Commit 247d1af2 authored by Roman Flury's avatar Roman Flury

update pkg source

parent 71e65e9c
Pipeline #2948 canceled with stage
Package: spam
Type: Package
Title: SPArse Matrix
Version: 2.5-0
Date: 2019-12-05
Version: 2.5-1
Date: 2019-12-12
Authors@R: c(person("Reinhard", "Furrer", role = c("aut", "cre"),
email = "reinhard.furrer@math.uzh.ch"),
person("Florian", "Gerber", role = c("aut"),
......@@ -59,4 +59,3 @@ LazyData: true
License: LGPL-2 | BSD_3_clause + file LICENSE
URL: https://www.math.uzh.ch/pages/spam/
BugReports: https://git.math.uzh.ch/reinhard.furrer/spam/issues
RoxygenNote: 6.1.1
# spam 2.5-1
BUG FIXES
* fixing fortran linking warning.
# spam 2.5-0
SIGNIFICANT USER-VISIBLE CHANGES
......
# HEADER ####################################################
# This is file spam/R/deprecated.R. #
# It is part of the R package spam, #
# --> https://CRAN.R-project.org/package=spam #
# --> https://CRAN.R-project.org/package=spam64 #
# --> https://git.math.uzh.ch/reinhard.furrer/spam #
# by Reinhard Furrer [aut, cre], Florian Gerber [aut], #
# Roman Flury [aut], Daniel Gerber [ctb], #
# Kaspar Moesinger [ctb] #
# HEADER END ################################################
validspamobject <- function( ...) {
# .Deprecated('validate_spam()')
message("`validspamobject()` is deprecated. Use `validate_spam()` directly")
validate_spam( ...)
}
spam.getOption <- function(...) {
# .Deprecated(msg="`spam.getOption( arg)` is deprecated.\n Use `getOption( spam.arg)` directly")
message("`spam.getOption( arg)` is deprecated. Use `getOption( spam.arg)` directly")
getOption(...)
}
spam.options <- function(...) {
# .Deprecated(msg="`spam.options( arg)` is deprecated.\n Use `options( spam.arg)` directly")
message("`spam.options( arg)` is deprecated. Use `options( spam.arg)` directly")
if (nargs() == 0) {
tmp <- names(options())
return(options()[ grep( "spam.", tmp)])
}
args <- list(...)
names(args) <- paste0("spam.", names(args))
do.call("options", args)
}
>spam_0.41: moved definitively to GIT. ChangeLog will consist of
`git log`
spam_0.41-0 2014-02-26 (RF)
- addressed several Rdevel CMD check --as-cran Notes.
- minor changes in tests/mle (improving speed)
- minor code tiding
- file header edits
spam_0.40-1 2014-02-20 (Florian Gerber)
- update grid_trace2() and grid_trace2.Rd
- eliminate bug in cov.mat() and correct typo in cov.Rd
add tests/covmat.R tests/covmat.Rout.save
changeset: 4:66173a00f913
tag: tip
user: Reinhard Furrer @ lappi <reinhard.furrer@math.uzh.ch>
date: Wed Aug 21 21:09:05 2013 +0200
summary: Adjusted DESCRIPTION, NEWS, ChangeLog for push to CRAN
changeset: 3:412496cbb8b3
user: Florian Gerber <florian.gerber@math.uzh.ch>
date: Tue Aug 20 15:36:34 2013 +0200
summary: gridBase NOT in dependency. comment germany.Rd about 'fields'
changeset: 2:2526f2c1d501
user: Florian Gerber <florian.gerber@math.uzh.ch>
date: Mon Aug 19 15:42:49 2013 +0200
summary: add plot grid_zoom() and grid_trace2() incl help files.
changeset: 1:2929fe7a2799
user: Florian Gerber <florian.gerber@math.uzh.ch>
date: Tue Aug 06 14:31:11 2013 +0200
summary: Test hg, small changes in spam0.30-0/man/mcmczoomPlot.Rd
changeset: 0:0029fc2741f4
user: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
date: Mon Aug 05 13:53:20 2013 +0200
summary: First Version that runs...
Dear Emacs, please make this -*-Text-*- mode!
