Package: SparseArray 1.7.2

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:Hervé Pagès [aut, cre], Vince Carey [fnd], Rafael A. Irizarry [fnd], Jacques Serizay [ctb]

SparseArray_1.7.2.tar.gz
SparseArray_1.7.2.zip(r-4.5)SparseArray_1.7.2.zip(r-4.4)SparseArray_1.7.2.zip(r-4.3)
SparseArray_1.7.2.tgz(r-4.4-x86_64)SparseArray_1.7.2.tgz(r-4.4-arm64)SparseArray_1.7.2.tgz(r-4.3-x86_64)SparseArray_1.7.2.tgz(r-4.3-arm64)
SparseArray_1.7.2.tar.gz(r-4.5-noble)SparseArray_1.7.2.tar.gz(r-4.4-noble)
SparseArray_1.7.2.tgz(r-4.4-emscripten)SparseArray_1.7.2.tgz(r-4.3-emscripten)
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'))

Peer review:

Bug tracker:https://github.com/bioconductor/sparsearray/issues

Uses libs:
  • openmp– GCC OpenMP (GOMP) support library

On BioConductor:SparseArray-1.7.0(bioc 3.21)SparseArray-1.6.0(bioc 3.20)

infrastructuredatarepresentationbioconductor-packagecore-package

11.44 score 8 stars 1.2k packages 45 scripts 75k downloads 99 exports 13 dependencies

Last updated 9 days agofrom:49e375d8e6. Checks:ERROR: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesFAILNov 15 2024
R-4.5-win-x86_64WARNINGNov 15 2024
R-4.5-linux-x86_64WARNINGNov 15 2024
R-4.4-win-x86_64WARNINGNov 15 2024
R-4.4-mac-x86_64WARNINGNov 15 2024
R-4.4-mac-aarch64WARNINGNov 15 2024
R-4.3-win-x86_64WARNINGNov 15 2024
R-4.3-mac-x86_64WARNINGNov 15 2024
R-4.3-mac-aarch64WARNINGNov 15 2024

Exports:abindapermaperm.COO_SparseArrayaperm.NaArrayaperm.SVT_SparseArrayArithas.array.COO_SparseArrayas.array.NaArrayas.array.SVT_SparseArraybindROWScbindcoercecolAllscolAnyNAscolAnyscolMaxscolMeanscolMeans2colMedianscolMinscolProdscolRangescolSdscolsumcolSumscolSums2colVarsCompareComplexCOO_SparseArrayextract_arrayextract_na_arrayextract_sparse_arrayget_SparseArray_nthreadis_nonnais_nonzerois_sparseLogicMathmeanmean.NaArraymean.SparseArrayNaArrayncharnnacountnnavalsnnavals<-nnawhichnzcoonzcountnzdatanzvalsnzvals<-nzwhichpmaxpminpoissonSparseArraypoissonSparseMatrixrandomSparseArrayrandomSparseMatrixrange.COO_SparseArrayrange.NaArrayrange.SVT_SparseArrayrbindread_block_as_sparsereadSparseCSVreadSparseTablerowAllsrowAnyNAsrowAnysrowMaxsrowMeansrowMeans2rowMediansrowMinsrowProdsrowRangesrowSdsrowsumrowsum.dgCMatrixrowsum.SparseMatrixrowSumsrowSums2rowVarssdset_SparseArray_nthreadshowSparseArraysparsitySVT_SparseArraytt.NaMatrixt.SVT_SparseMatrixtune_Array_dimstypetype<-varwhichwriteSparseCSV

Dependencies:abindBiocGenericscrayongenericsIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsXVectorzlibbioc

