2012-06-26  Douglas Bates  <bates@stat.wisc.edu>

	* DESCRIPTION, R/unit.test.R, inst/include/Eigen/*: Massive
	changes related to upgrade to Eigen-3.1.0

2012-03-08  Douglas Bates <bates@stat.wisc.edu>

	* inst/tests/test-solutions.R, inst/tests/test-transform.R,
	  inst/tests/test-wrap.R: Add testthat test files, temporarily disabled
	  for R CMD check because of an unknown conflict
	* DESCRIPTION, R/unit.test.R, inst/include/Eigen/Cholesky,
	 ..., src/Makevars: Massive changes in upgrade to Eigen-3.1.0-alpha2

2012-03-03  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/RcppEigenWrap.h: Correct a typo.

2012-02-28  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: Add as
	  templates for ArrayXd and ArrayXXd

2012-02-03  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/RcppEigenWrap.h, inst/unitTests/runit.sparse.R: Allow
	  import of compressed row sparse matrices. Add test of same.

2012-01-18  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/RcppEigenWrap.h: Allow for wrapping sparse row-major
	  matrices.

2011-12-31  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/RcppEigenCholmod.h: Minor typo in a comment

2011-12-23  Dirk Eddelbuettel  <edd@debian.org>

	* inst/unitTests/runTests.R: unit tests output 'fallback' directory
	changed to '..' and files are now in top-level of $pkg.Rcheck/

2011-11-14  Douglas Bates  <bates@stat.wisc.edu>

	* vignettes/RcppEigen-intro-nojss.Rnw: Many, many changes by Dirk
	and by Doug over the last two weeks to create a JSS paper and
	updated package.  Too many changes to list.

2011-10-26  Douglas Bates <bates@stat.wisc.edu>

	* inst/doc/Rcpp.bib, inst/doc/RcppEigen-Intro.Rnw,
	  inst/doc/RcppEigen-Intro.pdf: Add an introductory vignette.
	* src/fastLm.cpp, src/fastLm.h: Use a method for XtX but returning a
	  MatrixXd, not a view.
	* inst/doc/RcppEigen-Intro.Rnw: Describe the SymmEig method correctly.
	* src/fastLm.cpp, src/fastLm.h: Use a macro for XtX temporarily. Clean
	  up code.
	* inst/include/RcppEigenCholmod.h, inst/include/RcppEigenStubs.h: Update
	  to Matrix_1.0.2 versions
	* inst/include/Eigen, inst/include/unsupported: update to eigen 3.0.3
	* src/RcppEigen.cpp: Add externally callable functions for Eigen version
	  and SSE instruction sets in use.
	* inst/examples/lmBenchmark.R: Suppress messages and provide additional
	  information about Eigen version and SSE instructions in use.
	* R/fastLm.R: Allow optional arguments to be passed to printCoefmat;
	  adapt to new returned structure.

2011-09-16  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: Avoid
	  compiler warnings about comparing signed and unsigned values.

2011-09-13  Douglas Bates <bates@stat.wisc.edu>

	* src/Makevars: Force the -DNDEBUG flag to satisfy R CMD check in
	  R-2.14.0 and higher

2011-09-12  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h:
	  Remove the solvetype specification for the solve method (but type is
	  retained for solveInPlace).

2011-09-11  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/RcppEigenForward.h: Remove forward declaration of
	  non-existent templated function.

2011-09-02  Douglas Bates <bates@stat.wisc.edu>

	* DESCRIPTION, inst/include/Eigen/src/Core/util/Meta.h: New release.
	  ifdef the use of "long long" using RCPP_HAS_LONG_LONG_TYPES (thanks,
	  Dirk)

2011-08-31  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h:
	  Delete my addition of a CholmodAutoLLt mode, which is not needed (I
	  misunderstood something previously).

2011-08-28  Douglas Bates <bates@stat.wisc.edu>

	* many files in inst/include/Eigen and inst/include/unsupported:
	  Upgrade to Eigen release 3.0.2

2011-08-12  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h:
	  By-passing the const reference

2011-08-11  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: Add a
	  solveInPlace method to try to avoid memory problems.

2011-08-10  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h:
	  Attempted fix of problem of freeing Map'ed memory in the Cholmod
	  solve.

2011-07-31  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h:
	  Trying to fix the memory problems from the CholmodDecomposition solve
	  methods - apparently unsuccessfully.

2011-07-29  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: Add
	  LLtAuto method (which doesn't seem to work), more extractors and a
	  factorize_p method for a const_CHM_SP argument.
	* inst/include/RcppEigenCholmod.h: Add a declaration of log determinant
	  squared function.
	* inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h,
	  inst/unitTests/runit.sparse.R: Allow rectangular matrix in
	  CholmodDecomposition's factorize method. Test rectangular version of
	  KNex example.

