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revision 1243, Sun Apr 9 00:02:26 2006 UTC revision 1887, Thu Jun 7 09:04:34 2007 UTC
# Line 1  Line 1 
 -----  
 Modify the one-argument form of the anova method for lmer objects (yet  
   again) to calculate the F ratios.  It is the df, not the ratio that  
   is controversial.  
 Should there be an extractor function for the mean square error?  If  
 so,  
 -----  
1  Check for DimNames propagation in coercion and other operations.  Check for DimNames propagation in coercion and other operations.
 -----  
 - Revive the "lmer" and "glmer" classes.  Slots like "family" should  
   be in "glmer" only.  Many methods for "lmer" can be simplified as,  
   for example, they will always use the scale factor.  
   
 - Add a "pedigree" class and methods for it.  Allow a pedigree  
   argument in lmer.  
   
2  ------  ------
3  - Sparse matrix methods can now be based on the CHOLMOD package.  We  - rcond methods for sparseMatrix classes
    will need to migrate from the current code to CHOLMOD-based code  
    using #ifdef USE_CHOLMOD.  Some of the things to be done  
   
    - Move documentation from subdirectories of src to inst/doc  
    - Write utilities to create a cholmod_sparse pointer from a  
    dgCMatrix or lgCMatrix (or zgCMatrix) object without copying and  
    allocating.  
    - Start adding simple S4 methods (rcond, %*%, +, cbind, t).  
4    
5  - Report the problem in the Linux ldexp manual page.  The second and  - Report the problem in the Linux ldexp manual page.  The second and
6    third calls in the Synopsis should be to ldexpf and ldexpl.    third calls in the Synopsis should be to ldexpf and ldexpl.
# Line 32  Line 9 
9    
10  - consider moving alloc3Darray from ./src/Mutils.c to  - consider moving alloc3Darray from ./src/Mutils.c to
11    $(RSRC)/src/base/array.c    $(RSRC)/src/base/array.c
12    ------
 -------  
   
13  - provide methods for "dspMatrix" and "dppMatrix"!  - provide methods for "dspMatrix" and "dppMatrix"!
14    
15  - implement (more) methods for supporting "packed" (symmetric / triangular)  - implement (more) methods for supporting "packed" (symmetric / triangular)
# Line 43  Line 18 
18    
19    (have some dtr* <-> dtp*)    (have some dtr* <-> dtp*)
20    
21  ---  -----
22    
23  - combine the C functions for multiplication by special forms and  - combine the C functions for multiplication by special forms and
24    solution wrt special forms by using a 'right' argument and a    solution wrt special forms by using a 'right' argument and a
# Line 59  Line 34 
34    and "/" and "%/%" at least when the RHS is non-zero a scalar.    and "/" and "%/%" at least when the RHS is non-zero a scalar.
35    Challenge: nice implementation (``common non-0''; but Tsparse* is not uniq).    Challenge: nice implementation (``common non-0''; but Tsparse* is not uniq).
36    
37  ---  -----
38    
39  - "Math2" , "Math", "Arith":  - "Math2" , "Math", "Arith":
40     keep triangular and symmetric Matrices when appropriate:     keep triangular and symmetric Matrices when appropriate:
# Line 81  Line 56 
56    calling Lapack's DGEMM for "dense"    calling Lapack's DGEMM for "dense"
57    [2005-12-xx: done for dgeMatrix at least]    [2005-12-xx: done for dgeMatrix at least]
58    
 - "ltTmatrix" :  
   2) new("ltTMatrix", diag = "U", Dim = c(2:2, 2:2)) shows lack of ltTM*_validate  
   