**************************************************
* *
* SPAM VERSION 0.21 *
* *
**************************************************
o New functions bandwidth, permutation, mle[.nomean][.spam],
neg2loglikelihood[.spam].
o Renamed adiag.spam to bdiag.spam.
o Cleaned up argument naming with the rmvnorm.*
suite.
o Varios Fortran code, R code and help file
improvements.
**************************************************
* *
* SPAM VERSION 0.20 *
* *
**************************************************
CHANGES IN R VERSION 0.20-3
o Resolved dependency issues.
CHANGES IN R VERSION 0.20-1,2
o Minor changes to pass the CRAN test.
CHANGES IN R VERSION 0.20-0
o New demos, test functions, datasets.
o Method t for spam.chol.NgPeyton.
o Method Math2 now with signature digits="ANY".
o Update in rmvnorm.canonical, can take a Cholesky structure
as argument.
o New functionality for a sparse times a full matrix
multiplication.
o Minor ajustment in memory allocation of chol.
**************************************************
* *
* SPAM VERSION 0.15 *
* *
**************************************************
CHANGES IN R VERSION 0.15-6
o Minor change in Fortran routines to accomodate some Intel
compilers (pointed out by Tim Hoar).
CHANGES IN R VERSION 0.15-5
o New function adiag.spam, creation of block diagonal sparse
matrices. No method though.
o New functions rmvnorm.spam, rmvnorm.canonical and
rmvnorm.prec to draw multivariate normals.
o New function apply.spam, similar functionality as apply.
o drop is implemented now when subsetting a sparse matrix
with a binary matrix.
o Major overhaul to nearest.dist: zeros are not included.
Old parameters are kept for backwards compatibility.
o Orders/complexities of major algorithms are now described
in the help 'complexity'.
o Using packageStartupMessage in .onAttach.
o Code clean up and help improvements. Changes reflecting the
change to UZH.
o Bugfix in assinging via a nx2 matrix.
CHANGES IN R VERSION 0.15-4
o Changes in help files. Minor code improvements.
o New function powerboost.
o Changes to if(getRversion() >= "x.y"), required for R 2.10.
CHANGES IN R VERSION 0.15-3
o Several bug fixes in the demos due to the changes in
the previous versions.
o Several minior changes in the help files to compile with
the new help parser and to correct for typos.
o Added the demos into the tests directory. Additionally,
tests contains now the proper Rout.saves files.
o In test files, library( spam, warn.conflict=FALSE)
is used to avoid masking messages in R-2.8.0.
Timing output in test files is suppressed.
o Added trivial headers to most files.
o Bug fix in spam.list(), negative values were not correctly
handled.
o Bug fix in subsetting (occured when subsetting very
sparse matrices, memory allocation problem).
CHANGES IN R VERSION 0.15-2
o Method all.equal for matrix-spam signature.
o Bug fix in Fortran function of nearest.dist. Numerical
instabilities could return NaN on diagonal. Additionally,
overhaul of tests/dist.R.
o Several minor improvements in the help files as well
as in function nearest.dist and tests/*.R.
CHANGES IN R VERSION 0.15-1
o Improvements in the nearest.dist function. The diagonals
are now handled consistenly.
o Symmetry check criterion for Cholesky decomposition has been
relaxed from (2+eps)*eps to 100*eps for an easier handling when
working with great circle distance induced covariance matrices.
Same cutoff is used with eigen. Instead of using norm,
we use essentially an isSymmetric.spam test.
o Methods isSymmetric and all.equal for spam.
o Methods image and display for spam.chol.NgPeyton.
o Method as.spam for distance class implemented.
o Complete rewrite of spam.list. Method as.spam for lists
are implemented as well.
o Method spam for spam objects (possibility to rearrange the
dimension) has been eliminated. The approach was based on
creating the full matrix and assigning it back to a spam
object.
o Binary subsetting and subassigning is implemented.
o Bug fix: the Cholesky Fortran routine checks if diagonal
elements are available (and positive).
o Bug fix: in dim<-.spam
o Minor improvements in the help files as well as the following
R functions: norm, .spam.matmul.
CHANGES IN R VERSION 0.15-0
o The devel versions of 14-x have been sitting around for
a while and I was inconsistent with the devel/gold numbering.
To avoid any confusion, I have decided to go to the next
minor version. An additional reason supporting this is
that the version number identification has changed over
the 0.14-devel.
