Package: SparseArray 1.5.35
Hervé Pagès
SparseArray: High-performance sparse data representation and manipulation in R
The SparseArray package provides array-like containers for efficient in-memory representation of multidimensional sparse data in R (arrays and matrices). The package defines the SparseArray virtual class and two concrete subclasses: COO_SparseArray and SVT_SparseArray. Each subclass uses its own internal representation of the nonzero multidimensional data: the "COO layout" and the "SVT layout", respectively. SVT_SparseArray objects mimic as much as possible the behavior of ordinary matrix and array objects in base R. In particular, they suppport most of the "standard matrix and array API" defined in base R and in the matrixStats package from CRAN.
Authors:
SparseArray_1.5.35.tar.gz
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SparseArray.pdf |SparseArray.html✨
SparseArray/json (API)
NEWS
| # Install 'SparseArray' in R: |
| install.packages('SparseArray', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/sparsearray/issues
On BioConductor:SparseArray-1.5.34(bioc 3.20)SparseArray-1.4.8(bioc 3.19)
infrastructuredatarepresentationbioconductor-packagecore-package
Last updated 1 days agofrom:f5fe6b4298. Checks:OK: 1 NOTE: 6 WARNING: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 14 2024 |
| R-4.5-win-x86_64 | WARNING | Sep 14 2024 |
| R-4.5-linux-x86_64 | NOTE | Sep 14 2024 |
| R-4.4-win-x86_64 | WARNING | Sep 14 2024 |
| R-4.4-mac-x86_64 | NOTE | Sep 14 2024 |
| R-4.4-mac-aarch64 | NOTE | Sep 14 2024 |
| R-4.3-win-x86_64 | NOTE | Sep 14 2024 |
| R-4.3-mac-x86_64 | NOTE | Sep 14 2024 |
| R-4.3-mac-aarch64 | NOTE | Sep 14 2024 |
Exports:abindapermaperm.COO_SparseArrayaperm.NaArrayaperm.SVT_SparseArrayArithas.array.COO_SparseArrayas.array.NaArrayas.array.SVT_SparseArraybindROWScbindcoercecolAllscolAnyNAscolAnyscolMaxscolMeanscolMeans2colMedianscolMinscolProdscolRangescolSdscolsumcolSumscolSums2colVarsCompareComplexCOO_SparseArrayextract_arrayextract_na_arrayextract_sparse_arrayget_SparseArray_nthreadis_sparseLogicMathmeanmean.NaArraymean.SparseArrayNaArrayncharnnacountnnawhichnzcoonzcountnzdatanzvalsnzvals<-nzwhichpmaxpminpoissonSparseArraypoissonSparseMatrixrandomSparseArrayrandomSparseMatrixrange.COO_SparseArrayrange.NaArrayrange.SVT_SparseArrayrbindread_block_as_sparsereadSparseCSVreadSparseTablerowAllsrowAnyNAsrowAnysrowMaxsrowMeansrowMeans2rowMediansrowMinsrowProdsrowRangesrowSdsrowsumrowsum.dgCMatrixrowsum.SparseMatrixrowSumsrowSums2rowVarssdset_SparseArray_nthreadshowSparseArraysparsitySVT_SparseArraytt.NaMatrixt.SVT_SparseMatrixtune_Array_dimstypetype<-varwhichwriteSparseCSV
Dependencies:abindBiocGenericscrayonIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| COO_SparseArray objects | as.array,COO_SparseArray-method as.array.COO_SparseArray class:COO_SparseArray class:COO_SparseMatrix coerce,ANY,COO_SparseArray-method coerce,ANY,COO_SparseMatrix-method coerce,COO_SparseArray,COO_SparseMatrix-method coerce,COO_SparseMatrix,COO_SparseArray-method coerce,COO_SparseMatrix,dgCMatrix-method coerce,COO_SparseMatrix,dgRMatrix-method coerce,COO_SparseMatrix,lgCMatrix-method coerce,COO_SparseMatrix,lgRMatrix-method coerce,COO_SparseMatrix,SparseArray-method coerce,dgCMatrix,COO_SparseMatrix-method coerce,dgRMatrix,COO_SparseMatrix-method coerce,lgCMatrix,COO_SparseMatrix-method coerce,lgRMatrix,COO_SparseMatrix-method coerce,Matrix,COO_SparseArray-method COO_SparseArray COO_SparseArray-class COO_SparseMatrix COO_SparseMatrix-class nzcoo nzcoo,COO_SparseArray-method nzcount,COO_SparseArray-method nzdata nzdata,COO_SparseArray-method nzvals,COO_SparseArray-method nzvals<-,COO_SparseArray-method nzwhich,COO_SparseArray-method type,COO_SparseArray-method type<-,COO_SparseArray-method |
