eps, the tolerance parameter determining which
elements are set to zero has been increased. New default is
spam.eps=100*.Machine$double.eps
Operations from S4 Group Generic Functions Logic and
Arith now all return a regular matrix if one of the objects
is a full spam object.
spam 2.11-3
INTERNAL CHANGES
Minor changes in diff coherent form as in
base::diff. Patch
https://bugs.r-project.org/show_bug.cgi?id=18972. (flagged by
testthat.
spam 2.11-2
BUG FIXES
Addressed sprintf() warnings due to unused arguments
(preset in print(, minimal=FALSE) and
print_nnzpos()).
INTERNAL CHANGES
Adding a few IGNORE_RDIFFs in examples.
Minor code cleaning.
spam 2.11-1
INTERNAL CHANGES
Minor improvements on *.Rout.save, addressing
differences.
spam 2.11-0
SIGNIFICANT USER-VISIBLE CHANGES
rbind() now works properly with spam64 for
two spam matrices.
INTERNAL CHANGES
Minor improvements on documentation.
Adjustements of *.Rout.save, according to new
format.
spam 2.10.0
SIGNIFICANT USER-VISIBLE CHANGES
nearest.dist() has now a super fast Rcpp implementation
by Annina Cincera.
BUG FIXES
One particular operation from S4 Group Generic Functions
Arith yielded wrong results if the sparse matrix was full,
see below. (Thanks to Ethan Heinzen.)
INTERNAL CHANGES
Changes in CITATION according to new
format.
Eliminated kind constructs in the Fortran code
(addressing _R_CHECK_FORTRAN_KIND_DETAILS_)
Added ... argument to
[t]crossprod.spam() as by generic.
spam 2.9.2
BUG FIXES
Certain operations from S4 Group Generic Functions
Logic and Arith yielded wrong results if the
sparse matrix was full. (Thanks to Ethan Heinzen.)
spam 2.9.1
BUG FIXES
Use of ## IGNORE_RDIFF_BEGIN and eps=1e-15
in the help files to assure coherence among different systems.
spam 2.9.0
SIGNIFICANT USER-VISIBLE CHANGES
New functions rmvt.spam() and rmvt()
sampling from a multivariate t-distribution. Approach is similar to
mvtnorm::rmvt().
INTERNAL CHANGES
Cleaning of help inconsistencies.
BUG FIXES
A zero sparse matrix caused severe errors within low level code of
spam.eigen.
spam 2.8-3
Prelease for version 2.9, only available on
https://git.math.uzh.ch/reinhard.furrer/spam.
spam 2.8-2
SIGNIFICANT USER-VISIBLE CHANGES
New function rgrf() to sample a Gaussian random
field (minimalistic replacement of geoR::grf().
New implementation of the Matern covariance function for
half-integer smoothness: cov.mat12() (wrapps to
cov.exp()) cov.mat32() and
cov.mat52() for nu=1/2, 3/2, and 5/2, respectively. The
function are factor 10 faster than cov.mat() with
corresponding smoothness.
New function cov.finnmat() using the parametrization
sqrt(8smoothness)h/range for as argument for the Bessel
function.
All *likelihood*() and mle*() functions
have now an argument cov.args= which will be passed to the
covariance function. This creates a larger flexibility to fine-tune
covariance functions.
New function neg2likelihood.nomean(), similar to
neg2likelihood().
spam 2.8-1
BUG FIXES
All covariance functions now call cov.nug(), when range
is smaller than eps.
spam 2.8-0
SIGNIFICANT USER-VISIBLE CHANGES
Minor improvements in the help files. (2.8-1)
The function chol.spam() has a much better verbose
offering.
The function determinant.spam() does not take any
arguments for the Cholesky factorization, if needed, pass via
chol(), i.e., det(chol(., args=))^2.
New function rmvnorm.conditional() to sample from a
multivariate conditional normal random variable.
The functions rmvnorm() and
rmvnorm.spam() have now arguments mean and
sigma (equivalent to mu and
Sigma), to match mvtnorm::rmvnorm().
Demo article-jss has been renamed
jss10-figures-table. Deprecated demos
article-jss-example1, article-jss-example2 and
jss10-example2 have been eliminated.