**************************************************
* *
* SPAM VERSION 0.14 *
* *
**************************************************
CHANGES IN R VERSION 0.14-x
o A few rudimentary functions to change between the compressed
sparse row formats of the packages SparseM and Matrix.
Just the functions, no S3/S4 constructs available.
o Functionality to read matrices stored in the Harwell-Boeing
or MatrixMarket formats.Read MatrixMarket.
o Rewritten cbind.spam and rbind.spam. Both can take now
numeric and spam objects. cbind.spam calls now Fortran
code and is now very fast. Rewrite of their help.
o Implemented spam.list to go from a index based list to a
spam matrix. The function triplets does the inverse.
o forwardsolve and backsolve methods for spam objects.
o Implemented the function 'dim<-' for spam objects.
o Method diag and as.matrix for spam.chol.NgPeyton.
o eps is now tested for being at least double precision.
o as.spam.xxx and spam.yyy functions have been streamlined.
o Initializing an empty spam matrix causes a warning but still
coerces to a zero matrix, see new("spam",entries=rep(1,0))
o Eliminated bug in subsetting (occuring when subsetting
for an empty matrix). Clean out subsetting and assigning.
o Include a inst subdirectory containing this file, which
is renamed to NEWS. Once we have reached a stable version
I will maintain a proper CHANGELOG file in the root
directory.
o Proper method handling for kronecker and bug fixes in
kronecker.spam.
o Saved the datasets UScounties.storder/ndorder as spam
objects as assumed by demo article-jss.
o Implemented many 'identical' structures and homogenized zero
matrix handling, throughout the R code. int0, ..., int2 are
internally defined integers.
o Similar changes as for 13-3. Additionally, considerable
improvements in help, file structure, tests, timing, etc.
CHANGES IN R VERSION 0.14-0
Major revision. Slight loss of backwards compatibility.
o New demo article-jss.
o New variable spam.version, similar to the R version
variable.
o Change and adding of a few option names, for example
cholsymmetrycheck, cholpivotcheck, cholupdatesingular,
dopivoting, safemode, ...
See help files for details.
o Complete rewrite of chol. The argument ordering is
now called pivot, more consistent with the generic
function. Two different orderings are implemented.
Uses the new option cholsymmetrycheck.
o Similar changes as in chol in determinant.spam.
o New function update.spam.chol.NgPeyton.
o Invisible/minor changes in method c for spam, in solve.spam,
determinant.chol.NgPeyton
o The class spam.chol.NgPeyton is defined differently.
Accordingly, print and summary methods are updated.
Notably, fill-in ratios are given with summary.
Summary also hands back the length of the vectors holding the
factor and the column indices.
o New methods for spam.chol.NgPeyton, namely, dim, length, c,
dim<-, and length<-. The latter two giving simply errors.
o Along the redefinition of the class spam.chol.NgPeyton,
forwardsolve.spam and backsolve.spam are updated.
Use now the option dopivoting.
o kronecker.r is implemented.
o nearest.dist, a function to calculate close distances
within one or two sets of locations is implemented.
Roughly speaking, it is the union of dist in base and
rdist/rdist.earth in fields. (comes with options
nearestdistincreasefactor and nearestdistnnz).
o print and show now emphasize that the non-zero elements
are row-wise printed.
o UScounties is a dataset containing the adjacency matrix
of the first and second order neighbors of the counties
of the lower 48 US states.
o Some changes in help files, especially in the *-class
files.
o Eliminated warnings issued when compiling.
o Minor R and Fortran code cleaning.
o Along the new features, update of CHANGELOG, todo,
NAMESPACE files, etc.
**************************************************
* *
* SPAM VERSION SERIES 0.13 *
* *
**************************************************
CHANGES IN R VERSION 0.13-3
o Minor changes in R and Fortran code to eliminate warnings.
o In diag()'s argument list, drop the explicit default (' = n').
As is now in R-2.7.
CHANGES IN R VERSION 0.13-2
o New spam.options and getOption functions. .Spam
as a variable is not visible anymore.
o Retrieving information from the DESCRIPTION file directly
(thanks to Roger Bivand).
CHANGES IN R VERSION 0.13-1
o Minor Fortran Changes for g77 compatibility. Thanks to
Roger Bivand.
o Updated DESCRIPTION file.
