Package: matter 2.9.1
Kylie A. Bemis
matter: Out-of-core statistical computing and signal processing
Toolbox for larger-than-memory scientific computing and visualization, providing efficient out-of-core data structures using files or shared memory, for dense and sparse vectors, matrices, and arrays, with applications to nonuniformly sampled signals and images.
Authors:
matter_2.9.1.tar.gz
matter_2.9.1.zip(r-4.5)matter_2.9.1.zip(r-4.4)matter_2.7.9.zip(r-4.3)
matter_2.9.1.tgz(r-4.4-x86_64)matter_2.9.1.tgz(r-4.4-arm64)matter_2.7.9.tgz(r-4.3-x86_64)matter_2.7.9.tgz(r-4.3-arm64)
matter_2.9.1.tar.gz(r-4.5-noble)matter_2.9.1.tar.gz(r-4.4-noble)
matter_2.9.1.tgz(r-4.4-emscripten)matter_2.7.9.tgz(r-4.3-emscripten)
matter.pdf |matter.html✨
matter/json (API)
NEWS
| # Install 'matter' in R: |
| install.packages('matter', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kuwisdelu/matter/issues
On BioConductor:matter-2.9.0(bioc 3.21)matter-2.8.0(bioc 3.20)
infrastructuredatarepresentationdataimportdimensionreductionpreprocessingcpp
Last updated 16 days agofrom:bcfe9fb4a2. Checks:OK: 4 NOTE: 2 ERROR: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 05 2024 |
| R-4.5-win-x86_64 | NOTE | Dec 05 2024 |
| R-4.5-linux-x86_64 | NOTE | Dec 05 2024 |
| R-4.4-win-x86_64 | OK | Dec 05 2024 |
| R-4.4-mac-x86_64 | OK | Dec 05 2024 |
| R-4.4-mac-aarch64 | OK | Dec 05 2024 |
| R-4.3-win-x86_64 | ERROR | Oct 16 2024 |
| R-4.3-mac-x86_64 | ERROR | Oct 16 2024 |
| R-4.3-mac-aarch64 | ERROR | Oct 16 2024 |
Exports:.colDists.colStats.rowDists.rowStatsadataadd_alphaadd_facetsadd_markaindexapprox1approx2Aritharray_indas_facetsas_layersas.altrepas.arrayas.data.frameas.factoras.listas.matrixas.matteras.sharedas.sparseas.vectorasearchatomdataatomdata<-atomindexatomindex<-atomsavgbinpeaksbinvecbpislocalbplocalizedbptrystartbptrystopbsearchcbind2checksumchunk_applychunk_colapplychunk_lapplychunk_mapplychunk_rowapplychunk_writerchunkApplychunked_listchunked_matchunked_vecchunkifychunkLapplychunkMapplycoldistcoldist_atcolDistscolMeanscolscalecolStatscolSumscolsweepcombineconvolve_atcoscorecpalcpalscv_docwtdescribe_for_displaydimsdomaindomain<-downsampledpaldpalsdrledroplevelsEncodingEncoding<-enhance_adaptenhance_adjenhance_histestbase_hullestbase_locestbase_medestbase_snipestdimestnoise_diffestnoise_filtestnoise_madestnoise_quantestnoise_sdestreseval_ateval_exprsfastmapfetchfilt1_adaptfilt1_bifilt1_convfilt1_difffilt1_gaussfilt1_guidefilt1_mafilt1_pagfilt1_sgfilt2_adaptfilt2_bifilt2_convfilt2_difffilt2_gaussfilt2_guidefilt2_mafiltn_adaptfiltn_bifiltn_convfiltn_gaussfiltn_mafindbinsfindpeaksfindpeaks_cwtfindpeaks_knnfindridgesflashgetRNGStreamhex2rawicorinpolyiQuoteis_griddedis.drleis.matteris.sharedis.sparseisoclosisofunkdsearchkdtreeknnmaxknnminknnsearchlevelslinear_indlocmaxlocminmattermatter_arrmatter_defaultsmatter_errormatter_fctmatter_listmatter_logmatter_loggermatter_matmatter_messagematter_shared_resourcematter_shared_resource_listmatter_shared_resource_poolmatter_strmatter_vecmatter_warnmeanmemmem_realizedmemclmemtimemergepeaksmimi_learnnndsvdnnmf_alsnnmf_multnnpairsnnzeronscentroidsopls_nipalspanel_dimpanel_getpanel_gridpanel_nextpanel_prevpanel_setparse_formulapathpath<-peakareaspeakheightspeakwidthspinvplotplot_imageplot_signalpls_kernelpls_nipalspls_simplspointerspointers<-prcompprcomp_lanczospredscorepreplotpreview_for_displayprofmemqmadqmedianqorderqrankqselectraw2hexrbind2read_atomread_atomsreadonlyreadonly<-reldiffrescale_iqrrescale_rangerescale_refrescale_rmsrescale_sumrickerRNGStreamsrocscorerollrollvecrowdistrowdist_atrowDistsrowMajrowMeansrowscalerowStatsrowSumsrowsweeps_alls_anys_colstatss_maxs_means_mins_nnzeros_prods_ranges_rowstatss_sds_stats_sums_varsamplersampler<-sdseq_relset_channelset_coordset_engineset_parset_titlesetRNGStreamsgmixsgmixnshinglesshm_usedsimple_loggersimspecsimspec1size_bytessizeofSnowfastParamsparse_matsparse_vecstat_cstructttempmemto_rasterto_raster3tolerancetolerance<-trans2dtypetype<-uuidvarvipvizivizi_enginevizi_parvizi_stylevm_usedwarp1_cowwarp1_dtwwarp1_locwarp2_transwrite_atomwrite_atoms