2011-07-28  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: Added
	  a solveType member - there will be better ways of doing this
	* inst/include/RcppEigenForward.h: Include the stubs unconditionally
	* inst/include/RcppEigenStubs.cpp:
	* inst/include/RcppEigenStubs.h: Inlined the function definitions so it
	  is a header file now
	* inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h:
	  Extended CholmodDecomposition analyzePattern and factorize to support
	  rectangular matrices. Added factorize_p method, primarily for the
	  factorization of A'A + I.
	* DESCRIPTION, NAMESPACE, R/SHLIB.R, R/inline.R,
	  inst/include/RcppEigen.h, inst/include/RcppEigenConfig.h,
	  inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h,
	  inst/include/unsupported/Eigen/SparseExtra,
	  inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h,
	  inst/skeleton/Makevars, inst/unitTests/runit.sparse.R: Add support for
	  Cholmod functions linked through the Matrix package. Tests for same.
	  Wrap of an Eigen::SparseMatrix now returns an S4 dgCMatrix object.
	* inst/include/RcppEigenCholmod.h, inst/include/RcppEigenStubs.cpp:
	  Create stubs and the Cholmod header. (To Do: make the stubs inline
	  functions in a header file.)

2011-07-27  Douglas Bates <bates@stat.wisc.edu>

	* inst/unitTests/runit.sparse.R: Separate the tests for sparse matrices.
2011-07-26  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/unsupported/Eigen/src/SparseExtra/SimplicialCholesky.h:
	  Added matrixLDL method

2011-07-18  Douglas Bates <bates@stat.wisc.edu>

	* src/fastLm.cpp: clean up code, taking advantage of the more general
	  wrap methods

2011-07-15  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h,
	  inst/unitTests/runit.RcppEigen.R: added as methods for
	  Eigen::SparseMatrix and Eigen::MappedSparseMatrix classes and tests of
	  same

2011-07-13  Douglas Bates <bates@stat.wisc.edu>

	* DESCRIPTION, inst/include/RcppEigenWrap.h,
	  inst/unitTests/runit.RcppEigen.R: Dispatch on wrap to vector according
	  to T::ColsAtCompileTime; modify tests to avoid the .eval() methods;
	  bump Rcpp version dependence

2011-07-13  Romain Francois  <romain@r-enthusiasts.com>

	* inst/include/RcppEigenWrap.h: dispatch sparse/dense and generalizes
	  dealing with sparse objects
	* inst/include/RcppEigenWrap.h: comment non generic implementations
	* inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: comment
	  non generic implementations
	* inst/include/RcppEigenWrap.h: deal with dimensions in
	  eigen_wrap_is_plain
	* inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: first
	  steps into dealing with Eigen expressions

2011-07-10  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/PlainObjectBaseAddon.h: Added some begin and end methods
	  to PlainObjectBase template through the extension mechanism. Should
	  make these legitimate iterators to simplify some wrap methods (need a
	  value_type member).
	* inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h,
	  inst/unitTests/runit.RcppEigen.R: Added as methods for mapped vectors
	  and mapped matrices (still some code duplication) and tests of same.

2011-07-09  Dirk Eddelbuettel  <edd@debian.org>

	* inst/unitTests/runit.RcppEigen.R: s/Armadillo/Eigen/ in a few places

2011-07-09  Douglas Bates <bates@stat.wisc.edu>

	* inst/unitTests/runit.RcppEigen.R: Added tests of wrap and as. Need to
	  create an as method for mapped arrays.

2011-07-08  Douglas Bates <bates@stat.wisc.edu>

	* DESCRIPTION: Prepare for a new release.
	* inst/include/RcppEigen.h, inst/include/RcppEigenForward.h,
	  inst/include/RcppEigenWrap.h: Add wrap methods for mapped Eigen
	  objects; Initial support for as<> with some Eigen classes.
	* inst/include/unsupported/Eigen/src/SparseExtra/SimplicialCholesky.h:
	  Commit interim version of the SimplicialLLT and SimplicialLDLT classes
	  that will appear in Eigen 3.0.2

2011-06-30  Douglas Bates <bates@stat.wisc.edu>

	* src/fastLm.cpp: Code simplification suggested by Gael Guennebaud

2011-06-29  Dirk Eddelbuettel  <edd@debian.org>

	* DESCRIPTION: make Maintainers equal to Authors (but keep our joint
	  email address)

2011-06-29  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/RcppEigenWrap.h: Syntax errors corrected.

2011-06-28  Douglas Bates <bates@stat.wisc.edu>

	* inst/examples/lmBenchmark.R: Print the results from do_bench() so
	  echo=TRUE is not needed when sourcing; add a suppressSVD argument to
	  do_bench().

2011-06-27  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: Add a
	  wrap method (compiles but currently untested) for
	  Eigen::SparseMatrix<T>
	* src/fastLm.cpp: Include sample code for the Moore-Penrose inverse.
	  There are better ways of doing this but I can't work out the syntax.

