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Merge branch 'master' into Eigen3.4.0
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‎.codecov.yml

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coverage:
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precision: 1
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comment: false
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coverage:
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status:
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project:
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default:
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target: 70% # the (on purpose low) required coverage value
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threshold: 2% # the permitted delta in hitting the target
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patch:
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default:
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target: 0% # the (on purpose low) required coverage value
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ignore:
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- "inst/include/Eigen/"
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- "inst/include/unsupported/Eigen/"
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codecov:
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token: 0b726434-b483-4a82-9cfe-e8312f3b3e9b
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# layout: "header, diff, tree, changes"
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# behavior: default
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# require_changes: false # if true: only post the comment if coverage changes
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# branches: null
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# flags: null
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# paths: null

‎.github/workflows/ci.yaml

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pull_request:
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env:
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USE_BSPM: "true"
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_R_CHECK_FORCE_SUGGESTS_: "false"
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jobs:
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runs-on: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v3
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- name: Get Script
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run: curl -OLs https://eddelbuettel.github.io/r-ci/run.sh && chmod 0755 run.sh
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- name: Bootstrap
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run: |
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curl -OLs https://eddelbuettel.github.io/r-ci/run.sh
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chmod 0755 run.sh
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./run.sh bootstrap
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run: ./run.sh bootstrap
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- name: Dependencies
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run: ./run.sh install_all

‎.travis.yml

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‎ChangeLog

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2021-10-26 Yixuan Qiu <[email protected]>
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2024-01-17 Yixuan Qiu <[email protected]>
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* DESCRIPTION (Version, Date): Release candidate 0.3.3.99.0
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* patches/eigen-3.4.0.diff: Carried local CRAN patches forward
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* patches/howToDiff.md: Idem
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2023-11-01 Dirk Eddelbuettel <[email protected]>
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* DESCRIPTION (Version, Date): CRAN Release 0.3.3.9.4
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* inst/NEWS.Rd: Release 0.3.3.9.4
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2023-10-05 Mikael Jagan <[email protected]>
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* DESCRIPTION: Package 'Matrix' is now only a Suggests:
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* NAMESPACE: Remove unconditional imports from package Matrix
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* inst/include/Eigen/CholmodSupport: No longer need to include
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RcppEigenCholmod.h
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* inst/include/Eigen/src/CholmodSupport/CholmodSupport.h: Small
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wrapper adjustments conditional on Matrix use
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* inst/include/RcppEigenCholmod.h: Updated
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* inst/include/RcppEigenForward.h: Simplified
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* inst/include/RcppEigenWrap.h: Ditto
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* inst/include/RcppEigenStubs.cpp: New shorter helper
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* inst/include/RcppEigenStubs.h: Removed
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2023-07-21 Dirk Eddelbuettel <[email protected]>
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* DESCRIPTION (Date, Version): Roll micro version and date
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* README.md: Add r-universe badge
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2023-07-20 Dirk Eddelbuettel <[email protected]>
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* src/RcppEigen.cpp (EigenNbThreads): Add simple threads reporter
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* R/fastLm.R (fastLmPure): Simpler call to `fastLm_Impl()`
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* src/init.c: Replaced by auto-generated section in RcppExports.cpp
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* src/RcppExports.cpp: Regenerated
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* R/RcppExports.R: Idem
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* src/Makevars: Document possible use of '-fopenmp'
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* src/Makevars.win: Idem
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2023-04-18 Dirk Eddelbuettel <[email protected]>
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* README.md: Use app.codecov.io as base for codecov link
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2023-03-10 Dirk Eddelbuettel <[email protected]>
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* DESCRIPTION (Date, Version): Roll minor version
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* R/RcppEigen.package.skeleton.R: No longer set Imports: RcppEigen in
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DESCRIPTION and NAMESPACE
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2023-02-12 Dirk Eddelbuettel <[email protected]>
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* inst/CITATION: Convert to bibentry() style with person()
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2022-11-04 Dirk Eddelbuettel <[email protected]>
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* DESCRIPTION (Version, Date): CRAN Release 0.3.3.9.3
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* inst/NEWS.Rd: Release 0.3.3.9.3
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* src/init.c: Add 'void' for proper prototype pleasing clang-15
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* R/fastLm.R (summary.fastLm,print.fastLm): Refer to correct and full
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variable name df.residual in the returned object
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* .github/workflows/ci.yaml (jobs): Update to actions/checkout@v3
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2022-09-15 Jonah Gabry <[email protected]>
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* inst/skeleton/rcppeigen_hello_world.cpp: Correct typo
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2022-04-08 Dirk Eddelbuettel <[email protected]>
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* DESCRIPTION (Depends): Add a versioned dependency on R 3.6.0 or
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later because of our use of FCONE to support USE_FC_LEN_T
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2022-04-05 Dirk Eddelbuettel <[email protected]>
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* DESCRIPTION (Version, Date): CRAN Release 0.3.3.9.2
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* inst/NEWS.Rd: Release 0.3.3.9.2
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2022-04-04 Dirk Eddelbuettel <[email protected]>
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* src/fastLm.cpp: Add FCONE in two calls for improved Fortran and C
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character interface per Writing R Extensions, Section 6.6.1
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2022-01-16 Dirk Eddelbuettel <[email protected]>
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* inst/tinytest/test_wrap.R: Added (optional) large memory wrap tests
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* inst/tinytest/cpp/wrap.cpp: Added C++ part of test
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* .codecov.yml: Added to not trigger PR fail for small additions
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2022-01-16 Mikael Jagan <[email protected]>
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* inst/include/RcppEigenWrap.h: Refine use plain dense wrap() change
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2022-01-15 Mikael Jagan <[email protected]>
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* inst/include/RcppEigenWrap.h: Use R_xlen_t for vectors rows + cols
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2021-12-29 Dirk Eddelbuettel <[email protected]>
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* README.md: Add total downloads badge
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2021-12-08 Dirk Eddelbuettel <[email protected]>
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* README.md: Remove unused continuous integration artifact and badge
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2021-10-13 Dirk Eddelbuettel <[email protected]>
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* inst/CITATION: Refinment of doi use
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2021-10-10 Dirk Eddelbuettel <[email protected]>
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* inst/CITATION: Switch JSS url to doi form per JSS request

