91 
Done(20060103) 
Done(20060103) 
92 


93 
 new("ltTMatrix") now at least prints 
 new("ltTMatrix") now at least prints 
94 


95 

 Done by version 0.9951  
96 


97 


98 

 Migration of lmer from the mer representation to the mer2 
99 

representation and the use of the CHOLMOD code for the sparse 
100 

matrix decomposition. Some of the things that need to be done. 
101 


102 

 Matrices in the mer2 representation are classed matrices, in the 
103 

mer representation they were unclassed. Any parts inside the C 
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code that would access, for example, 
105 

REAL(GET_SLOT(x, Matrix_RXXSym)) 
106 

need to be modified to access 
107 

REAL(GET_SLOT(GET_SLOT(x, Matrix_RXXSym), Matrix_xSym)) 
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This is especially important for Omega but I think I have done 
109 

those changes already. 
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111 

 The components named *X* in an mer object refers to an augmented 
112 

design matrix of p+1 columns. In the mer2 object there are 
113 

separate slots for rZy and rXy. The scalar y'y is the first 
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element of devComp. 
115 


116 

 Presently nc is of length nf+1 and the last element is n, the 
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number of observations. This value should be moved to devComp and 
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nc made of length nf. 
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120 

 The slot L is a list of length 1 that contains an ExternalPointer 
121 

to a cholmod_factor object. This contains a permutation which is 
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most easily accessible through cholmod_solve(CHOLMOD_P,...) or 
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cholmod_solve(CHOLMOD_Pt,...). The ZtX, Zty, RZX and rZy slots actually 
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contain P%*%RZX and P%*%rZy 
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