INTERNAL CHANGES
determinant.spam() and chol.spam() now use
the common routine .spam.chol.basis().
Added 64 bit support for back solve routines. Not fully tested.
Switched from URL to DOI for JJS references.
Some additional unit tests.
Demo files have been deprived from the unnecessary footer.
BUG FIXES
Memory allocation for nnzcolindicies was corrected (as
in versions <=2.6). The change in 2.7 was working well for huge
matrices. This addresses bug reported by Curtis Storlie, Martin Boer and
Paul Eilers.
Help of determinant.spam() now reflects what is
calculated.
determinant.spam() should now work with 64-bit as
well.
In case of insufficient memory allocation chol.spam()
now has appropriate 64-bit support for the subsequent iterations.
Addressing heap-buffer-overflow and allocating larger arrays in
eigen_approx. Debian package 2.7.0-2 contains the patch.
Thanks to Sébastien Villemot.
now works for length(s)>1, see PR#18272 for
base::all.equal.numeric(), thanks to Michael Chirico.
spam 2.7
SIGNIFICANT USER-VISIBLE CHANGES
spam package citeEntry.
updated examples and description of covmat() and
nearest.dist().
new functions rmvnorm(), cor.sph().
better memory allocation for Cholesky factorization.
INTERNAL CHANGES
covmat() with elementary if() clauses
instead of ifelse(), for stable memory usage.
nearest.dist() unleashed for spam64.
reorganized functions in R source files. Cleaned unnecessary
comments.
BUG FIXES
spam 2.6-0
SIGNIFICANT USER-VISIBLE CHANGES
print.spam() is able to print non-zero entries of a
spam matrix.
new fast Fortran routines used in new gmult() to
multiply specific spam submatrices with different factors.
INTERNAL CHANGES
renaming man files such that pkgdown is linking correctly.
spam 2.5-1
BUG FIXES
fixing fortran linking warning.
spam 2.5-0
SIGNIFICANT USER-VISIBLE CHANGES
improved examples for spam_random() and
eigen.spam().
Fortran code used by eigen.spam() for non-symmetric
matrices is now stable.
INTERNAL CHANGES
fixing real comparison warnings in Fortran.
removing remaining and unused print/count/timing variables in
Fortran.
implement dimension upper bound for eigen.spam() due to
BLAS/LAPACK routines, which are used in Arnoldi iteration (ARPACK).
BUG FIXES
adjusting spam.Rmd vignette to pandoc2.8.
correct class checking for matrices.
cleaning and consolidation of init.c with spam64 (LTO’s).
spam 2.4-0
INTERNAL CHANGES
cleaning GCC-10 Fortran warnings.
spam 2.3-0
NEW FEATURES
New function spam_random() to create a random spam
matrix.
SIGNIFICANT USER-VISIBLE CHANGES
Deprecated functions spam.options(),
spam.getOption() are removed.
Deprecated function validspamobject() is now
defunct.
todo() and spam.history() are
removed.
summary.spam() prints whether it is a 32 or 64-bit spam
object.
INTERNAL CHANGES
Fortran modification to address LTO issues.
Not exported deprecated function subset.rows.spam() is
now defunct.
BUG FIXES
Dataset UScounties.ndorder contained no-zeros on the
diagonal. Now entire diagonal is zero.
spam 2.2-2
BUG FIXES
in testthat/test-constructors.R, which uses
base::sample()
(http://developer.r-project.org/blosxom.cgi/R-devel/2019/02/26#n2019-02-26).
spam 2.2-1
SIGNIFICANT USER-VISIBLE CHANGES
New vignette including illustrations and examples
Improved documentation for covariance functions like
cov.exp().
BUG FIXES
det(spam(1)) bug fix & default of
diag.spam(x) in spam_diag() removed.
INTERNAL CHANGES
Spam fit for pkgdown website.
Replacing some internal functions by their primitive
equivalent.
spam 2.2-0
SIGNIFICANT USER-VISIBLE CHANGES
Implementation of ‘eigen.spam()’ and ‘eigen_approx()’ to calculate
eigenvalues and eigenvectors for sparse matrices.
spam 2.1-4
SIGNIFICANT USER-VISIBLE CHANGES
‘germany.plot’ has new argument ‘cex.main’.