Dependencies:BHBiocGenericsBiocParallelcodetoolscpp11digestformatRfutile.loggerfutile.optionsgenericsirlbalambda.rlatticeMatrixProtGenericssnow
Matter 2: User guide for flexible out-of-memory data structures
Rendered frommatter2-guide.Rmdusingknitr::rmarkdownon Dec 05 2024.Last update: 2024-07-18
Started: 2024-07-18
Matter 2: Signal and image processing
Rendered frommatter2-signal.Rmdusingknitr::rmarkdownon Dec 05 2024.Last update: 2024-07-18
Started: 2024-07-18
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Resampling in 1D with Interpolation | approx1 |
| Resampling in 2D with Interpolation | approx2 |
| Central Tendency | avg |
| Peak Processing | binpeaks mergepeaks |
| Binned Summaries of a Vector | binvec |
| Binary Search with Approximate Matching | bsearch reldiff |
| Calculate Checksums and Cryptographic Hashes | checksum checksum,atoms-method checksum,character-method checksum,matter_-method |
| Apply Functions Over Chunks of a List, Vector, or Matrix | chunkApply chunkLapply chunkMapply chunk_apply chunk_colapply chunk_lapply chunk_mapply chunk_rowapply chunk_writer |
| Chunked Vectors, Arrays, and Lists | as.list,chunked-method chunked chunked-class chunked_arr chunked_arr-class chunked_list chunked_list-class chunked_mat chunked_mat-class chunked_vec chunked_vec-class chunkify class:chunked class:chunked_arr class:chunked_list class:chunked_mat class:chunked_vec describe_for_display,chunked-method length,chunked-method lengths,chunked-method preview_for_display,chunked-method preview_for_display,chunked_list-method [,chunked,ANY,ANY,ANY-method [[,chunked_list-method [[,chunked_mat-method [[,chunked_vec-method |
| Scaling and Centering by Row or Column Based on Grouping | colscale colscale,ANY-method rowscale rowscale,ANY-method |
| Row and Column Summary Statistics Based on Grouping | .colStats .rowStats colStats colStats,ANY-method colStats,matter_mat-method colStats,sparse_mat-method rowStats rowStats,ANY-method rowStats,matter_mat-method rowStats,sparse_mat-method |
| Sweep out Matrix Summaries Based on Grouping | colsweep colsweep,ANY-method colsweep,matter_mat-method colsweep,sparse_mat-method rowsweep rowsweep,ANY-method rowsweep,matter_mat-method rowsweep,sparse_mat-method |
| Convolution at Arbitrary Indices | convolve_at |
| Colocalization Coefficients | coscore |
| Color Palettes | add_alpha cpal cpals dpal dpals |
| Perform Cross Validation | cv_do fitted.cv |
| Deferred Operations on ``matter'' Objects | Arith Arith,array,matter_arr-method Arith,array,sparse_arr-method Arith,matter_arr,array-method Arith,matter_arr,vector-method Arith,sparse_arr,array-method Arith,sparse_arr,vector-method Arith,vector,matter_arr-method Arith,vector,sparse_arr-method Compare Logic Ops |
| Deprecated and defunct objects in matter | asearch deprecated nnpairs profmem sgmixn |
| Downsample a Signal | downsample findbins |
| Delta Run Length Encoding | as.data.frame,drle-method as.factor,drle_fct-method as.integer,drle-method as.list,drle-method as.numeric,drle-method as.vector,drle-method c,drle-method class:drle class:drle_fct combine,drle,drle-method combine,drle,numeric-method combine,drle_fct,drle_fct-method combine,numeric,drle-method drle drle-class drle_fct drle_fct-class droplevels,drle_fct-method is.drle length,drle-method levels,drle_fct-method levels<-,drle_fct-method type,drle-method [,drle,ANY,ANY,ANY-method [,drle_fct,ANY,ANY,ANY-method |