‎DESCRIPTION

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Type: Package
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Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library
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Version: 0.3.3.99.0
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Date: 2021-10-26
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Date: 2024-01-17
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Author: Douglas Bates, Dirk Eddelbuettel, Romain Francois, and Yixuan Qiu;
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the authors of Eigen for the included version of Eigen
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Maintainer: Dirk Eddelbuettel <[email protected]>
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such matrices, and solutions of linear systems. Its performance on many
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algorithms is comparable with some of the best implementations based on
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'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header
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files from the 'Eigen' C++ template library (currently version 3.3.4). Thus
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users do not need to install 'Eigen' itself in order to use 'RcppEigen'.
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Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License
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(version 2); earlier version were licensed under the GNU LGPL version 3 or
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later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under
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the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
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files from the 'Eigen' C++ template library. Thus users do not need to
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install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1,
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'Eigen' is licensed under the Mozilla Public License (version 2); earlier
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version were licensed under the GNU LGPL version 3 or later. 'RcppEigen'
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(the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL
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version 2 or later, as is the rest of 'Rcpp'.
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License: GPL (>= 2) | file LICENSE
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LazyLoad: yes
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Depends: R (>= 3.6.0)
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LinkingTo: Rcpp
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Imports: Rcpp (>= 0.11.0), stats, utils
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Suggests: Matrix, inline, tinytest, pkgKitten, microbenchmark

