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Added new fast DecontX functions which utilized RcppArmadillo sparse matrix operations

Joshua D. Campbell authored on 03/01/2020 14:08:34
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-## With Rcpp 0.11.0 and later, we no longer need to set PKG_LIBS as there is
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-## no user-facing library. The include path to headers is already set by R.
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-#PKG_LIBS = 
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 ## With R 3.1.0 or later, you can uncomment the following line to tell R to 
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-## enable compilation with C++11 (or even C++14) where available
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-#CXX_STD = CXX11
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+## enable compilation with C++11 (where available)
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+##
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+## Also, OpenMP support in Armadillo prefers C++11 support. However, for wider
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+## availability of the package we do not yet enforce this here.  It is however
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+## recommended for client packages to set it.
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+##
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+## And with R 3.4.0, and RcppArmadillo 0.7.960.*, we turn C++11 on as OpenMP
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+## support within Armadillo prefers / requires it
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+CXX_STD = CXX11
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+
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+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) 
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+PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
Browse code

Fast matrix multiplication with RcppEigen (#247)

* Require class check on count matrix.

Require that all provided count matrices are checked to see if they're integer type, and if not, casting them to be that type.
Explicitly cast simulateCells() simulated count matrices to integer. Added unit tests to ensure this happens for this function.

* Updating documentation

* Fixing broken unit tests

* Moving dangling references to process.counts param

* Set integer storage.mode in processCounts()

* RcppEigen for fast matrix multiplication in celda_C EM

Use RcppEigen to do fast matrix multiplication in the newly implemented EM optimizations in celda_C.

* Fixed call to eigenMatMultInt. Added documentation.

* Rename rowsum functions. Documentation for eigenMatMultInt.

* Fixing loading of C++ function


Former-commit-id: 5481ad715488d093fdd1efebeb6ca60a4faad06f

Sean authored on 31/05/2018 21:56:55 • GitHub committed on 31/05/2018 21:56:55
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+## With Rcpp 0.11.0 and later, we no longer need to set PKG_LIBS as there is
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+## no user-facing library. The include path to headers is already set by R.
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+#PKG_LIBS = 
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+
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+## With R 3.1.0 or later, you can uncomment the following line to tell R to 
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+## enable compilation with C++11 (or even C++14) where available
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+#CXX_STD = CXX11