Readme and manuals

Help Manual

Help pageTopics
COO_SparseArray objectsas.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,dgTMatrix-method coerce,COO_SparseMatrix,lgCMatrix-method coerce,COO_SparseMatrix,lgRMatrix-method coerce,COO_SparseMatrix,lgTMatrix-method coerce,COO_SparseMatrix,ngCMatrix-method coerce,COO_SparseMatrix,ngRMatrix-method coerce,COO_SparseMatrix,ngTMatrix-method coerce,COO_SparseMatrix,SparseArray-method coerce,COO_SparseMatrix,sparseMatrix-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 coerce,ngCMatrix,COO_SparseMatrix-method coerce,ngRMatrix,COO_SparseMatrix-method coerce,RsparseMatrix,SparseMatrix-method coerce,TsparseMatrix,COO_SparseMatrix-method COO_SparseArray COO_SparseArray-class COO_SparseMatrix COO_SparseMatrix-class is_nonzero,COO_SparseArray-method 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
is_nonna() and the nna*() functionsis_nonna is_nonna,ANY-method nnacount nnacount,ANY-method nnavals nnavals,ANY-method nnavals<- nnavals<-,ANY-method nnawhich nnawhich,ANY-method
is_nonzero() and the nz*() functionsis_nonzero is_nonzero,ANY-method is_nonzero,sparseMatrix-method nzcount nzcount,ANY-method nzcount,CsparseMatrix-method nzcount,RsparseMatrix-method nzcount,TsparseMatrix-method nzvals nzvals,ANY-method nzvals,dgCMatrix-method nzvals,lgCMatrix-method nzvals,nMatrix-method nzvals<- nzvals<-,ANY-method nzwhich nzwhich,ANY-method nzwhich,CsparseMatrix-method nzwhich,RsparseMatrix-method sparsity
NaArray objectsas.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 is_nonna,NaArray-method NaArray NaArray-class NaMatrix NaMatrix-class nnacount,NaArray-method nnawhich,NaArray-method show,NaArray-method type,NaArray-method type<-,NaArray-method
Combine multidimensional NaArray objectsabind,NaArray-method bindROWS,NaArray-method cbind,NaArray-method NaArray-abind NaArray-combine NaArray_abind NaArray_combine rbind,NaArray-method
NaArray transpositionaperm,NaArray-method aperm.NaArray NaArray-aperm NaArray-transposition NaArray_aperm NaArray_transposition t,NaMatrix-method t.NaMatrix
'Arith' operations on NaArray objects+,NaArray,missing-method -,NaArray,missing-method Arith,array,NaArray-method Arith,NaArray,array-method Arith,NaArray,NaArray-method Arith,NaArray,SVT_SparseArray-method Arith,NaArray,vector-method Arith,SVT_SparseArray,NaArray-method Arith,vector,NaArray-method NaArray-Arith NaArray-arith NaArray-Arith-methods NaArray-arith-methods NaArray_Arith NaArray_arith NaArray_Arith-methods NaArray_arith-methods
'Compare' operations on NaArray objectsCompare,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 NaArray-Compare-methods NaArray-compare-methods NaArray_Compare NaArray_compare NaArray_Compare-methods NaArray_compare-methods
'Logic' operations on NaArray objects!,NaArray-method Logic,array,NaArray-method Logic,NaArray,array-method Logic,NaArray,NaArray-method Logic,NaArray,SVT_SparseArray-method Logic,NaArray,vector-method Logic,SVT_SparseArray,NaArray-method Logic,vector,NaArray-method NaArray-Logic NaArray-logic NaArray-Logic-methods NaArray-logic-methods NaArray_Logic NaArray_logic NaArray_Logic-methods NaArray_logic-methods
'Math' and 'Math2' methods for NaArray objectsMath,NaArray-method Math2,NaArray-method NaArray-Math NaArray-math NaArray-Math-methods NaArray-math-methods NaArray-Math2 NaArray-math2 NaArray-Math2-methods NaArray-math2-methods NaArray_Math NaArray_math NaArray_Math2 NaArray_math2 NaArray_Math2_methods NaArray_math2_methods NaArray_Math_methods NaArray_math_methods round,NaArray-method signif,NaArray-method
NaArray col/row summarizationcolAlls,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 rowAnyNAs,NaArray-method rowMaxs,NaArray-method rowMins,NaArray-method rowRanges,NaArray-method rowSums,NaArray-method rowSums2,NaArray-method
Miscellaneous operations on a NaArray objectis.infinite,NaArray-method is.na,NaArray-method is.nan,NaArray-method NaArray-misc NaArray-misc-methods NaArray_misc NaArray_misc_methods