‎R/RcppEigen.package.skeleton.R

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## RcppEigen.package.skeleton.R: makes a skeleton for a package that wants to use RcppEigen
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##
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## Copyright (C) 2011 - 2021 Douglas Bates, Dirk Eddelbuettel and Romain Francois
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## Copyright (C) 2011 - 2023 Douglas Bates, Dirk Eddelbuettel and Romain Francois
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##
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## This file is part of RcppEigen.
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##
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DESCRIPTION <- file.path(root, "DESCRIPTION")
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if (file.exists(DESCRIPTION)) {
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x <- cbind(read.dcf(DESCRIPTION),
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"Imports" = sprintf("Rcpp (>= %s), RcppEigen",
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"Imports" = sprintf("Rcpp (>= %s)",
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packageDescription("Rcpp")[["Version"]]),
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"LinkingTo" = "Rcpp, RcppEigen")
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write.dcf(x, file = DESCRIPTION)
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lines <- readLines(NAMESPACE)
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if (!any(grepl("useDynLib", lines))) {
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lines <- c(sprintf("useDynLib(%s)", name),
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"import(RcppEigen)",
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"importFrom(Rcpp, evalCpp)", ## ensures Rcpp instantiation
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lines)
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writeLines(lines, con = NAMESPACE)

‎R/RcppExports.R

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# This file was generated by Rcpp::compileAttributes
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# Generated by using Rcpp::compileAttributes() -> do not edit by hand
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# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
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fastLm_Impl <- function(X, y, type) {
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.Call('RcppEigen_fastLm_Impl', PACKAGE = 'RcppEigen', X, y, type)
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}
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eigen_version <- function(single) {
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.Call('RcppEigen_eigen_version', PACKAGE = 'RcppEigen', single)
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.Call(`_RcppEigen_eigen_version`, single)
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}
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Eigen_SSE <- function() {
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.Call('RcppEigen_Eigen_SSE', PACKAGE = 'RcppEigen')
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.Call(`_RcppEigen_Eigen_SSE`)
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}
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EigenNbThreads <- function() {
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.Call(`_RcppEigen_EigenNbThreads`)
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}
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fastLm_Impl <- function(X, y, type) {
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.Call(`_RcppEigen_fastLm_Impl`, X, y, type)
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}
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‎R/fastLm.R

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## fastLm.R: Rcpp/Eigen implementation of lm()
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##
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## Copyright (C) 2011 - 2017 Douglas Bates, Dirk Eddelbuettel and Romain Francois
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## Copyright (C) 2011 - 2023 Douglas Bates, Dirk Eddelbuettel and Romain Francois
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##
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## This file is part of RcppEigen.
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##
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stopifnot(is.matrix(X), is.numeric(y), NROW(y)==nrow(X))
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.Call("RcppEigen_fastLm_Impl", X, y, method, PACKAGE="RcppEigen")
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fastLm_Impl(X, y, method)
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}
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object$coefficients <- cbind(Estimate = coef,
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"Std. Error" = se,
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"Pr(>|t|)" = 2*pt(-abs(tval), df=object$df))
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"Pr(>|t|)" = 2*pt(-abs(tval), df=object$df.residual))
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## cf src/stats/R/lm.R and case with no weights and an intercept
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object$r.squared <- mss/(mss + rss)
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n <- length(f)
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rdf <- object$df
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rdf <- object$df.residual
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object$adj.r.squared <- 1 - (1 - object$r.squared) * ((n - df.int)/rdf)
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class(object) <- "summary.fastLm"
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object
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printCoefmat(x$coefficients, P.values=TRUE, has.Pvalue=TRUE, ...)
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cat("\nResidual standard error: ", formatC(x$s, digits=digits), " on ",
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formatC(x$df), " degrees of freedom\n", sep="")
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formatC(x$df.residual), " degrees of freedom\n", sep="")
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cat("Multiple R-squared: ", formatC(x$r.squared, digits=digits),
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",\tAdjusted R-squared: ",formatC(x$adj.r.squared, digits=digits),
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"\n", sep="")