2011-06-25  Douglas Bates <bates@stat.wisc.edu>

	* inst/examples, inst/examples/lmBenchmark.R: Add lm benchmark example
	* src/fastLm.cpp: tighten code a bit

2011-06-23  Douglas Bates <bates@stat.wisc.edu>

	* src/fastLm.cpp: Don't try to extract names that aren't there.
	* man/fastLm.Rd: Add a simple example.
	* src/fastLm.cpp, src/fastLm.h: Add the SymmEig lm method. Preliminary
	  support for setting a tolerance for the rank calculation.
	* src/RcppEigen.cpp: Use the correct macros for eigen_version.
	* man/fastLm.Rd, tests/simple.R: Add examples and test cases for simple
	  crossprod and tcrossprod functions
	* inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: bypass
	  the incomplete exporter functions to support as<>

2011-06-21  Douglas Bates <bates@stat.wisc.edu>

	* src/fastLm.cpp, src/fastLm.h: Add an SVD method for fastLm
	* DESCRIPTION: Minor fix in punctuation.
	* R/fastLm.R, inst/unitTests/runit.fastLm.R, man/fastLm.Rd,
	  src/fastLm.cpp, src/fastLm.h: Refactoring of the fastLm code to allow
	  algorithms to be added easily. Adjust docs and R code accordingly.

2011-06-17  Douglas Bates <bates@stat.wisc.edu>

	* inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: Add
	  wrap instantiations for ArrayXd, ArrayXXd classes in Eigen

2011-06-15  Douglas Bates <bates@stat.wisc.edu>

	* DESCRIPTION, R/RcppEigen.package.skeleton.R, R/SHLIB.R, R/fastLm.R,
	  R/inline.R, R/unit.test.R, inst/doc/RcppEigen-unitTests.Rnw,
	  inst/include/RcppEigen.h, inst/include/RcppEigenConfig.h,
	  inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h,
	  inst/unitTests/runit.fastLm.R, man/fastLm.Rd, src/RcppEigen.cpp,
	  src/fastLm.cpp: Change references to Armadillo into Eigen; author
	  order in copyright statements.

2011-06-15  Dirk Eddelbuettel  <edd@debian.org>

	* tests/doRUnit.R: oops: s/Armadillo/Eigen/

2011-06-15  Douglas Bates <bates@stat.wisc.edu>

	* src/fastLm.cpp: Initial (not very good) implementation of "fastLmSVD",
	  which isn't really that fast.
	* man/fastLm.Rd: Minor clarification.

2011-06-15  Douglas Bates <bates@stat.wisc.edu>

	* cleanup, inst/doc/*: Documentation based on unit tests.
	* R/SHLIB.R, R/inline.R, R/unit.test.R: Add support for inline package
	* inst/include/RcppEigen.h: Add support for sparse Cholesky and LU
	* inst/include/unsupported, inst/include/unsupported/*: Add
	  support for sparse Cholesky and LU
	* man/RcppEigen-package.Rd: Add reference to web page
	* NAMESPACE, R/RcppEigen.package.skeleton.R, inst/skeleton/*,
	  man/RcppEigen.package.skeleton.Rd: Add RcppEigen.package.skeleton and
	  support files.
	* DESCRIPTION: Remove Conrad's text about Armadillo, as suggested by
	  Dirk

2011-06-15  Dirk Eddelbuettel  <edd@debian.org>

	* inst/unitTests/runit.fastLm.R: better way to load trees dataset
	* man/fastLm.Rd: better way to load trees dataset
	* inst/unitTests/runit.fastLm.R, man/fastLm.Rd: added unit tests for
	  fastLm{Bench,Chol1,Chol2}
	* ChangeLog, inst/unitTests, inst/unitTests/runTests.R,
	  inst/unitTests/runit.fastLm.R, tests, tests/doRUnit.R: added initial
	  unit tests

2011-06-14  Dirk Eddelbuettel  <edd@debian.org>

	* inst/unitTests/*: Added initial unit tests
	* tests/doRUnit.R: Added hook to run RUnit tests

2011-06-14  Douglas Bates <bates@stat.wisc.edu>

	* src/fastLm.cpp: Cosmetic fixes.
	* DESCRIPTION: New version.
	* man/fastLm.Rd: Change order of fastLmPure arguments in the example.
	  Dirk said I would miss one of these. :-)
	* R/fastLm.R, man/fastLm.Rd, src/fastLm.cpp: Change order of fastLmPure
	  arguments and the various fastLm* C++ functions. Add fastLmChol1 and
	  fastLmChol2.

2011-06-13  Douglas Bates <bates@stat.wisc.edu>

	* ChangeLog: Add ChangeLog
	* src/fastLm.cpp: Handle the rank-deficient case.
	* inst/include/Eigen/src/LU/arch/Inverse_SSE.h: Use an _m128d type
	  instead of long long int for the mask.
	* R/fastLm.R: Associate names with coefficients. Clean up fastLm.
	  Forward the object through summary.
	* inst/include/Eigen/src/Core/util/Meta.h: Suppress use of long long
