# SCM Repository

# Annotation of /pkg/Done

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1 : | maechler | 511 | - check to see if the .onLoad function to require the methods package |

2 : | (in the AllClass.R file) is needed | ||

3 : | -- no, it is not: "Depends: " in DESCRIPTION suffices. | ||

4 : | bates | 529 | |

5 : | - Should the uplo and diag slots continue to be stored as character? | ||

6 : | An alternative is to use a factor as in the enum values for the | ||

7 : | cblas. | ||

8 : | -- Leave as character but use care in determining the default cases | ||

9 : | -- E.g. Checks for diag slot should check for 'U' or 'u' vs. anything else | ||

10 : | |||

11 : | - Organization of the source code files - right now they are organized | ||

12 : | according to class (e.g. dgeMatrix.R, dgeMatrix.h, dgeMatrix.c). Is | ||

13 : | there a better way? | ||

14 : | -- This seems ok. | ||

15 : | |||

16 : | - Fix the calculation of the Dim slot for the crossprod method for | ||

17 : | dgCMatrix objects (too tired to do that now). | ||

18 : | -- Done | ||

19 : | bates | 530 | |

20 : | - spelling style: Should "coersion" be "coercion" ? | ||

21 : | -- Yes. Watch for this. | ||

22 : | |||

23 : | bates | 536 | - src/Metis/ : one of the two Makefiles needs fixing, as changing |

24 : | src/Metis/*.c does not lead to recompilation. | ||

25 : | --DB - it seems both Makefiles need fixing. I think I have the | ||

26 : | src/Metis/Makefile fixed but not src/Makefile | ||

27 : | --DB - now have both working, I believe. | ||

28 : | bates | 530 | |

29 : | maechler | 538 | - man/Matrix.Rd : has example with dimnames, but we just drop them! |

30 : | MM thinks dimnames should be supported (but then ...) | ||

31 : | -- added 'Dimnames' slot (2005-02-10) | ||

32 : | maechler | 540 | |

33 : | - bCrosstab(): yes, we really do want the diagonal "V:V" crosstabs. | ||

34 : | -- explained a bit more in man/bCrosstab.Rd | ||

35 : | |||

36 : | bates | 561 | - Clean up vestigial functions (pdFactor, pdMatrix, matrix<-) from the |

37 : | nlme package. | ||

38 : | maechler | 675 | |

39 : | - create a class of permutation matrices for use in expand. The | ||

40 : | current expand method for the LU factorization is not complete | ||

41 : | because it does not provide the permutation. | ||

42 : | |||

43 : | - tcrossprod() now works: C code now "exported" via init.c | ||

44 : | maechler | 869 | |

45 : | maechler | 946 | - Fixed: dtpMatrix(... diag = "U") (i.e., unit-diagonal packed triangular) |

46 : | *does* need 'x' entries for the diagonal but these are never looked at. | ||

47 : | maechler | 869 | -> changed doc -- Lapack also says they are not referenced but assumed 1. |

48 : | bates | 881 | |

49 : | |||

50 : | - in lmer.c check all instances of the use of ZtX and XtX and change | ||

51 : | them so that having a negative last element of nc means use the | ||

52 : | response only (but look for it in the right place). | ||

53 : | maechler | 935 | |

54 : | - Solved: | ||

55 : | |||

56 : | Currently the show() method fail sometime after coercion: | ||

57 : | e.g. 'sy' show()s wrongly, even though it "str()" fine : | ||

58 : | |||

59 : | (po <- crossprod(Matrix(0:3, 2))) # ok | ||

60 : | (ge <- as(po, "dgeMatrix")) # ok | ||

61 : | (sy <- as(po, "dsyMatrix")) # BAD | ||

62 : | str(sy) # looks fine | ||

63 : | |||

64 : | or | ||

65 : | example(expand) # -> ex$L and ex$U look bad, however | ||

66 : | as(ex$L, "dgeMatrix") # `works' | ||

67 : | |||

68 : | {Of course, we don't need a workaround but must understand | ||

69 : | and solve the problem} | ||

70 : | |||

71 : | maechler | 976 | - slot "factors" maybe should move up to "Matrix" -- done, 2005-09-28 |

72 : | maechler | 935 | |

73 : | maechler | 976 | - group generics: "Arith", also "Compare", "Math" etc; |

74 : | see ?Math and the examples in ?SetGeneric | ||

75 : | |||

76 : | - methods for rbind and cbind where they make sense: | ||

77 : | R 2.2.0 (and newer) provide cbind2() and rbind2() generics and default | ||

78 : | methods [following John Chambers's proposition], and we have implemented | ||

79 : | methods for them. | ||

80 : | |||

81 : | maechler | 935 | - arithmetic for sparse matrices: |

82 : | done for <sparseMatrix> o <scalar> | ||

83 : | {more needed: see TODO} | ||

84 : | |||

85 : | maechler | 1109 | - rcond() of a singular dpoMatrix gives a LaPack error instead of just 0: |

86 : | MM <- crossprod(M <- Matrix(c(1:4,9:6), 2,4)) ; rcond(MM) | ||

87 : | Done(2005-10-03): The error message is more helpful now. | ||

88 : | maechler | 976 | |

89 : | maechler | 1109 | - implement diagonal Matrix class "ddiMatrix" etc |

90 : | using constructor function Diagonal() {and extractor diag()}. | ||

91 : | Done(2006-01-03) | ||

92 : | |||

93 : | - new("ltTMatrix") now at least prints | ||

94 : | bates | 1224 | |

95 : | -- Done by version 0.995-1 --- | ||

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 | ||

104 : | 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)) | ||

108 : | This is especially important for Omega but I think I have done | ||

109 : | those changes already. | ||

110 : | |||

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 | ||

114 : | element of devComp. | ||

115 : | |||

116 : | - Presently nc is of length nf+1 and the last element is n, the | ||

117 : | number of observations. This value should be moved to devComp and | ||

118 : | nc made of length nf. | ||

119 : | |||

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 | ||

122 : | most easily accessible through cholmod_solve(CHOLMOD_P,...) or | ||

123 : | cholmod_solve(CHOLMOD_Pt,...). The ZtX, Zty, RZX and rZy slots actually | ||

124 : | contain P%*%RZX and P%*%rZy | ||

125 : | |||

126 : | maechler | 1226 | - "[<-" Methods for dgC* and dgT* the former building on the latter |

127 : | using j = .Call("Matrix_expand_pointers", x@p, PACKAGE = "Matrix") | ||

128 : | where needed | ||

129 : | bates | 1224 | |

130 : | maechler | 1228 | - Put the matrix 'mm' and the response vector 'y' into 'KNex', a list. |

131 : | Modified all examples and tests that used them and the Comparisons vignette. |

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