diff --git a/ChangeLog b/ChangeLog index ea2e006f..706d45b7 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,10 @@ +2026-04-18 Dirk Eddelbuettel + + * vignettes/rmd/RcppArmadillo.bib: Refresh some URLs + * vignettes/rmd/RcppArmadillo-sparseMatrix.rmd: Idem + * vignettes/RcppArmadillo-intro.pdf: Regenerated + * vignettes/RcppArmadillo-sparseMatrix.pdf: Idem + 2026-04-16 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll micro version and date diff --git a/vignettes/RcppArmadillo-intro.pdf b/vignettes/RcppArmadillo-intro.pdf index 7d27e9ce..b178e2e9 100644 Binary files a/vignettes/RcppArmadillo-intro.pdf and b/vignettes/RcppArmadillo-intro.pdf differ diff --git a/vignettes/RcppArmadillo-sparseMatrix.pdf b/vignettes/RcppArmadillo-sparseMatrix.pdf index f440ea4a..2519d688 100644 Binary files a/vignettes/RcppArmadillo-sparseMatrix.pdf and b/vignettes/RcppArmadillo-sparseMatrix.pdf differ diff --git a/vignettes/rmd/RcppArmadillo-sparseMatrix.Rmd b/vignettes/rmd/RcppArmadillo-sparseMatrix.Rmd index c3d070aa..259c9fc9 100644 --- a/vignettes/rmd/RcppArmadillo-sparseMatrix.Rmd +++ b/vignettes/rmd/RcppArmadillo-sparseMatrix.Rmd @@ -17,12 +17,12 @@ address: - code: b address: \url{https://github.com/dselivanov} - code: c - address: \url{http://dirk.eddelbuettel.com} + address: \url{https://dirk.eddelbuettel.com} - code: d address: \url{https://github.com/thirdwing} - + lead_author_surname: Ni, Selivanov, Eddelbuettel and Kou - + doi: "https://cran.r-project.org/package=RcppArmadillo" footer_contents: "RcppArmadillo Vignette" @@ -42,7 +42,7 @@ bibliography: RcppArmadillo.bib header-includes: \newcommand{\proglang}[1]{\textsf{#1}} \newcommand{\pkg}[1]{\textbf{#1}} - \newcommand{\R}{\proglang{R}\ } + \newcommand{\R}{\proglang{R}\ } \newcommand{\Rns}{\proglang{R}} vignette: > @@ -64,8 +64,8 @@ library(Matrix) The documentation is intended for the convenience of RcppArmadillo sparse matrix users based on integration of the documentation of library -[Matrix](https://cran.r-project.org/web/packages/Matrix/Matrix.pdf) \citep{CRAN:Matrix} and -[Armadillo](http://arma.sourceforge.net/docs.html#SpMat) +[Matrix](https://cran.r-project.org/package=Matrix/Matrix.pdf) \citep{CRAN:Matrix} and +[Armadillo](https://arma.sourceforge.net/docs.html#SpMat) \citep{Sanderson:2010:Armadillo,Sanderson+Curtin:2016}. There are 31 types of sparse matrices in the [Matrix](https://cran.r-project.org/package=Matrix) @@ -73,7 +73,7 @@ package that can be used directly. But for now, only 12 of them are supported in `dgCMatrix`, `dtCMatrix`, `dsCMatrix`, `dgTMatrix`, `dtTMatrix`, `dsTMatrix`, `dgRMatrix`, `dtRMatrix`, `dsRMatrix`, `indMatrix`, `pMatrix`, `ddiMatrix`. -In the [Armadillo](http://arma.sourceforge.net/docs.html#SpMat) library, sparse matrix content is +In the [Armadillo](https://arma.sourceforge.net/docs.html#SpMat) library, sparse matrix content is currently stored as [CSC](https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_column_.28CSC_or_CCS.29) format. Such kind of format is quite similar to numeric column-oriented sparse matrix in the library @@ -103,12 +103,12 @@ or `arma::` as appropriate. - Description: general column-oriented numeric sparse matrix. - Constructor\vspace{-4pt} - - `new("dgCMatrix", ...)