‎README.md

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## RcppEigen: R and Eigen via Rcpp
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[![Build Status](https://travis-ci.org/RcppCore/RcppEigen.svg)](https://travis-ci.org/RcppCore/RcppEigen)
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[![CI](https://github.com/RcppCore/RcppEigen/workflows/ci/badge.svg)](https://github.com/RcppCore/RcppEigen/actions?query=workflow%3Aci)
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[![License](https://img.shields.io/badge/license-GPL%20%28%3E=%202%29-brightgreen.svg?style=flat)](https://www.gnu.org/licenses/gpl-2.0.html)
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[![License](https://img.shields.io/badge/license-MPL2-brightgreen.svg?style=flat)](https://www.mozilla.org/MPL/2.0/)
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[![CRAN](https://www.r-pkg.org/badges/version/RcppEigen)](https://cran.r-project.org/package=RcppEigen)
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[![r-universe](https://rcppcore.r-universe.dev/badges/RcppEigen)](https://rcppcore.r-universe.dev/RcppEigen)
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[![Dependencies](https://tinyverse.netlify.com/badge/RcppEigen)](https://cran.r-project.org/package=RcppEigen)
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[![Coverage Status](https://codecov.io/gh/RcppCore/RcppEigen/graph/badge.svg)](https://codecov.io/github/RcppCore/RcppEigen?branch=master)
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[![Coverage Status](https://codecov.io/gh/RcppCore/RcppEigen/graph/badge.svg)](https://app.codecov.io/github/RcppCore/RcppEigen?branch=master)
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[![Debian package](https://img.shields.io/debian/v/r-cran-rcppeigen/sid?color=brightgreen)](https://packages.debian.org/sid/r-cran-rcppeigen)
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[![Last Commit](https://img.shields.io/github/last-commit/RcppCore/RcppEigen)](https://github.com/RcppCore/RcppEigen)
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[![Downloads](https://cranlogs.r-pkg.org/badges/RcppEigen?color=brightgreen)](https://www.r-pkg.org:443/pkg/RcppEigen)
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[![Downloads (monthly)](https://cranlogs.r-pkg.org/badges/RcppEigen?color=brightgreen)](https://www.r-pkg.org:443/pkg/RcppEigen)
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[![Downloads (total)](https://cranlogs.r-pkg.org/badges/grand-total/RcppEigen?color=brightgreen)](https://www.r-pkg.org:443/pkg/RcppEigen)
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[![CRAN use](https://jangorecki.gitlab.io/rdeps/RcppEigen/CRAN_usage.svg?sanitize=true)](https://cran.r-project.org/package=RcppEigen)
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[![BioConductor use](https://jangorecki.gitlab.io/rdeps/RcppEigen/BioC_usage.svg?sanitize=true)](https://cran.r-project.org/package=RcppEigen)
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[![StackOverflow](https://img.shields.io/badge/stackoverflow-rcpp-orange.svg)](https://stackoverflow.com/questions/tagged/rcpp)

‎inst/CITATION

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citHeader("To cite RcppEigen in publications use:")
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citEntry(entry = "Article",
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title = "Fast and Elegant Numerical Linear Algebra Using the {RcppEigen} Package",
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author = personList(as.person("Douglas Bates"),
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as.person("Dirk Eddelbuettel")),
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journal = "Journal of Statistical Software",
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year = "2013",
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volume = "52",
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number = "5",
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pages = "1--24",
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url = "https://doi.org/10.18637/jss.v052.i05",
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textVersion =
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paste("Douglas Bates, Dirk Eddelbuettel (2013).",
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"Fast and Elegant Numerical Linear Algebra Using the RcppEigen Package.",
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"Journal of Statistical Software, 52(5), 1-24.",
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"URL https://doi.org/10.18637/jss.v052.i05/.")
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)
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bibentry("Article",
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title = "Fast and Elegant Numerical Linear Algebra Using the {RcppEigen} Package",
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author = c(person("Douglas", "Bates",
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comment = c(ORCID = "0000-0001-8316-9503")),
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person("Dirk", "Eddelbuettel",
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email = "[email protected]",
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comment = c(ORCID = "0000-0001-6419-907X"))),
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journal = "Journal of Statistical Software",
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year = "2013",
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volume = "52",
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number = "5",
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pages = "1--24",
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doi = "10.18637/jss.v052.i05")

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