CHANGES IN R VERSION 0.13
o Updated NAMESPACE (for versions > 2.5).
o Some changes in help files.
o Cleaned Fortran source files (eliminated unused
subroutines and used the posted complier output to
straighten details).
o Implemented more efficient transpose Fortran code.
This also eliminates a bug when transposing a 1 row
matrix.
o Eliminated bug when assigning with a 1 row matix.
o Eliminated bug (Fortran code) that could potentially
occur when assigning.
o Eliminated bug when plotting a 1 row matix.
o Minor R code cleaning.
**************************************************
* *
* SPAM VERSION 0.12 *
* *
**************************************************
o Updated NAMESPACE and DESCRIPTION file.
o print and summary pass back NULL instead of the
object.
o Changed to prod(x@dimension) instead of nrow*ncol to
overcome integer overflow for very large matrices.
o Introduced a prototype in the definition of spam
and spam.chol.*.
o .Spam$safemode also determines if a spam object is
tested for validity, as well as for NAOK.
o In many functions sparse matrix construction is
done manually using slots (and check=FALSE, if
approprate).
o Increased the value of symmetry criteria to
(2+eps)*eps, as each element can be off by eps,
subtraction leads to a 2*eps offset and yet we are
symmetric.
o Major restructuration of chol/det with elimination
of auxiliarychol.
o Methods chol/backsolve/forwarsolve now call the *.spam
functions.
o Many internal changes to favour speed and efficiency.
o Bug fix in .spam.elemul. occuring when the result is the
zero matrix.
CHANGES IN VERSION 2.2-0
SIGNIFICANT USER-VISIBLE CHANGES
o Implementation of 'eigen.spam' and 'eigen_approx' to calculate
eigenvalues and eigenvectors for sparse matrices.
o 'germany.plot' has new argument 'cex.main'.
BUG FIXES
o 'NAOK=TRUE' did not properly dispatch in all matrix multiplications.
o '.newSpam()' was not always properly called, causing possible errors
when creating empty 'spam' objects.
INTERNAL CHANGES
o Code cleaning and coherence improvements.
CHANGES IN VERSION 2.1-2
SIGNIFICANT USER-VISIBLE CHANGES
o In case 64bits are required, issues an error to load package
'spam64' first.
o Minor fixes in help files and other documentation.
INTERNAL CHANGES
o Improved registering of compiled functions
o Compatibility with new versions of package 'testthat'.
CHANGES IN VERSION 2.1-1
SIGNIFICANT USER-VISIBLE CHANGES
o With the addon of the package spam64, we have truly 64 bits
available!
o Dependency on dotCall64.
o Different option handling, we use now the classical R setting.
For the moment, the old functionality throws a message but in
upcoming versions we use `.Deprecated`.
'spam.options' -> 'options', 'spam.getOption' -> 'getOption'
o 'validate_spam' superseeds 'validspamobject'.
o Added the list of Fortran contributors.
INTERNAL CHANGES
o Many... many. More still to come.
o Unit testing with testthat.
o Change of archaic trig functions to standard.
Minor edits to great circle dist.
CHANGES IN VERSION 1.4-0
INTERNAL CHANGES
o Fortran modification to address more pedantic compilations.
CHANGES IN VERSION 1.3-0
BUG FIXES
o Adding nonsparse to sparse matrices did not always dispatch
properly and caused some errors. Thanks to Johan Lindström
for pointing out.
SIGNIFICANT USER-VISIBLE CHANGES
o Help improvements
o Added additional method dispatching for 'all.equal'.
CHANGES IN VERSION 1.2-0 and 1.2-1
SIGNIFICANT USER-VISIBLE CHANGES
o Renaming of demos from JSS10 paper.
o Continuing to implement 'spam_xxx' function names:
Like 'spam_rdist' there is now 'spam_diag'.
o 'subset.rows.spam' deprecated. There is an internal function
'subset_rows.spam'.
INTERNAL CHANGES
o Ample minor modifications in 'DESCRIPTION' and 'NAMESPACE'
for CRAN check conformity.
o Elimination of a few unnecessary functions (not exported).
o Minor modifications in tests.
CHANGES IN VERSION 1.1-0
SIGNIFICANT USER-VISIBLE CHANGES
o Upload of vignette linked to JSS15 paper. Related demos
and tests.
o "DUP=FALSE" is deprecated and will be disabled in future