Movatterモバイル変換

spam 3.0 (UPCOMING)

SIGNIFICANT USER-VISIBLE CHANGES

• eps, the tolerance parameter determining whichelements are set to zero has been increased. New default isspam.eps=100*.Machine$double.eps

• Operations from S4 Group Generic FunctionsLogic andArith now all return a regular matrix if one of the objectsis a fullspam object.

spam 2.11-1

INTERNAL CHANGES

• Minor improvements on*.Rout.save, addressingdifferences.

spam 2.11-0

SIGNIFICANT USER-VISIBLE CHANGES

• rbind() now works properly withspam64 fortwo spam matrices.

INTERNAL CHANGES

• Minor improvements on documentation.

• Adjustements of*.Rout.save, according to newformat.

spam 2.10.0

SIGNIFICANT USER-VISIBLE CHANGES

• nearest.dist() has now a super fast Rcpp implementationby Annina Cincera.

BUG FIXES

• One particular operation from S4 Group Generic FunctionsArith yielded wrong results if the sparse matrix was full,see below. (Thanks to Ethan Heinzen.)

INTERNAL CHANGES

• Changes inCITATION according to newformat.

• Eliminatedkind 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 FunctionsLogic andArith yielded wrong results if thesparse matrix was full. (Thanks to Ethan Heinzen.)

spam 2.9.1

BUG FIXES

• Use of## IGNORE_RDIFF_BEGIN andeps=1e-15in the help files to assure coherence among different systems.

spam 2.9.0

SIGNIFICANT USER-VISIBLE CHANGES

• New functionsrmvt.spam() andrmvt()sampling from a multivariate t-distribution. Approach is similar tomvtnorm::rmvt().

INTERNAL CHANGES

• Cleaning of help inconsistencies.

BUG FIXES

• A zero sparse matrix caused severe errors within low level code ofspam.eigen.

spam 2.8-3

Prelease for version 2.9, only available onhttps://git.math.uzh.ch/reinhard.furrer/spam.

spam 2.8-2

SIGNIFICANT USER-VISIBLE CHANGES

• New functionrgrf() to sample a Gaussian randomfield (minimalistic replacement ofgeoR::grf().

• New implementation of the Matern covariance function forhalf-integer smoothness:cov.mat12() (wrapps tocov.exp())cov.mat32() andcov.mat52() for nu=1/2, 3/2, and 5/2, respectively. Thefunction are factor 10 faster thancov.mat() withcorresponding smoothness.

• New functioncov.finnmat() using the parametrizationsqrt(8smoothness)h/range for as argument for the Besselfunction.

• All*likelihood*() andmle*() functionshave now an argumentcov.args= which will be passed to thecovariance function. This creates a larger flexibility to fine-tunecovariance functions.

• New functionneg2likelihood.nomean(), similar toneg2likelihood().

spam 2.8-1

BUG FIXES

• All covariance functions now callcov.nug(), when rangeis smaller thaneps.

spam 2.8-0

SIGNIFICANT USER-VISIBLE CHANGES

• Minor improvements in the help files. (2.8-1)

• The functionchol.spam() has a much better verboseoffering.

• The functiondeterminant.spam() does not take anyarguments for the Cholesky factorization, if needed, pass viachol(), i.e.,det(chol(., args=))^2.

• New functionrmvnorm.conditional() to sample from amultivariate conditional normal random variable.

• The functionsrmvnorm() andrmvnorm.spam() have now argumentsmean andsigma (equivalent tomu andSigma), to matchmvtnorm::rmvnorm().

• Demoarticle-jss has been renamedjss10-figures-table. Deprecated demosarticle-jss-example1,article-jss-example2 andjss10-example2 have been eliminated.