BUG FIXES
‘NAOK=TRUE’ did not properly dispatch in all matrix
multiplications.
‘.newSpam()’ was not always properly called, causing possible errors
when creating empty ‘spam’ objects.
INTERNAL CHANGES
Code cleaning and coherence improvements.
spam 2.1-2
SIGNIFICANT USER-VISIBLE CHANGES
In case 64bits are required, issues an error to load package
‘spam64’ first.
Minor fixes in help files and other documentation.
INTERNAL CHANGES
Improved registering of compiled functions.
Compatibility with new versions of package ‘testthat’.
spam 2.1-1
SIGNIFICANT USER-VISIBLE CHANGES
With the addon of the package spam64, we have truly 64 bits
available!
Dependency on dotCall64.
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’
‘validate_spam’ superseeds ‘validspamobject’.
Added the list of Fortran contributors.
INTERNAL CHANGES
Many… many. More still to come.
Unit testing with testthat.
Change of archaic trig functions to standard. Minor edits to great
circle dist.
spam 1.4-0
INTERNAL CHANGES
Fortran modification to address more pedantic compilations.
spam 1.3-0
BUG FIXES
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
Help improvements
Added additional method dispatching for ‘all.equal’.
spam 1.2-0 and 1.2-1
SIGNIFICANT USER-VISIBLE CHANGES
Renaming of demos from JSS10 paper.
Continuing to implement ‘spam_xxx’ function names: Like
‘spam_rdist’ there is now ‘spam_diag’.
‘subset.rows.spam’ deprecated. There is an internal function
‘subset_rows.spam’.
INTERNAL CHANGES
Ample minor modifications in ‘DESCRIPTION’ and ‘NAMESPACE’ for CRAN
check conformity.
Elimination of a few unnecessary functions (not exported).
Minor modifications in tests.
spam 1.1-0
SIGNIFICANT USER-VISIBLE CHANGES
Upload of vignette linked to JSS15 paper. Related demos and
tests.
“DUP=FALSE” is deprecated and will be disabled in future versions of
R. All “DUP” arguments have been eliminated. You have to expect a
slightly slower version of spam.
spam 1.0 and 1.0-1
This version is up to ‘DESCRIPTION’ and its implied changes
identical to 0.90-1. With the upcoming JSS article “Pitfalls in the
implementation of Bayesian hierarchical modeling of areal count data. An
illustration using BYM and Leroux models.” a “major” version jump is
adequate.
Referencing to spam data through spam::…
Implemented 1.1.3.1 Suggested packages approach.
spam 0.70/0.80/0.90/0.90-1
SIGNIFICANT USER-VISIBLE CHANGES
Introduction of many as(‘spam’,‘…’) functions.
Coercion function as.vector for spam objects.
Wrapper functions spam_rdist and
’spam_rdist.earthfor smooth use infields`.
The use of update(A, B) without assignment has been
eliminated. This is one way to address the change in memory handling
changes from R 3.0.2 to R 3.1.0. There is a slight overhead in memory.
If this causes problems, let me know.
Adjustment of the license.
NEW FEATURES
Arguments diag and eps in
nearest.dist cause now an error.
Further augmented help pages.
BUG FIXES
The demo now points to the new JSS article.
INTERNAL CHANGES
Set ‘structurebased=TRUE’ for the demos.
Link to upcoming JSS article in one of the demos.
‘update.spam.chol.NgPeyton’ preserves the structure (pointed out by
Chris Paciorek), see above.
Using similar License approach as SparseM. New files
README, inst/0LICENSE.
File renaming (OChangeLog -> 0ChangeLog)
Adjusted error messages for precmat.RW2
spam 0.60-0
SIGNIFICANT USER-VISIBLE CHANGES
Using the flag ‘structurebased’, the behavior of spam is now more
consistent.
“Arith”, “Compare”, “Logic” (getGroupMembers(“Ops”)) have now a
consistent behavior.