| NaArray objects | as.array,NaArray-method as.array.NaArray class:NaArray class:NaMatrix coerce,array,NaArray-method coerce,matrix,NaMatrix-method coerce,NaArray,NaMatrix-method coerce,NaMatrix,NaArray-method dim,NaArray-method dimnames,NaArray-method dimnames<-,NaArray,ANY-method NaArray NaArray-class NaMatrix NaMatrix-class nnacount nnacount,NaArray-method nnawhich nnawhich,ANY-method nnawhich,NaArray-method show,NaArray-method type,NaArray-method type<-,NaArray-method |
| Combine multidimensional NaArray objects | abind,NaArray-method bindROWS,NaArray-method cbind,NaArray-method NaArray-abind NaArray-combine NaArray_abind NaArray_combine rbind,NaArray-method |
| NaArray transposition | aperm,NaArray-method aperm.NaArray NaArray-aperm NaArray-transposition NaArray_aperm NaArray_transposition t,NaMatrix-method t.NaMatrix |
| 'Compare' operations on NaArray objects | Compare,array,NaArray-method Compare,NaArray,array-method Compare,NaArray,NaArray-method Compare,NaArray,SVT_SparseArray-method Compare,NaArray,vector-method Compare,SVT_SparseArray,NaArray-method Compare,vector,NaArray-method NaArray-Compare NaArray-Compare-methods NaArray_Compare NaArray_Compare-methods |
| NaArray col/row summarization | colAlls,NaArray-method colAnyNAs,NaArray-method colAnys,NaArray-method colMaxs,NaArray-method colMeans,NaArray-method colMeans2,NaArray-method colMins,NaArray-method colProds,NaArray-method colRanges,NaArray-method colSds,NaArray-method colSums,NaArray-method colSums2,NaArray-method colVars,NaArray-method NaArray-matrixStats NaArray_matrixStats rowSums,NaArray-method rowSums2,NaArray-method |
| Subsetting an NaArray object | extract_array,NaArray-method extract_na_array extract_na_array,NaArray-method NaArray-subsetting NaArray_subsetting tune_Array_dims,NaArray-method [,NaArray,ANY,ANY,ANY-method |
| NaArray summarization methods | anyNA,NaArray-method mean,NaArray-method mean.NaArray NaArray-summarization NaArray_summarization range,NaArray-method range.NaArray sd,NaArray-method var,NaArray,ANY-method |
| Random SparseArray object | poissonSparseArray poissonSparseMatrix randomSparseArray randomSparseMatrix |
| Read/write a sparse matrix from/to a CSV file | readSparseCSV readSparseTable writeSparseCSV |
| rowsum() methods for sparse matrices | colsum colsum,dgCMatrix-method colsum,SparseMatrix-method rowsum rowsum,dgCMatrix-method rowsum,SparseMatrix-method rowsum-methods rowsum.dgCMatrix rowsum.SparseMatrix rowsum_methods |
| SparseArray objects | class:SparseArray class:SparseMatrix dim,SparseArray-method dimnames,SparseArray-method dimnames<-,SparseArray,ANY-method is_sparse,SparseArray-method nzcount nzcount,CsparseMatrix-method nzcount,RsparseMatrix-method nzvals nzvals,ANY-method nzvals,dgCMatrix-method nzvals,lgCMatrix-method nzvals,ngCMatrix-method nzvals,ngRMatrix-method nzvals<- nzvals<-,ANY-method nzwhich nzwhich,ANY-method nzwhich,CsparseMatrix-method nzwhich,RsparseMatrix-method show,SparseArray-method SparseArray SparseArray-class SparseMatrix SparseMatrix-class sparsity |