INTERNAL CHANGES

• determinant.spam() andchol.spam() now usethe 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 fornnzcolindicies was corrected (asin versions <=2.6). The change in 2.7 was working well for hugematrices. This addresses bug reported by Curtis Storlie, Martin Boer andPaul Eilers.
• Help ofdeterminant.spam() now reflects what iscalculated.
• determinant.spam() should now work with 64-bit aswell.
• In case of insufficient memory allocationchol.spam()now has appropriate 64-bit support for the subsequent iterations.
• Addressing heap-buffer-overflow and allocating larger arrays ineigen_approx. Debian package 2.7.0-2 contains the patch.Thanks to Sébastien Villemot.
• now works forlength(s)>1, see PR#18272 forbase::all.equal.numeric(), thanks to Michael Chirico.

spam 2.7

SIGNIFICANT USER-VISIBLE CHANGES

• spam packageciteEntry.
• updated examples and description ofcovmat() andnearest.dist().
• new functionsrmvnorm(),cor.sph().
• better memory allocation for Cholesky factorization.

INTERNAL CHANGES

• covmat() with elementaryif() clausesinstead ofifelse(), for stable memory usage.
• nearest.dist() unleashed for spam64.
• reorganized functions in R source files. Cleaned unnecessarycomments.

BUG FIXES

spam 2.6-0

SIGNIFICANT USER-VISIBLE CHANGES

• print.spam() is able to print non-zero entries of aspam matrix.
• new fast Fortran routines used in newgmult() tomultiply 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 forspam_random() andeigen.spam().
• Fortran code used byeigen.spam() for non-symmetricmatrices is now stable.

INTERNAL CHANGES

• fixing real comparison warnings in Fortran.
• removing remaining and unused print/count/timing variables inFortran.
• implement dimension upper bound foreigen.spam() due toBLAS/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 functionspam_random() to create a random spammatrix.

SIGNIFICANT USER-VISIBLE CHANGES

• Deprecated functionsspam.options(),spam.getOption() are removed.
• Deprecated functionvalidspamobject() is nowdefunct.
• todo() andspam.history() areremoved.
• summary.spam() prints whether it is a 32 or 64-bit spamobject.

INTERNAL CHANGES

• Fortran modification to address LTO issues.
• Not exported deprecated functionsubset.rows.spam() isnow defunct.

BUG FIXES

• DatasetUScounties.ndorder contained no-zeros on thediagonal. Now entire diagonal is zero.

spam 2.2-2

BUG FIXES

• in testthat/test-constructors.R, which usesbase::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 likecov.exp().

BUG FIXES

• det(spam(1)) bug fix & default ofdiag.spam(x) inspam_diag() removed.

INTERNAL CHANGES

• Spam fit for pkgdown website.
• Replacing some internal functions by their primitiveequivalent.

spam 2.2-0

SIGNIFICANT USER-VISIBLE CHANGES

• Implementation of ‘eigen.spam()’ and ‘eigen_approx()’ to calculateeigenvalues 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 matrixmultiplications.
• ‘.newSpam()’ was not always properly called, causing possible errorswhen 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 bitsavailable!
• Dependency on dotCall64.
• Different option handling, we use now the classical R setting. Forthe moment, the old functionality throws a message but in upcomingversions 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 greatcircle 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 properlyand 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 CRANcheck 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 andtests.
• “DUP=FALSE” is deprecated and will be disabled in future versions ofR. All “DUP” arguments have been eliminated. You have to expect aslightly slower version of spam.

spam 1.0 and 1.0-1

• This version is up to ‘DESCRIPTION’ and its implied changesidentical to 0.90-1. With the upcoming JSS article “Pitfalls in theimplementation of Bayesian hierarchical modeling of areal count data. Anillustration using BYM and Leroux models.” a “major” version jump isadequate.
• Referencing to spam data through spam::…
• Implemented1.1.3.1 Suggested packages approach.

spam 0.70/0.80/0.90/0.90-1

SIGNIFICANT USER-VISIBLE CHANGES

• Introduction of many as(‘spam’,‘…’) functions.
• Coercion functionas.vector for spam objects.
• Wrapper functionsspam_rdist and’spam_rdist.earthfor smooth use infields`.
• The use ofupdate(A, B) without assignment has beeneliminated. This is one way to address the change in memory handlingchanges 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

• Argumentsdiag andeps innearest.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 byChris Paciorek), see above.
• Using similar License approach as SparseM. New filesREADME,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 moreconsistent.
• “Arith”, “Compare”, “Logic” (getGroupMembers(“Ops”)) have now aconsistent behavior.