NEW FEATURES
Few new S3 functions for simplicity: ‘var.spam’, ‘eigen.spam’,
…
New constructor functions ‘colindices<-’ etc. Maybe additional
tests may be required.
Operators from ‘Arith’ obey now the structure based
calculation.
BUG FIXES
‘inefficiencywarning’ passes message correctly.
INTERNAL CHANGES
many more spam/tests/*.
Consistent use of ‘spam’ and ‘vector’ siglist for ‘Ops’.
Minor cleaning of Fortran code.
Renaming/restructuring/cleaning of files…
Fortran arguments are copied when updating the cholesky
structure.
spam 0.50-0
SIGNIFICANT USER-VISIBLE CHANGES
Using the flag ‘structurebased=FALSE’, the behavior of spam is now
much, much closer to regular matrix calculations. This is illustrated
when calculating gamma of a sparse matrix.
Along the same lines, the flag ‘NAOK=TRUE’ allows the use of the
“not finite numbers” (NA, NaN, Inf). We have tested many, many functions
but full fledged use is not yet guaranteed.
Currently, we can still guarantee backwards compatibility…
NEW FEATURES
New functions ‘crossprod’ and ‘tcrossprod’ as well as according
method definitions.
New constructor functions ‘rowpointers<-’ etc.
Better option handling. The option ‘safemode’ is now
‘safemodevalidity’. Additionally, new option ‘NAOK’.
Help pages have been improved.
Operators from ‘Summary’ and ‘Math’ obey now the structure based
calculation. (‘Math2’ inherently does).
BUG FIXES
rmvnorm.[].const now work properly for any number of constraints and
n.
Assignment handles properly recycling.
todo() now works properly.
INTERNAL CHANGES
eliminated {d,i}check by equivalent coercion.
Consistent use of NAOK in Fortran calls.
Minor cleaning of Fortran code.
Renaming/restructuring of files…
spam 0.42-0
NEW FEATURES
More consistent handling of subsetting. Warning is issued if
subsetting with NA
BUG FIXES
Fixed several issues when rowsubsetting…
INTERNAL CHANGES
Additional tests for positive definiteness in ‘chol’.
spam 0.41-0
NEW FEATURES
Functions grid_trace2() received more functionality.
BUG FIXES
Eliminated bug in cov.mat(). Pointed out by Joshua French.
INTERNAL CHANGES
Updated DESCRIPTION: added Florian Gerber [ctb].
Minor code and help cleanup. Additional testing files. File header
edits.
Addressed Rdevel CMD check –as-cran Notes, especially workaround for
DUP=FALSE.
spam 0.40-0
BUG FIXES
A severe bug in subsetting a spam object with a nx2 matrix crept in
spam in version 0.29-3. Thanks to Andrew Hong and Beat Briner for
pointing out.
To simplify communication, we have switched increased the tenth
version number.
All other changes are of cosmetic nature.
spam 0.30-x
SIGNIFICANT USER-VISIBLE CHANGES
Added several plots to visualize several MCMC chains (‘grid_trace2’,
‘grid_zoom’, …).
NEW FEATURES
New function ‘germany.plot’ to draw the landkreise. (‘map.landkreis’
is now obsolete).
Switched from ‘tim.colors’ to ‘colorRampPalette’ in
‘germany.plot’.
Metadata in ‘germany.info’, polygon definitions in ‘germany.poly’
(‘germany’ kept for backwards compatibility).
INTERNAL CHANGES
Switched to mercurial for maintaining the package.
Updated ChangeLog file (hg log).
Increased dependency to >= R 2.15.
Minor code and help cleanup.
spam 0.29-0, 0.29-1, 0.29-2,
0.29-3
SIGNIFICANT USER-VISIBLE CHANGES
There is a generic conflict with ‘backsolve’ between spam and
other packages (e.g., bdsmatrix). To avoid the issue, we use the
standard generic implemented in ‘methods’ which requires an additional
argument for version 0.29-0 (see also PR#14883). However to maintain
backwards compatibility with packages that depend on spam, this was
reverted in 0.29-1. Currently, this conflict is not properly solved. I
propose to load ‘spam’ first then the other packages, followed by
manually calling:
now work. They are, however, somewhat inefficient.