` - - `Matrix(*, sparse = TRUE)` + - `new("dgCMatrix", ...)` + - `Matrix(*, sparse = TRUE)` - `sparseMatrix()` - Coercion\vspace{-4pt} - - `as(*, "CsparseMatrix")` - - `as(*, "dgCMatrix")` + - `as(*, "CsparseMatrix")` + - `as(*, "dgCMatrix")` ### C++ Code @@ -125,10 +125,10 @@ arma::sp_mat sqrt_(arma::sp_mat X) { R> i <- c(1,3:8) R> j <- c(2,9,6:10) R> x <- 7 * (1:7) -R> A <- sparseMatrix(i, j, x = x) +R> A <- sparseMatrix(i, j, x = x) R> sqrt_(A) 8 x 10 sparse Matrix of class "dgCMatrix" - + [1,] . 2.645751 . . . . . . . . [2,] . . . . . . . . . . [3,] . . . . . . . . 3.741657 . @@ -145,13 +145,13 @@ R> sqrt_(A) - Description: triangular column-oriented numeric sparse matrix. - Constructor\vspace{-4pt} - - `new("dtCMatrix", ...)` - - `Matrix(*, sparse = TRUE)` + - `new("dtCMatrix", ...)` + - `Matrix(*, sparse = TRUE)` - `sparseMatrix(*, triangular=TRUE)` - Coercion\vspace{-4pt} - - `as(*, "triangularMatrix")` - - `as(*, "dtCMatrix")` - + - `as(*, "triangularMatrix")` + - `as(*, "dtCMatrix")` + ### C++ Code @@ -185,8 +185,8 @@ R> symmatl_(dtC) - Description: symmetric column-oriented numeric sparse matrix. - Constructor\vspace{-4pt} - - `new("dsCMatrix", ...)` - - `Matrix(*, sparse = TRUE)` + - `new("dsCMatrix", ...)` + - `Matrix(*, sparse = TRUE)` - `sparseMatrix(*, symmetric = TRUE)` - Coercion\vspace{-4pt} - `as(*, "symmetricMatrix")` @@ -194,7 +194,7 @@ R> symmatl_(dtC) ### C++ Code -```cpp +```cpp // [[Rcpp::export]] arma::sp_mat trimatu_(arma::sp_mat X) { return arma::trimatu(X); @@ -210,7 +210,7 @@ R> x <- 7 * (1:7) R> dsC <- sparseMatrix(i, j, x = x, symmetric = TRUE) R> trimatu_(dsC) 10 x 10 sparse Matrix of class "dgCMatrix" - + [1,] . 7 . . . . . . . . [2,] . . . . . . . . . . [3,] . . . . . . . . 14 . @@ -230,8 +230,8 @@ R> trimatu_(dsC) - Description: general numeric sparse matrix in triplet form. - Constructor\vspace{-6pt} - - `new("dgTMatrix", ...)` - - `sparseMatrix(*, giveCsparse=FALSE)` + - `new("dgTMatrix", ...)` + - `sparseMatrix(*, giveCsparse=FALSE)` - `spMatrix()` - Coercion\vspace{-6pt} - `as(*, "TsparseMatrix")` @@ -259,7 +259,7 @@ int trace_(arma::sp_mat X) { ### R Code ```r -R> dgT <- new("dgTMatrix", i = c(1L,1L,0L,3L,3L), j = c(2L,2L,4L,0L,0L), +R> dgT <- new("dgTMatrix", i = c(1L,1L,0L,3L,3L), j = c(2L,2L,4L,0L,0L), x=10*1:5, Dim=4:5) R> dgT_t <- trans_(dgT) R> prod <- multiply(dgT, dgT_t) @@ -273,9 +273,9 @@ R> trace_(prod) ### Synopsis - Description: triangular numeric sparse matrix in triplet form. -- Constructor\vspace{-4pt} - - `new("dtTMatrix", ...)` - - `code{sparseMatrix(*, triangular=TRUE, giveCsparse=FALSE)` +- Constructor\vspace{-4pt} + - `new("dtTMatrix", ...)` + - `code{sparseMatrix(*, triangular=TRUE, giveCsparse=FALSE)` - Coercion\vspace{-4pt} - `as(*, "triangularMatrix")` - `as(*, "dtTMatrix")` @@ -310,7 +310,7 @@ R> diag_ones(dtT) - Description: symmetric numeric sparse matrix in triplet form. - Constructor\vspace{-4pt} - - `new("dsTMatrix", ...)