r-cran-spam 2.1-2-1 / usr / lib / R / site-library / spam / NEWS

	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 
    	versions of R. All "DUP" arguments have been eliminated.
	You have to expect a slightly slower version of spam.



 
	CHANGES IN VERSION 1.0 and 1.0-1
 
    o   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.


    o   Referencing to spam data through spam::...


    o	Implemented `1.1.3.1 Suggested packages` approach.




	CHANGES IN VERSION 0.70/0.80/0.90/0.90-1

SIGNIFICANT USER-VISIBLE CHANGES

    o	Introduction of many as('spam','...') functions.

    o   Coercion function `as.vector` for spam objects. 

    o   Wrapper functions `spam_rdist` and 'spam_rdist.earth`
	for smooth use in `fields`.

    o   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.

    o   Adjustment of the license.


NEW FEATURES

   o    Arguments `diag` and `eps` in `nearest.dist` cause now
	an error.

   o    Further augmented help pages.


BUG FIXES

   o    The demo now points to the new JSS article.


INTERNAL CHANGES

    o	Set 'structurebased=TRUE' for the demos.

    o   Link to upcoming JSS article in one of the demos. 

    o 	'update.spam.chol.NgPeyton' preserves the structure
	(pointed out by Chris Paciorek), see above.

    o   Using similar License approach as SparseM. New files
	`README`, `inst/0LICENSE`.

    o   File renaming (OChangeLog -> 0ChangeLog) 


    o   Adjusted error messages for precmat.RW2


	CHANGES IN VERSION 0.60-0

SIGNIFICANT USER-VISIBLE CHANGES

   o	Using the flag 'structurebased', the behavior 
	of spam is now more consistent.

   o    "Arith", "Compare", "Logic" (getGroupMembers("Ops")) 
	have now a consistent behavior.



NEW FEATURES

   o    Few new S3 functions for simplicity: 
	'var.spam', 'eigen.spam', ...

   o 	New constructor functions 'colindices<-' etc.
	Maybe additional tests may be required.

   o 	Operators from 'Arith' obey now the 
   	structure based calculation. 


BUG FIXES

   o    'inefficiencywarning' passes message correctly.


INTERNAL CHANGES

   o 	many more spam/tests/*.

   o    Consistent use of 'spam' and 'vector' siglist for 'Ops'.

   o    Minor cleaning of Fortran code.
    
   o    Renaming/restructuring/cleaning of files...

   o    Fortran arguments are copied when updating the cholesky 
	structure.

 


	CHANGES IN VERSION 0.50-0

SIGNIFICANT USER-VISIBLE CHANGES

   o	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.

   o    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.

   o    Currently, we can still guarantee backwards 
	compatibility...


NEW FEATURES

   o    New functions 'crossprod' and 'tcrossprod' as well
	as according method definitions.

   o 	New constructor functions 'rowpointers<-' etc.

   o 	Better option handling. The option 'safemode' is
	now 'safemodevalidity'. Additionally, new option
	'NAOK'.

   o    Help pages have been improved.

   o 	Operators from 'Summary' and 'Math' obey now the 
   	structure based calculation. 
	('Math2' inherently does).


BUG FIXES

   o    rmvnorm.[].const now work properly for any number of
	constraints and n.

   o	Assignment handles properly recycling.

   o	todo() now works properly.


INTERNAL CHANGES

   o 	eliminated {d,i}check by equivalent coercion.

   o    Consistent use of NAOK in Fortran calls.

   o    Minor cleaning of Fortran code.
    
   o    Renaming/restructuring of files...

 



	CHANGES IN VERSION 0.42-0

NEW FEATURES

   o    More consistent handling of subsetting. 
   	Warning is issued if subsetting with NA


BUG FIXES

   o    Fixed several issues when rowsubsetting...


INTERNAL CHANGES

   o 	Additional tests for positive definiteness in 'chol'.




	CHANGES IN VERSION 0.41-0


NEW FEATURES

   o    Functions grid_trace2() received more functionality.


BUG FIXES

   o    Eliminated bug in cov.mat(). Pointed out by Joshua French


INTERNAL CHANGES

   o 	Updated DESCRIPTION: added Florian Gerber [ctb]

   o    Minor code and help cleanup. Additional testing files. 
   	File header edits.

   o	Addressed Rdevel CMD check --as-cran Notes, especially
   	workaround for DUP=FALSE





	CHANGES IN VERSION 0.40-0



BUG FIXES
   
   o    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.




	CHANGES IN VERSION 0.30-x


SIGNIFICANT USER-VISIBLE CHANGES

   o	Added several plots to visualize several MCMC chains
   	('grid_trace2', 'grid_zoom', ...). 