| Combine multidimensional SparseArray objects | abind,SparseArray-method bindROWS,SparseArray-method cbind,SparseArray-method rbind,SparseArray-method SparseArray-abind SparseArray-combine SparseArray_abind SparseArray_combine |
| SparseArray transposition | aperm,COO_SparseArray-method aperm,SVT_SparseArray-method aperm.COO_SparseArray aperm.SVT_SparseArray SparseArray-aperm SparseArray-transposition SparseArray_aperm SparseArray_transposition t,SVT_SparseMatrix-method t.SVT_SparseMatrix |
| 'Arith' operations on SparseArray objects | +,SparseArray,missing-method -,SparseArray,missing-method Arith,array,SVT_SparseArray-method Arith,SVT_SparseArray,array-method Arith,SVT_SparseArray,SVT_SparseArray-method Arith,SVT_SparseArray,vector-method Arith,vector,SVT_SparseArray-method SparseArray-Arith SparseArray-Arith-methods SparseArray_Arith SparseArray_Arith-methods |
| 'Compare' operations on SparseArray objects | Compare,array,SVT_SparseArray-method Compare,SVT_SparseArray,array-method Compare,SVT_SparseArray,SVT_SparseArray-method Compare,SVT_SparseArray,vector-method Compare,vector,SVT_SparseArray-method SparseArray-Compare SparseArray-Compare-methods SparseArray_Compare SparseArray_Compare-methods |
| 'Complex' methods for SparseArray objects | Complex,SVT_SparseArray-method SparseArray-Complex SparseArray-Complex-methods SparseArray_Complex SparseArray_Complex_methods |
| 'Logic' operations on SparseArray objects | !,SparseArray-method Logic,array,SVT_SparseArray-method Logic,SVT_SparseArray,array-method Logic,SVT_SparseArray,SVT_SparseArray-method Logic,SVT_SparseArray,vector-method Logic,vector,SVT_SparseArray-method SparseArray-Logic SparseArray-Logic-methods SparseArray_Logic SparseArray_Logic-methods |
| 'Math' and 'Math2' methods for SparseArray objects | Math,SVT_SparseArray-method Math2,SVT_SparseArray-method round,SVT_SparseArray-method signif,SVT_SparseArray-method SparseArray-Math SparseArray-Math-methods SparseArray-Math2 SparseArray-Math2-methods SparseArray_Math SparseArray_Math2 SparseArray_Math2_methods SparseArray_Math_methods |
| SparseArray col/row summarization | colAlls colAlls,SparseArray-method colAnyNAs colAnyNAs,SparseArray-method colAnys colAnys,SparseArray-method colMaxs colMaxs,SparseArray-method colMeans colMeans,SparseArray-method colMeans2 colMeans2,SparseArray-method colMedians colMedians,SparseArray-method colMins colMins,SparseArray-method colProds colProds,SparseArray-method colRanges colRanges,SparseArray-method colSds colSds,SparseArray-method colSums colSums,SparseArray-method colSums2 colSums2,SparseArray-method colVars colVars,SparseArray-method rowAlls rowAlls,SparseArray-method rowAnyNAs rowAnyNAs,SparseArray-method rowAnys rowAnys,SparseArray-method rowMaxs rowMaxs,SparseArray-method rowMeans rowMeans,SparseArray-method rowMeans2 rowMeans2,SparseArray-method rowMedians rowMedians,SparseArray-method rowMins rowMins,SparseArray-method rowProds rowProds,SparseArray-method rowRanges rowRanges,SparseArray-method rowSds rowSds,SparseArray-method rowSums rowSums,SparseArray-method rowSums2 rowSums2,SparseArray-method rowVars rowVars,SparseArray-method SparseArray-matrixStats SparseArray_matrixStats |