` + - `new("dsTMatrix", ...)` - `sparseMatrix(*, symmetric=TRUE, giveCsparse=FALSE)` - Coercion\vspace{-4pt} - `as(*, "symmetricMatrix")` @@ -344,7 +344,7 @@ R> trace_(dsT) - `new("dgRMatrix", ...)` - Coercion\vspace{-4pt} - `as(*, "RsparseMatrix")` - - `as(*, "dgRatrix")` + - `as(*, "dgRatrix")` ### C++ Code @@ -375,7 +375,7 @@ R> square_(dgR) - Description: triangular row-oriented numeric sparse matrix. - Constructor\vspace{-4pt} - - `new("dtRMatrix", ...)` + - `new("dtRMatrix", ...)` ### C++ Code @@ -436,9 +436,9 @@ R> sign_(dsR) ### Synopsis - Description: index matrix. -- Constructor\vspace{-4pt} +- Constructor\vspace{-4pt} - new("indMatrix", ...) -- Coercion\vspace{-4pt} +- Coercion\vspace{-4pt} - `as(*, "indMatrix")` ### C++ Code @@ -455,7 +455,7 @@ arma::sp_mat multiply(arma::sp_mat A, arma::sp_mat B) { ```r R> ind <- as(2:4, "indMatrix") -R> dgT <- new("dgTMatrix", i = c(1L,1L,0L,3L,3L), j = c(2L,2L,4L,0L,0L), +R> dgT <- new("dgTMatrix", i = c(1L,1L,0L,3L,3L), j = c(2L,2L,4L,0L,0L), x=10*1:5, Dim=4:5) R> multiply(ind, dgT) 3 x 5 sparse Matrix of class "dgCMatrix" @@ -473,7 +473,7 @@ R> multiply(ind, dgT) - Description: permutation matrix. - Constructor\vspace{-4pt} - `new("pMatrix", ...)` -- Coercion\vspace{-4pt} +- Coercion\vspace{-4pt} - `as(*, "pMatrix")` ### C++ Code @@ -490,7 +490,7 @@ arma::sp_mat multiply(arma::sp_mat A, arma::sp_mat B) { ```r R> pM <- as(c(2,3,1,4), "pMatrix") -R> dgT <- new("dgTMatrix", i = c(1L,1L,0L,3L,3L), j = c(2L,2L,4L,0L,0L), +R> dgT <- new("dgTMatrix", i = c(1L,1L,0L,3L,3L), j = c(2L,2L,4L,0L,0L), x=10*1:5, Dim=4:5) R> multiply(pM, dgT) 4 x 5 sparse Matrix of class "dgCMatrix" diff --git a/vignettes/rmd/RcppArmadillo.bib b/vignettes/rmd/RcppArmadillo.bib index c86d0e92..291fd633 100644 --- a/vignettes/rmd/RcppArmadillo.bib +++ b/vignettes/rmd/RcppArmadillo.bib @@ -1,8 +1,8 @@ -@String{CRAN = "http://CRAN.R-Project.org/" } +@String{CRAN = "https://CRAN.R-Project.org/" } @String{manuals = CRAN # "doc/manuals/" } @String{RCoreTeam = "{R Development Core Team}" } @String{RFoundation = "R Foundation for Statistical Computing" } -@String{R-Forge = "http://R-Forge.R-Project.org/" } +@String{R-Forge = "https://R-Forge.R-Project.org/" } @String{DOI = "10.32614/CRAN.package." } @@ -293,7 +293,7 @@ @Article{Eddelbuettel+Francois:2011:Rcpp volume = 40, number = 8, pages = {1--18}, - url = {http://www.jstatsoft.org/v40/i08/}, + url = {https://www.jstatsoft.org/v40/i08/}, doi = {10.18637/jss.v040.i08} } @@ -494,7 +494,7 @@ @TechReport{Sanderson:2010:Armadillo Experiments }, institution = {{NICTA}}, year = 2010, - url = "http://arma.sourceforge.net" + url = "https://arma.sourceforge.net/" } @article{Sanderson+Curtin:2016, @@ -624,7 +624,7 @@ @Misc{Tierney:2012:ByteCompiler title = {A Byte-Code Compiler for {R}}, howpublished = {Manuscript, Department of Statistics and Actuarial Science, University of Iowa}, year = 2012, - url = {www.stat.uiowa.edu/~luke/R/compiler/compiler.pdf}, + url = {https://homepage.divms.uiowa.edu/~luke/R/compiler/compiler.pdf}, annote = {Accessed 2012-06-25.}, }