Package: SparseArray 1.5.14
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_1.5.14.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-1.5.11(bioc 3.20)SparseArray-1.4.8(bioc 3.19)
Last updated 6 days agofrom:5987be2462
Exports:abindapermaperm.COO_SparseArrayaperm.SVT_SparseArrayArithas.array.COO_SparseArrayas.array.SVT_SparseArraybindROWScbindcoercecolAllscolAnyNAscolAnyscolMaxscolMeanscolMedianscolMinscolProdscolRangescolSdscolSumscolVarsCompareComplexCOO_SparseArrayextract_arrayextract_sparse_arrayget_SparseArray_nthreadis_sparseLogicMathmeanncharnzcoonzcountnzdatanzvalsnzvals<-nzwhichpmaxpminpoissonSparseArraypoissonSparseMatrixrandomSparseArrayrandomSparseMatrixrange.COO_SparseArrayrange.SVT_SparseArrayrbindread_block_as_sparsereadSparseCSVreadSparseTablerowAllsrowAnyNAsrowAnysrowMaxsrowMeansrowMediansrowMinsrowProdsrowRangesrowSdsrowsumrowsum.dgCMatrixrowsum.SVT_SparseMatrixrowSumsrowVarssdset_SparseArray_nthreadshowSparseArraysparsitySVT_SparseArraytt.SVT_SparseMatrixtypetype<-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 |
| SparseArray col/row summarization methods | colAlls colAlls,SVT_SparseArray-method colAnyNAs colAnyNAs,SVT_SparseArray-method colAnys colAnys,SVT_SparseArray-method colMaxs colMaxs,SVT_SparseArray-method colMeans colMeans,SVT_SparseArray-method colMedians colMedians,SVT_SparseArray-method colMins colMins,SVT_SparseArray-method colProds colProds,SVT_SparseArray-method colRanges colRanges,SVT_SparseArray-method colSds colSds,SVT_SparseArray-method colSums colSums,SVT_SparseArray-method colVars colVars,SVT_SparseArray-method matrixStats-methods matrixStats_methods rowAlls rowAlls,SVT_SparseArray-method rowAnyNAs rowAnyNAs,SVT_SparseArray-method rowAnys rowAnys,SVT_SparseArray-method rowMaxs rowMaxs,SVT_SparseArray-method rowMeans rowMeans,SVT_SparseArray-method rowMedians rowMedians,SVT_SparseArray-method rowMins rowMins,SVT_SparseArray-method rowProds rowProds,SVT_SparseArray-method rowRanges rowRanges,SVT_SparseArray-method rowSds rowSds,SVT_SparseArray-method rowSums rowSums,SVT_SparseArray-method rowVars rowVars,SVT_SparseArray-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 | rowsum,dgCMatrix-method rowsum,SVT_SparseMatrix-method rowsum-methods rowsum.dgCMatrix rowsum.SVT_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 |
| 'Complex' methods for SparseArray objects | Complex,SVT_SparseArray-method SparseArray-Complex SparseArray-Complex-methods SparseArray_Complex SparseArray_Complex_methods |
| Add/drop ineffective dims to/from a SparseArray object | dim-tuning dim<- dim_tuning drop ineffective-dims ineffective_dims SparseArray-dim-tuning SparseArray-ineffective-dims SparseArray_dim_tuning SparseArray_ineffective_dims |
| 'Math' and 'Math2' methods for SparseArray objects | Math,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 |
| 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 |
| 'Ops' methods for SparseArray objects | !,SparseArray-method +,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 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 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-Arith SparseArray-Compare SparseArray-Logic SparseArray-Ops SparseArray-Ops-methods SparseArray_Arith SparseArray_Compare SparseArray_Logic SparseArray_Ops SparseArray_Ops_methods |
| SparseArray subassignment | SparseArray-subassignment SparseArray_subassignment [<-,SVT_SparseArray,ANY,ANY,ANY-method |
| 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 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,SVT_SparseMatrix-method %*%,matrix,SVT_SparseMatrix-method %*%,SVT_SparseMatrix,ANY-method %*%,SVT_SparseMatrix,matrix-method %*%,SVT_SparseMatrix,SVT_SparseMatrix-method crossprod crossprod,ANY,SVT_SparseMatrix-method crossprod,matrix,SVT_SparseMatrix-method crossprod,SVT_SparseMatrix,ANY-method crossprod,SVT_SparseMatrix,matrix-method crossprod,SVT_SparseMatrix,missing-method crossprod,SVT_SparseMatrix,SVT_SparseMatrix-method SparseMatrix-mult SparseMatrix_mult tcrossprod tcrossprod,ANY,SVT_SparseMatrix-method tcrossprod,matrix,SVT_SparseMatrix-method tcrossprod,SVT_SparseMatrix,ANY-method tcrossprod,SVT_SparseMatrix,matrix-method tcrossprod,SVT_SparseMatrix,missing-method tcrossprod,SVT_SparseMatrix,SVT_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 |
