2013-02-03 Dirk Eddelbuettel * DESCRIPTION: New minor version 0.3.1.2.1 for upload to CRAN and JSS * NEWS.org: Updated 2013-01-26 Dirk Eddelbuettel * vignettes/jss835/: Regroup all related files in this directory * .Rbuildignore: Ignore vignettes/jss835 2013-01-14 Dirk Eddelbuettel * inst/CITATION: Added as provided by JSS editor * man/fastLm.Rd: Added reference to JSS paper * man/RcppEigen-package.Rd: Idem 2012-11-29 Douglas Bates * DESCRIPTION: New version * inst/include/Eigen, inst/include/unsupported: Update to version 3.1.2 of Eigen. 2012-11-29 Romain Francois * include/RcppEigenWrap.h: compatibility issue with Rcpp 0.10.1 2012-08-14 Dirk Eddelbuettel * R/flags.R: Add two (unexported) functions CxxFlags() and RcppEigenCxxFlags() for use in Makefiles etc 2012-07-30 Douglas Bates * inst/include/RcppEigenWrap.h, inst/unitTests/runit.RcppEigen.R: Another suggestion from Gael Guennebaud to allow row vectors to be wrapped. 2012-07-28 Douglas Bates * inst/include/RcppEigenWrap.h, inst/unitTests/runit.RcppEigen.R: More fixes to RcppEigenWrap.h and adjustment of tests accordingly. The changes allow RowMajor matrices to be wrapped (thanks to Gael Guennebaud) but cannot handle RowVector types. There will need to be more template metaprogramming done to redirect the case of RowVector, which cannot be changed to a ColMajor form. * src/Makevars: Because of changes in R, -DNDEBUG is automatic. One must override it with -UNDEBUG in the local ~/.R/Makevars to activate the debugging code. * inst/doc/code.R: New version of wrap code provides correct answer to the badtrans example * DESCRIPTION: Bump the date. 2012-07-27 Douglas Bates * inst/include/Eigen/*: Changed to released version of Eigen-3.1.0 using the MPL2 license. 2012-07-19 Dirk Eddelbuettel * R/fastLm.R: correct residual standard error display * R/fastLm.R: improved test for intercept once more with a tip of the hat to Doug 2012-07-17 Dirk Eddelbuettel * R/fastLm.R: Corrections for R^2 in no-intercept case 2012-06-26 Douglas Bates * DESCRIPTION, R/unit.test.R, inst/include/Eigen/*: Massive changes related to upgrade to Eigen-3.1.0 2012-03-13 Douglas Bates * inst/include/RcppEigenWrap.h: Change the wrap methods to avoid creating Rcpp::Dimension objects (which are implicitly created by the Rcpp::Matrix constructor). * inst/tests/test-solutions.R: Clean up. I defined the results then reevaluated them. 2012-03-08 Douglas Bates * inst/include/RcppEigenForward.h: Remove an include of RcppEigenConfig.h which is no longer needed. * ChangeLog, NEWS, NEWS.org: Update Changelog and NEWS which is generated from an org-mode file NEWS.org * inst/include/RcppEigenConfig.h, inst/include/unsupported/Eigen/MoreVectorization, inst/include/unsupported/Eigen/src/MoreVectorization/CMakeLists.txt: Delete the unsupported/Eigen/src/MoreVectorization module which we don't need * inst/include/unsupported/Eigen/src/MoreVectorization/MathFunctions.h: Delete the unsupported/Eigen/src/MoreVectorization module which we don't need * 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 * inst/include/RcppEigenWrap.h: Correct a typo. 2012-02-28 Douglas Bates * inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: Add as templates for ArrayXd and ArrayXXd 2012-02-03 Douglas Bates * 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 * inst/include/RcppEigenWrap.h: Allow for wrapping sparse row-major matrices. 2011-12-31 Douglas Bates * inst/include/RcppEigenCholmod.h: Minor typo in a comment 2011-12-23 Dirk Eddelbuettel * 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 * 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 * 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 * inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: Avoid compiler warnings about comparing signed and unsigned values. 2011-09-13 Douglas Bates * src/Makevars: Force the -DNDEBUG flag to satisfy R CMD check in R-2.14.0 and higher 2011-09-12 Douglas Bates * 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 * inst/include/RcppEigenForward.h: Remove forward declaration of non-existent templated function. 2011-09-02 Douglas Bates * 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 * 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 * many files in inst/include/Eigen and inst/include/unsupported: Upgrade to Eigen release 3.0.2 2011-08-12 Douglas Bates * inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: By-passing the const reference 2011-08-11 Douglas Bates * inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: Add a solveInPlace method to try to avoid memory problems. 2011-08-10 Douglas Bates * 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 * 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 * 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 * 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 * inst/unitTests/runit.sparse.R: Separate the tests for sparse matrices. 2011-07-26 Douglas Bates * inst/include/unsupported/Eigen/src/SparseExtra/SimplicialCholesky.h: Added matrixLDL method 2011-07-18 Douglas Bates * src/fastLm.cpp: clean up code, taking advantage of the more general wrap methods 2011-07-15 Douglas Bates * 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 * 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 * 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 * 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 * inst/unitTests/runit.RcppEigen.R: s/Armadillo/Eigen/ in a few places 2011-07-09 Douglas Bates * 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 * 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 * src/fastLm.cpp: Code simplification suggested by Gael Guennebaud 2011-06-29 Dirk Eddelbuettel * DESCRIPTION: make Maintainers equal to Authors (but keep our joint email address) 2011-06-29 Douglas Bates * inst/include/RcppEigenWrap.h: Syntax errors corrected. 2011-06-28 Douglas Bates * 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 * inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: Add a wrap method (compiles but currently untested) for Eigen::SparseMatrix * 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 * inst/examples, inst/examples/lmBenchmark.R: Add lm benchmark example * src/fastLm.cpp: tighten code a bit 2011-06-23 Douglas Bates * 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 * 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 * inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: Add wrap instantiations for ArrayXd, ArrayXXd classes in Eigen 2011-06-15 Douglas Bates * 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 * tests/doRUnit.R: oops: s/Armadillo/Eigen/ 2011-06-15 Douglas Bates * 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 * 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 * 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 * inst/unitTests/*: Added initial unit tests * tests/doRUnit.R: Added hook to run RUnit tests 2011-06-14 Douglas Bates * 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 * 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