NEW FEATURES

• Few new S3 functions for simplicity: ‘var.spam’, ‘eigen.spam’,…
• New constructor functions ‘colindices<-’ etc. Maybe additionaltests may be required.
• Operators from ‘Arith’ obey now the structure basedcalculation.

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 choleskystructure.

spam 0.50-0

SIGNIFICANT USER-VISIBLE CHANGES

• Using the flag ‘structurebased=FALSE’, the behavior of spam is nowmuch, much closer to regular matrix calculations. This is illustratedwhen 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 functionsbut full fledged use is not yet guaranteed.
• Currently, we can still guarantee backwards compatibility…

NEW FEATURES

• New functions ‘crossprod’ and ‘tcrossprod’ as well as accordingmethod 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 basedcalculation. (‘Math2’ inherently does).

BUG FIXES

• rmvnorm.[].const now work properly for any number of constraints andn.
• 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 ifsubsetting 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 headeredits.
• Addressed Rdevel CMD check –as-cran Notes, especially workaround forDUP=FALSE.

spam 0.40-0

BUG FIXES

• A severe bug in subsetting a spam object with a nx2 matrix crept inspam in version 0.29-3. Thanks to Andrew Hong and Beat Briner forpointing out.
• To simplify communication, we have switched increased the tenthversion 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 andother packages (e.g., bdsmatrix). To avoid the issue, we use thestandard generic implemented in ‘methods’ which requires an additionalargument for version 0.29-0 (see also PR#14883). However to maintainbackwards compatibility with packages that depend on spam, this wasreverted in 0.29-1. Currently, this conflict is not properly solved. Ipropose to load ‘spam’ first then the other packages, followed bymanually calling:

• setMethod(“backsolve”,“spam.chol.NgPeyton”,backsolve.spam)setMethod(“backsolve”,“spam”,backsolve.spam)

Stay tuned...

• Calls like:

• mat <- diag.spam(4) diag(mat[-1, ]) <- 3 diag.spam(mat[ ,-1]) <-2

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 severalbugs, pointed out by Steve Geinitz and Andrea Riebler. I’ll post anupdated sampler in a future release.

NEW FEATURES

• New functions ‘rmvnorm.const’, ‘rmvnorm.prec.const’ and‘rmvnorm.canonical.const’ to draw constrained multivariate normalvariates.
• New functions ‘precmat’ (wrapper to), ‘precmat.RW1’, ‘precmat.RW2’,‘precmat.season’, ‘precmat.IGMRFreglat’ and ‘precmat.IGMRFirreglat’ tocreate 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 incase of an inefficient calculation.
• New option ‘structurebased’: should operations be performed on thenonzero entries or on including the zeros. Classical example: whatshould the cosine of a sparse matrix look like? In the near future, alloperations from Math and Ops will include this option. Some loss ofbackwards compatibility might be lost in the future.

INTERNAL CHANGES

• New much faster approach to extract rows. For not too sparse largematrices 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 havenon-intersecting structures (pointed out by Corentin Barbu).
• Bug fix in triangular backsolves involving ‘spam’ objects and rhsmatrices.
• Bug fix in triangular backsolve causing errors on somearchitectures.

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 unnecessarysubroutines and write calls.

BUG FIXES

• Bug fix that may occure when extracting zero elements (pointed outby 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 Rversions.

spam 0.22

NEW FEATURES

• Improved versions of demos. Synchronized with the JSS article.
• Additional changes and improvements in the help files (thanks toSteve Geinitz).

spam 0.21

NEW FEATURES

• New NEWS file, to work better with news() command. The previous isavailable 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).