NEW FEATURES

   o    New function 'germany.plot' to draw the landkreise.
   	('map.landkreis' is now obsolete).

   o	Switched from 'tim.colors' to 'colorRampPalette'
   	in 'germany.plot'.

   o 	Metadata in 'germany.info', polygon definitions in
   	'germany.poly' ('germany' kept for backwards 
	compatibility).


INTERNAL CHANGES

   o 	Switched to mercurial for maintaining the package.

   o    Updated ChangeLog file (hg log).

   o 	Increased dependency to >= R 2.15.

   o    Minor code and help cleanup.





	CHANGES IN VERSION 0.29-0, 0.29-1, 0.29-2, 0.29-3

SIGNIFICANT USER-VISIBLE CHANGES

   o	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:

	  setMethod("backsolve","spam.chol.NgPeyton",backsolve.spam)
	  setMethod("backsolve","spam",backsolve.spam)

	Stay tuned...

   o	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.

   o	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

   o	New functions 'rmvnorm.const', 'rmvnorm.prec.const' and
   	'rmvnorm.canonical.const' to draw constrained multivariate
	normal variates.

   o	New functions 'precmat' (wrapper to), 'precmat.RW1', 'precmat.RW2', 
    	'precmat.season', 'precmat.IGMRFreglat' and 'precmat.IGMRFirreglat'
   	to create precision matrices for IGMRF.

   o	New methods 'rowSums', 'colSums' and  'rowMeans', 'colMeans' for
   	'spam' objects.

   o	New methods 'head' and 'tail' for 'spam' and 'spam.chol.NgPeyton' 
   	objects.

   o 	New method 'chol2inv' for 'spam' object.

   o	New option 'inefficiencywarning': handling of warnings issued 
   	in case of an inefficient calculation. 

   o	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

   o	New much faster approach to extract rows. For not too sparse 
   	large matrices improvements over two orders of magnitudes are
	achieved.
	
   o 	Elininated '.Internal()' calls that induce a 'Note' on CRAN
   	checks. This also implied a minor rewrite of 'image.spam'.	

   o 	Minor code improvements. 

   o	Eliminated non-API calls (29.1).

   o	Rewritten .C("bincode",...) call as suggested by Brian Ripley
   	(29.2).
  

BUG FIXES

   o 	Bug fix that occures when multiplying elementwise matrices 
   	that have non-intersecting structures (pointed out by 
	Corentin Barbu).

   o	Bug fix in triangular backsolves involving 'spam' objects 
   	and rhs matrices.

   o	Bug fix in triangular backsolve causing errors on some
   	architectures.




	CHANGES IN VERSION 0.28

NEW FEATURES

   o	New function 'cleanup' (suggested by Simon Barthelme). 

   o 	Extending help files.

   o 	Improved functionality of 'isSymmetric'.


INTERNAL CHANGES

   o	Proper storage of data files.

   o 	Cleaning up argument names within spam functions.	 

   o    Cleaning up old Fortran code, i.e., eliminating
   	unnecessary subroutines and write calls.


BUG FIXES

   o 	Bug fix that may occure when extracting zero elements 
        (pointed out by Corentin Barbu).




	CHANGES IN VERSION 0.27

NEW FEATURES

    o	Requires now R2.10 and higher.

    o	Functions to create Toeplitz and circulant matrices.

    o 	Function to create precision matrices for gridded GMRF.

    o	Improvements in the mle.* functions.

    o	Method diff for sparse matrices (suggested by Paul Eilers).

    o 	Improvement of help pages. 

    o	Eliminated some help aliases to base functions 
    	(for which no 'usage' is given). 


INTERNAL CHANGES

    o  	Change to iL coding.

    o	Start to using 'identical'.

    o 	Code cleaning due to requirement of R2.10 and higher.


BUG FIXES

    o   Bug fix in as.spam.list (thanks to Paul Eilers).

    o 	Bug fix in demo(spam) (thanks to Thomas Gsponer).





	CHANGES IN VERSION 0.24, 0.25 and 0.26
	
    o 	Devel versions, not released.	





	CHANGES IN VERSION 0.23

NEW FEATURES

    o	Further improved versions of demos. 

    o	Some improvements to meet Rd standards.
        Adjustments for future R versions. 





	CHANGES IN VERSION 0.22

NEW FEATURES

    o	Improved versions of demos. Synchronized with the JSS article.

    o   Additional changes and improvements in the help files (thanks
    	to Steve Geinitz).


    




	CHANGES IN VERSION 0.21

	
NEW FEATURES

    o	New NEWS file, to work better with news() command.
    	The previous is available under ONEWS.


    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.


INTERNAL CHANGES

    o   Various Fortran code, R code and help file 
    	improvements.


BUG FIXES

    o	Minor change in one of the demos (solves a 64bit issue).