| Miscellaneous operations on a SparseArray object | is.infinite is.infinite,COO_SparseArray-method is.infinite,SVT_SparseArray-method is.na is.na,COO_SparseArray-method is.na,SVT_SparseArray-method is.nan is.nan,COO_SparseArray-method is.nan,SVT_SparseArray-method nchar nchar,COO_SparseArray-method pmax pmax,SparseArray-method pmin pmin,SparseArray-method SparseArray-misc SparseArray-misc-methods SparseArray_misc SparseArray_misc_methods tolower tolower,COO_SparseArray-method toupper toupper,COO_SparseArray-method |
| SparseArray subassignment | SparseArray-subassignment SparseArray_subassignment |
| Subsetting a SparseArray object | extract_array,COO_SparseArray-method extract_array,SVT_SparseArray-method extract_sparse_array,COO_SparseArray-method extract_sparse_array,SVT_SparseArray-method SparseArray-subsetting SparseArray_subsetting [,SVT_SparseArray,ANY,ANY,ANY-method |
| SparseArray summarization methods | anyNA,SparseArray-method mean,SparseArray-method mean.SparseArray range,COO_SparseArray-method range,SVT_SparseArray-method range.COO_SparseArray range.SVT_SparseArray sd,SparseArray-method SparseArray-summarization SparseArray_summarization var,SparseArray,ANY-method |
| SparseMatrix multiplication and cross-product | %*% %*%,ANY,SparseMatrix-method %*%,matrix,SparseMatrix-method %*%,SparseMatrix,ANY-method %*%,SparseMatrix,matrix-method %*%,SparseMatrix,SparseMatrix-method crossprod crossprod,ANY,SparseMatrix-method crossprod,matrix,SparseMatrix-method crossprod,SparseMatrix,ANY-method crossprod,SparseMatrix,matrix-method crossprod,SparseMatrix,missing-method crossprod,SparseMatrix,SparseMatrix-method SparseMatrix-mult SparseMatrix_mult tcrossprod tcrossprod,ANY,SparseMatrix-method tcrossprod,matrix,SparseMatrix-method tcrossprod,SparseMatrix,ANY-method tcrossprod,SparseMatrix,matrix-method tcrossprod,SparseMatrix,missing-method tcrossprod,SparseMatrix,SparseMatrix-method |
| SVT_SparseArray objects | as.array,SVT_SparseArray-method as.array.SVT_SparseArray class:NULL_OR_list class:SVT_SparseArray class:SVT_SparseMatrix coerce,ANY,SparseArray-method coerce,ANY,SparseMatrix-method coerce,array,SVT_SparseArray-method coerce,COO_SparseArray,SVT_SparseArray-method coerce,COO_SparseMatrix,SVT_SparseMatrix-method coerce,CsparseMatrix,SVT_SparseMatrix-method coerce,Matrix,SVT_SparseArray-method coerce,matrix,SVT_SparseMatrix-method coerce,RsparseMatrix,SparseArray-method coerce,RsparseMatrix,SparseMatrix-method coerce,SVT_SparseArray,COO_SparseArray-method coerce,SVT_SparseArray,SVT_SparseMatrix-method coerce,SVT_SparseMatrix,COO_SparseMatrix-method coerce,SVT_SparseMatrix,dgCMatrix-method coerce,SVT_SparseMatrix,lgCMatrix-method coerce,SVT_SparseMatrix,ngCMatrix-method coerce,SVT_SparseMatrix,SparseArray-method coerce,SVT_SparseMatrix,SVT_SparseArray-method NULL_OR_list NULL_OR_list-class nzcount,SVT_SparseArray-method nzwhich,SVT_SparseArray-method SVT_SparseArray SVT_SparseArray-class SVT_SparseMatrix SVT_SparseMatrix-class type,SVT_SparseArray-method type<-,SVT_SparseArray-method |
| Number of threads used by SparseArray operations | get_SparseArray_nthread set_SparseArray_nthread thread-control thread_control |
