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[matrix] Annotation of /pkg/TODO
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Annotation of /pkg/TODO

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1 : bates 1233 -----
2 : bates 1339 Modify mcmcsamp to return the deviance in the sample only when the
3 :     optional argument 'deviance' is TRUE (default FALSE).
4 :     -----
5 :     Replace the use of the unexported replacement function LMEoptimize<-
6 :     in lmer.R by the function LMEopt, which always returns NULL but
7 :     (in contradiction to the language specification) modifies its first argument.
8 :     -----
9 : bates 1243 Modify the one-argument form of the anova method for lmer objects (yet
10 :     again) to calculate the F ratios. It is the df, not the ratio that
11 :     is controversial.
12 :     Should there be an extractor function for the mean square error? If
13 : bates 1322 so, what should it be called?
14 : bates 1243 -----
15 : bates 1236 Check for DimNames propagation in coercion and other operations.
16 :     -----
17 : bates 1233 - Revive the "lmer" and "glmer" classes. Slots like "family" should
18 :     be in "glmer" only. Many methods for "lmer" can be simplified as,
19 :     for example, they will always use the scale factor.
20 :    
21 :     - Add a "pedigree" class and methods for it. Allow a pedigree
22 :     argument in lmer.
23 :    
24 : bates 984 ------
25 : bates 918 - Sparse matrix methods can now be based on the CHOLMOD package. We
26 :     will need to migrate from the current code to CHOLMOD-based code
27 :     using #ifdef USE_CHOLMOD. Some of the things to be done
28 :    
29 :     - Move documentation from subdirectories of src to inst/doc
30 :     - Write utilities to create a cholmod_sparse pointer from a
31 :     dgCMatrix or lgCMatrix (or zgCMatrix) object without copying and
32 :     allocating.
33 :     - Start adding simple S4 methods (rcond, %*%, +, cbind, t).
34 :    
35 : bates 344 - Report the problem in the Linux ldexp manual page. The second and
36 :     third calls in the Synopsis should be to ldexpf and ldexpl.
37 : maechler 472
38 : maechler 868 - [,] indexing: for sparse "works", but not yet for negative indices!
39 : maechler 472
40 : bates 536 - consider moving alloc3Darray from ./src/Mutils.c to
41 : maechler 538 $(RSRC)/src/base/array.c
42 : bates 536
43 : maechler 517 -------
44 :    
45 : maechler 634 - provide methods for "dspMatrix" and "dppMatrix"!
46 :    
47 : maechler 538 - implement (more) methods for supporting "packed" (symmetric / triangular)
48 : maechler 634 matrices; particularly something like pack() and unpack() [to/from our
49 :     classes from/to "numeric"] --- have already man/unpack.Rd but no method yet!
50 : maechler 538
51 : maechler 834 (have some dtr* <-> dtp*)
52 :    
53 : bates 645 ---
54 :    
55 :     - combine the C functions for multiplication by special forms and
56 :     solution wrt special forms by using a 'right' argument and a
57 :     'classed' argument.
58 : maechler 675 [done with dgeMatrix_matrix_mm(); not yet for other classes;
59 :     and for _crossprod()]
60 :    
61 :     - add more comprehensive examples / tests for Schur decomposition
62 : maechler 696
63 :     - arithmetic for sparse matrices:
64 : maechler 935 <sparseMatrix> o <same-dim-sparseMatrix>
65 : maechler 696 should return a sparse matrix for at least "+" and "*" , also %%,
66 :     and "/" and "%/%" at least when the RHS is non-zero a scalar.
67 : maechler 935 Challenge: nice implementation (``common non-0''; but Tsparse* is not uniq).
68 : maechler 696
69 : bates 712 ---
70 :    
71 : maechler 935 - "Math2" , "Math", "Arith":
72 :     keep triangular and symmetric Matrices when appropriate:
73 :     particularly desirable for "Math2": round(), signif()
74 : maechler 956
75 :     - "d" <-> "l" coercion for all "[TCR]" sparse matrices is really trivial:
76 :     "d" -> "l" : drops the 'x' slot
77 :     "l" -> "d" : construct an 'x' slot of all '1'
78 :     We currently have many of these conversions explicitly, e.g.
79 :     setAs("dsTMatrix", "lsTMatrix",
80 :     function(from) new("lsTMatrix", i = from@i, j = from@j, uplo = from@uplo,
81 :     Dim = from@Dim, Dimnames = from@Dimnames))
82 :     but I would rather want to automatically construct all these coercion
83 :     methods at once by a ``method constructor'', i.e.,
84 :     for all "dsparse*" -> "lsparse*" and vice versa.
85 :     How can one do this {in a documented way} ?
86 : maechler 1087
87 : maechler 1097 - tcrossprod(x, y) : do provide methods for y != NULL
88 :     calling Lapack's DGEMM for "dense"
89 : maechler 1109 [2005-12-xx: done for dgeMatrix at least]
90 :    
91 :     - "ltTmatrix" :
92 :     2) new("ltTMatrix", diag = "U", Dim = c(2:2, 2:2)) shows lack of ltTM*_validate
93 : maechler 1201
94 :     - BUGlet: Shouldn't lose factorization here:
95 :     h6 <- Hilbert(6); chol(h6) ; str(h6) # has factor
96 :     str(H6 <- as(h6, "dspMatrix")) # has lost factor
97 :     ## and the same in a similar situation involving "dpo", "dpp"
98 : maechler 1226
99 :     - "Compare" for dgC & dgT --- want to be able to do M[M > 10] etc
100 : maechler 1245
101 :     - Things like M[upper.tri(M)] are not really most useful for sparse
102 :     matrices. --> provide generic functions
103 :     upperTriMatrix(), lowerTriMatrix() both with argument 'diag = TRUE'
104 :     (which can be set to FALSE of course) which are used to extract a
105 :     triangle from an arbitrary sparse matrix and return a "dtCMatrix".
106 :    
107 :     - Factorizations: LU [ -> solve() ] and Schur() for *sparse* Matrices.
108 :     ----------------- LU-sparse is the purpose of all of ./src/UMFPACK/
109 :     --> ./inst/doc/UFsparse/*
110 : maechler 1315 Note that UMFPACK is a bit slow compared to TAUCS etc, according to
111 :     Gould et al.(2005)
112 : maechler 1245 And then, possibly eigen(), svd(), qr(), ... for sparse
113 :     {probably base some on the fast chol() of CHOLMOD}.
114 : maechler 1315 ./man/lu.Rd notes that lu() is not yet available for sparse
115 : maechler 1253
116 :     2006-04-15 : now with 'CSparse' { src/cs.c }, have at least solve( <dtC*> )
117 :    
118 : maechler 1290 - nicer pedigree examples and tests

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