Subsetting an NaArray objectextract_array,NaArray-method extract_na_array extract_na_array,NaArray-method NaArray-subsetting NaArray_subsetting tune_Array_dims,NaArray-method
NaArray summarization methodsanyNA,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 objectpoissonSparseArray poissonSparseMatrix randomSparseArray randomSparseMatrix
Read/write a sparse matrix from/to a CSV filereadSparseCSV readSparseTable writeSparseCSV
rowsum() methods for sparse matricescolsum colsum,dgCMatrix-method colsum,SparseMatrix-method rowsum rowsum,dgCMatrix-method rowsum,SparseMatrix-method rowsum-methods rowsum.dgCMatrix rowsum.SparseMatrix rowsum_methods
SparseArray objectsclass:SparseArray class:SparseMatrix dim,SparseArray-method dimnames,SparseArray-method dimnames<-,SparseArray,ANY-method is_sparse,SparseArray-method show,SparseArray-method SparseArray SparseArray-class SparseMatrix SparseMatrix-class
Combine multidimensional SparseArray objectsabind,SparseArray-method bindROWS,SparseArray-method cbind,SparseArray-method rbind,SparseArray-method SparseArray-abind SparseArray-combine SparseArray_abind SparseArray_combine
SparseArray transpositionaperm,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 SparseArray-Arith-methods SparseArray-arith-methods SparseArray_Arith SparseArray_arith SparseArray_Arith-methods SparseArray_arith-methods
'Compare' operations on SparseArray objectsCompare,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 SparseArray-Compare-methods SparseArray-compare-methods SparseArray_Compare SparseArray_compare SparseArray_Compare-methods SparseArray_compare-methods
'Complex' methods for SparseArray objectsComplex,SVT_SparseArray-method SparseArray-Complex SparseArray-complex SparseArray-Complex-methods SparseArray-complex-methods SparseArray_Complex SparseArray_complex SparseArray_Complex_methods 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 SparseArray-Logic-methods SparseArray-logic-methods SparseArray_Logic SparseArray_logic SparseArray_Logic-methods SparseArray_logic-methods
'Math' and 'Math2' methods for SparseArray objectsMath,SVT_SparseArray-method Math2,SVT_SparseArray-method round,SVT_SparseArray-method signif,SVT_SparseArray-method SparseArray-Math SparseArray-math SparseArray-Math-methods SparseArray-math-methods SparseArray-Math2 SparseArray-math2 SparseArray-Math2-methods SparseArray-math2-methods SparseArray_Math SparseArray_math SparseArray_Math2 SparseArray_math2 SparseArray_Math2_methods SparseArray_math2_methods SparseArray_Math_methods SparseArray_math_methods
SparseArray col/row summarizationcolAlls 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 objectis.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 subassignmentSparseArray-subassignment SparseArray_subassignment
Subsetting a SparseArray objectextract_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
SparseArray summarization methodsanyNA,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 objectsas.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,ANY,SVT_SparseArray-method coerce,ANY,SVT_SparseMatrix-method coerce,array,SparseArray-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,SparseArray-method coerce,matrix,SparseMatrix-method coerce,matrix,SVT_SparseMatrix-method coerce,sparseMatrix,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,dgTMatrix-method coerce,SVT_SparseMatrix,lgCMatrix-method coerce,SVT_SparseMatrix,lgTMatrix-method coerce,SVT_SparseMatrix,ngCMatrix-method coerce,SVT_SparseMatrix,ngTMatrix-method coerce,SVT_SparseMatrix,SparseArray-method coerce,SVT_SparseMatrix,SVT_SparseArray-method coerce,TsparseMatrix,SVT_SparseMatrix-method is_nonzero,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 operationsget_SparseArray_nthread set_SparseArray_nthread thread-control thread_control