#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_fitted (SEXP x, SEXP mmats, SEXP useRf) |
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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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.
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Assign the upper triangles of the Omega matrices. (Called coef for historical reasons.)
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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.
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Perform ECME steps for the REML or ML criterion.
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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.
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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 [{}]
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Calculate and return the fitted values.
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Extract the conditional estimates of the fixed effects
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Copy ZtZ to ZZpO and L. Inflate diagonal blocks of ZZpO by Omega. Update devComp[1].
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Create and insert initial values for Omega.
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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.
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Extract the conditional modes of the random effects.
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Extract the ML or REML conditional estimate of sigma
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Update the arrays ZtZ, ZtX, and XtX in an lme object according to a list of model matrices.
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Check validity of an lmer object.
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Return the unscaled variances
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