'toeplitz.spam' is to be prefered.
Pointed out by Florian Gerber.
The Gibbs sampler in the demo article-jss-example2 contains several
bugs, pointed out by Steve Geinitz and Andrea Riebler. I’ll post an
updated sampler in a future release.
NEW FEATURES
New functions ‘rmvnorm.const’, ‘rmvnorm.prec.const’ and
‘rmvnorm.canonical.const’ to draw constrained multivariate normal
variates.
New functions ‘precmat’ (wrapper to), ‘precmat.RW1’, ‘precmat.RW2’,
‘precmat.season’, ‘precmat.IGMRFreglat’ and ‘precmat.IGMRFirreglat’ to
create precision matrices for IGMRF.
New methods ‘rowSums’, ‘colSums’ and ‘rowMeans’, ‘colMeans’ for
‘spam’ objects.
New methods ‘head’ and ‘tail’ for ‘spam’ and ‘spam.chol.NgPeyton’
objects.
New method ‘chol2inv’ for ‘spam’ object.
New option ‘inefficiencywarning’: handling of warnings issued in
case of an inefficient calculation.
New option ‘structurebased’: should operations be performed on the
nonzero entries or on including the zeros. Classical example: what
should the cosine of a sparse matrix look like? In the near future, all
operations from Math and Ops will include this option. Some loss of
backwards compatibility might be lost in the future.
INTERNAL CHANGES
New much faster approach to extract rows. For not too sparse large
matrices improvements over two orders of magnitudes are achieved.
Elininated ‘.Internal()’ calls that induce a ‘Note’ on CRAN checks.
This also implied a minor rewrite of ‘image.spam’.
Minor code improvements.
Eliminated non-API calls (29.1).
Rewritten .C(“bincode”,…) call as suggested by Brian Ripley
(29.2).
BUG FIXES
Bug fix that occures when multiplying elementwise matrices that have
non-intersecting structures (pointed out by Corentin Barbu).
Bug fix in triangular backsolves involving ‘spam’ objects and rhs
matrices.
Bug fix in triangular backsolve causing errors on some
architectures.
spam 0.28
NEW FEATURES
New function ‘cleanup’ (suggested by Simon Barthelme).
Extending help files.
Improved functionality of ‘isSymmetric’.
INTERNAL CHANGES
Proper storage of data files.
Cleaning up argument names within spam functions.
Cleaning up old Fortran code, i.e., eliminating unnecessary
subroutines and write calls.
BUG FIXES
Bug fix that may occure when extracting zero elements (pointed out
by Corentin Barbu).
spam 0.27
NEW FEATURES
Requires now R2.10 and higher.
Functions to create Toeplitz and circulant matrices.
Function to create precision matrices for gridded GMRF.
Improvements in the mle.* functions.
Method diff for sparse matrices (suggested by Paul Eilers).
Improvement of help pages.
Eliminated some help aliases to base functions (for which no ‘usage’
is given).
INTERNAL CHANGES
Change to iL coding.
Start to using ‘identical’.
Code cleaning due to requirement of R2.10 and higher.
BUG FIXES
Bug fix in as.spam.list (thanks to Paul Eilers).
Bug fix in demo(spam) (thanks to Thomas Gsponer).
spam 0.24, 0.25 and 0.26
Devel versions, not released.
spam 0.23
NEW FEATURES
Further improved versions of demos.
Some improvements to meet Rd standards. Adjustments for future R
versions.
spam 0.22
NEW FEATURES
Improved versions of demos. Synchronized with the JSS article.
Additional changes and improvements in the help files (thanks to
Steve Geinitz).
spam 0.21
NEW FEATURES
New NEWS file, to work better with news() command. The previous is
available under ONEWS.
New functions bandwidth, permutation, mle[.nomean][.spam],
neg2loglikelihood[.spam].
Renamed adiag.spam to bdiag.spam.
Cleaned up argument naming with the rmvnorm.* suite.
INTERNAL CHANGES
Various Fortran code, R code and help file improvements.
BUG FIXES
Minor change in one of the demos (solves a 64bit issue).
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