition at line 1293 of file lmer.c.

References _, and c.

SEXP mer_MCMCsamp	(	SEXP	x,
		SEXP	fm
	)

Generate a Markov-chain Monte Carlo sample from an mer object.

Parameters:

	x	pointer to an merMCMC object
	fm	pointer to an mer object

Returns:: x with samples filled in

Definition at line 1316 of file lmer.c.

References DEV_SLOT, DIMS_SLOT, FIXEF_SLOT, lme4_devianceSym, lme4_sigmaSym, lme4_STSym, lmm_update_fixef_u(), MCMC_beta_u(), MCMC_S(), MCMC_T(), ML_POS, n_POS, np_POS, p_POS, pwrss_POS, q_POS, RANEF_SLOT, SLOT_REAL_NULL(), ST_getPars(), ST_setPars(), update_L(), update_ranef(), update_RX(), and update_u().

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SEXP mer_optimize	(	SEXP	x,
		SEXP	verbp
	)

Optimize the profiled deviance of an lmer object or the Laplace approximation to the deviance of a nlmer or glmer object.

Parameters:

	x	pointer to an mer object
	verbp	pointer to indicator of verbose output

Returns:: R_NilValue

Definition at line 1366 of file lmer.c.

References Alloca, cvg_POS, DEV_SLOT, DIMS_SLOT, FIXEF_SLOT, lme4_STSym, lmm_update_fixef_u(), mer_update_dev(), ML_POS, MUETA_SLOT, nf_POS, np_POS, p_POS, ST_getPars(), ST_setPars(), update_L(), update_RX(), update_u(), and V_SLOT.

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SEXP mer_postVar ( SEXP x )

Extract the conditional variances of the random effects in an mer object.

Some people called these posterior variances, hence the name.

Parameters:

pointer to an mer object

Returns:: pointer to a list of arrays

Definition at line 1434 of file lmer.c.

References Alloca, c, DEV_SLOT, DIMS_SLOT, Gp_SLOT, isREML_POS, L_SLOT, lme4_STSym, nf_POS, q_POS, sigmaML_POS, sigmaREML_POS, ST_nc_nlev(), and useSc_POS.

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SEXP mer_ST_chol ( SEXP x )

Return a list of (upper) Cholesky factors from the ST list.

Parameters:

an mer object

Returns:: a list of upper Cholesky factors

Definition at line 1495 of file lmer.c.

References Alloca, DIMS_SLOT, Gp_SLOT, lme4_STSym, nf_POS, and ST_nc_nlev().

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SEXP mer_ST_getPars ( SEXP x )

Extract the parameters from the ST slot of an mer object.

Parameters:

an mer object

Returns:: pointer to a REAL vector

Definition at line 1530 of file lmer.c.

References DIMS_SLOT, np_POS, and ST_getPars().

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SEXP mer_ST_initialize	(	SEXP	ST,
		SEXP	Gpp,
		SEXP	Zt
	)

Evaluate starting estimates for the elements of ST.

Parameters:

	ST	pointers to the nf ST factorizations of the diagonal elements of Sigma
	Gpp	length nf+1 vector of group pointers for the rows of Zt
	Zt	transpose of Z matrix

Definition at line 1548 of file lmer.c.

References Alloca, AZERO, lme4_DimSym, lme4_iSym, lme4_pSym, lme4_xSym, and ST_nc_nlev().

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SEXP mer_ST_setPars	(	SEXP	x,
		SEXP	pars
	)

Update the ST slot of an mer object from a REAL vector of parameters and update the sparse model matrix A.

Parameters:

	x	an mer object
	pars	a REAL vector of the appropriate length

Returns:: R_NilValue

Definition at line 1584 of file lmer.c.

References _, DIMS_SLOT, np_POS, and ST_setPars().

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SEXP mer_update_dev ( SEXP x )

Evaluate the discrepancy and log of the penalized discrepancy.

update_mu must be called first.

Parameters:

pointer to an mer object

Definition at line 1601 of file lmer.c.

References DEV_SLOT, DIMS_SLOT, disc_POS, ldL2_POS, lme4_devResid(), ML_POS, MU_SLOT, MUETA_SLOT, n_POS, nAGQ_POS, PWT_SLOT, usqr_POS, vTyp_POS, wrss_POS, and Y_SLOT.

Referenced by mer_optimize().

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SEXP mer_update_L ( SEXP x )

Externally callable update_L.

Update the A, L, sqrtrWt and resid slots. It is assumed that update_mu has already been called at the current values of u and the model parameters.

Parameters:

an mer object

Returns:: penalized weighted residual sum of squares

Definition at line 1637 of file lmer.c.

References update_L().

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SEXP mer_update_mu ( SEXP x )

Externally callable update_mu.

Update the eta, v, mu, resid and var slots according to the current values of the parameters and u. Also evaluate d[wrss_POS] using the current contents of sqrtrWt. The sqrtrWt slot is updated in update_L.

Parameters:

pointer to an mer object

Returns:: penalized, weighted residual sum of squares

Definition at line 1652 of file lmer.c.

References update_mu().

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SEXP mer_update_projection ( SEXP x )

Externally callable lmm_update_projection.

Create the projections onto the column spaces of the random effects and the fixed effects.

Parameters:

an mer object

Returns:: a list with two elements, both REAL vectors

Definition at line 1682 of file lmer.c.

References DIMS_SLOT, lmm_update_projection(), p_POS, and q_POS.

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SEXP mer_update_ranef ( SEXP x )

Externally callable update_ranef.

Update the contents of the ranef slot in an mer object. For a linear mixed model the conditional estimates of the fixed effects and the conditional mode of u are evaluated first.

Parameters:

an mer object