59  - BUGlet:  Shouldn't lose factorization here:  - BUGlet:  Shouldn't lose factorization here:
60    h6 <- Hilbert(6); chol(h6) ; str(h6) # has factor    h6 <- Hilbert(6); chol(h6) ; str(h6) # has factor
61    str(H6 <- as(h6, "dspMatrix"))       # has lost factor    str(H6 <- as(h6, "dspMatrix"))       # has lost factor
62    ## and the same in a similar situation involving  "dpo", "dpp"    ## and the same in a similar situation involving  "dpo", "dpp"
63    
64  - "Compare" for dgC & dgT  --- want to be able to do  M[M > 10]  etc  - Things like  M[upper.tri(M)] are not really most useful for  sparse
65      matrices.  --> provide generic functions
66      upperTriMatrix(), lowerTriMatrix()  both with argument  'diag = TRUE'
67      (which can be set to FALSE of course) which are used to extract a
68      triangle from an arbitrary sparse matrix and  return a  "dtCMatrix".
69    
70    - Factorizations: LU done; also Schur()  for  *sparse*  Matrices.
71    
72    - band(), triu(), tril() for *all* including "matrix", not just sparse matrices
73    
74    - is.na() method for all our matrices [ ==> which(*, arr.ind=TRUE) might work ]
75    
76    - When we have a packed matrix, it's a waste to go through "full" to "sparse":
77      ==> implement
78            setAs("dspMatrix", "sparseMatrix")
79            setAs("dppMatrix", "sparseMatrix")
80            setAs("dtpMatrix", "sparseMatrix")
81      and the same for "lsp" , "ltp"  and  "nsp" , "ntp" !
82    
83    - use  .Call(Csparse_drop, M, tol) in more places,
84      both with 'tol = 0.' to drop "values that happen to be 0" and for
85      zapsmall() methods for Csparse*
86    
87    - implement .Call(Csparse_scale, ....) interfacing to cholmod_scale()
88      in src/CHOLMOD/Include/cholmod_matrixops.h : for another function
89      specifically for multiplying a cholmod_sparse object by a diagonal matrix.
90      Use it in %*% and [t]crossprod methods.
91    
92    - chol() and determinant() should ``work'': proper result or "good" error
93      message.
94    
95    - Think of constructing  setAs(...) calls automatically in order to
96      basically enable all ``sensible'' as(fromMatrix, toMatrix)  calls,
97      possibly using canCoerce(.)
98    
99    - make sure *all* group methods have (maybe "bail-out") setMethod for "Matrix".
100      e.g. zapsmall(<pMatrix>) fails "badly"
101    
102    - speedup: pass class definition to non0ind() [check all calls ..]
103    
104    - sum(): implement methods which work for *all* our matrices.
105    
106    - Implement  expand(.) for the Cholesky() results
107      "dCHMsimpl" and  "dCHMsuper"  -- currently have no *decent* way to get at
108      the matrix factors of the corresponding matrix factorization !!
109    
110    - rbind(<sparse>, <dense>) does not work  (e.g. <dgC>, <dge>)
111    
112    - setAs(<Mcl>,  "[dln]Matrix" )  for <Mcl> in {Matrix or denseMatrix + sparseMatrix}
113    
114    - Tell users about the possibility to disable the "S4-generic but somewhat slow"
115      cbind/rbind, e.g. via
116    
117      setHook(packageEvent("Matrix", "onLoad"),
118              function(...) methods:::bind_activation(FALSE))
119    
120    - ensure that  M[0], M[FALSE], M[1:2]  works as for traditional Matrices
121    
122    - make sure  M[FALSE, FALSE]  works for all Matrices
123      {e.g. fails for M <- Diagonal(4)}
124    
125    - <sparse> %*% <dense>  {also in crossprod/tcrossprod}  currently always
126      returns <dense>, since --> Csparse_dense_prod --> cholmod_sdmult
127      and that does only return dense.
128      When the sparse matrix is very sparse, i.e. has many rows with only zero
129      entries, it would make much sense to return sparse.
130    
131    - sparse-symmetric + diagonal should stay sparse-symmetric
132      (only stays sparse): Matrix(0, 4, 4) + Diagonal(4, 1:4)
133      --> R/diagMatrix.R ('FIXME')
134      but also R/Ops.R  to ensure  sp-sym. + sp-sym. |-> sp-sym.  etc
135    
136    - For a square sparse matrix 'b' {typically dgCMatrix or dgTMatrix},
137      we'd want a function  "Mat_plus_t_Mat" <- function(b) {....}
138      which computes the symmetric sparse matrix   b + t(b)
139      in way that never works with size-doubled vectors from  b@i etc..
140    
141    - ! <symmetricMatrix>  loses symmetry, both for dense and sparse matrices.
142      !M  where M is "sparseMatrix", currently always gives dense. This only
143      makes sense when M is ``really sparse''.
144    
145    - column names of sparse matrices are not printed;
146      we now "mention" them (if they are non-empty).
147      Option:
148            build show( <sparseMatrix>) on a function, possibly
149            print.sparseMatrix(), which gets an argument such as
150            'col.names.show  = FALSE' which is documented and can be set to TRUE
151    
152    - 'arules' needs fast colSums() and rowSums() - for ngCMatrix;
153      do it for "nMatrix" and "lMatrix" and return *integer*

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