| Contrast Enhancement | enhance enhance_adapt enhance_adj enhance_hist |
| Continuum Estimation | estbase estbase_hull estbase_loc estbase_med estbase_snip |
| Estimate Raster Dimensions | estdim |
| Local Noise Estimation | estnoise estnoise_diff estnoise_filt estnoise_mad estnoise_quant estnoise_sd |
| Estimate Signal Resolution | estres |
| FastMap Projection | fastmap predict.fastmap |
| Move Data Between Shared Memory and File Storage | fetch fetch,array-method fetch,character-method fetch,factor-method fetch,list-method fetch,logical-method fetch,matrix-method fetch,numeric-method fetch,raw-method flash flash,array-method flash,character-method flash,factor-method flash,list-method flash,logical-method flash,matrix-method flash,numeric-method flash,raw-method |
| Smoothing Filters in 1D | filt1 filt1_adapt filt1_bi filt1_conv filt1_diff filt1_gauss filt1_guide filt1_ma filt1_pag filt1_sg |
| Smoothing Filters in 2D | filt2 filt2_adapt filt2_bi filt2_conv filt2_diff filt2_gauss filt2_guide filt2_ma |
| Smoothing Filters using K-nearest neighbors | filtn filtn_adapt filtn_bi filtn_conv filtn_gauss filtn_ma |
| Peak Detection | findpeaks locmax locmin |
| CWT-based Peak Detection | cwt findpeaks_cwt findridges ricker |
| Peak Detection using K-nearest neighbors | findpeaks_knn knnmax knnmin |
| Point in polygon | inpoly |
| Quote Identifiers | iQuote |
| Isolate Closures for Serialization | isoclos isofun |
| K-Dimensional Nearest Neighbor Search | kdsearch kdtree knnsearch |
| Out-of-Core Arrays | %*%,matrix,matter_mat-method %*%,matter_mat,matrix-method %*%,matter_mat,vector-method %*%,vector,matter_mat-method as.array,matter_arr-method as.integer,matter_arr-method as.logical,matter_arr-method as.matrix,matter_arr-method as.numeric,matter_arr-method as.raw,matter_arr-method as.vector as.vector,matter_arr-method c,matter_arr-method cbind2,matter_mat,matter_mat-method cbind2,matter_mat,matter_vec-method cbind2,matter_vec,matter_mat-method cbind2,matter_vec,matter_vec-method class:matter_arr class:matter_mat class:matter_vec combine,matter_arr,ANY-method crossprod,ANY,matter_mat-method crossprod,matter_mat,ANY-method dim,matter_vec-method dim<-,matter_arr-method dim<-,matter_vec-method exp,matter_arr-method fetch,matter_arr-method fetch,matter_mat-method fetch,matter_vec-method flash,matter_arr-method flash,matter_mat-method flash,matter_vec-method log,matter_arr-method log10,matter_arr-method log1p,matter_arr-method log2,matter_arr-method matter_arr matter_arr-class matter_mat matter_mat-class matter_vec matter_vec-class rbind2,matter_mat,matter_mat-method rbind2,matter_mat,matter_vec-method rbind2,matter_vec,matter_mat-method rbind2,matter_vec,matter_vec-method rowMaj rowMaj,Matrix-method rowMaj,matrix-method rowMaj,matter_arr-method t,matter_arr-method t,matter_vec-method tcrossprod,ANY,matter_mat-method tcrossprod,matter_mat,ANY-method [,matter_arr,ANY,ANY,ANY-method [,matter_arr-method [,matter_mat,ANY,ANY,ANY-method [,matter_mat-method [<-,matter_arr,ANY,ANY,ANY-method [<-,matter_arr-method [<-,matter_mat,ANY,ANY,ANY-method [<-,matter_mat-method |
| Out-of-Core Factors | as.factor,matter_fct-method as.vector,matter_fct-method class:matter_fct combine,matter_fct,ANY-method fetch,matter_fct-method flash,matter_fct-method levels,matter_fct-method levels<-,matter_fct-method matter_fct matter_fct-class [,matter_fct,ANY,ANY,ANY-method [,matter_fct-method [<-,matter_fct,ANY,ANY,ANY-method [<-,matter_fct-method |
| Out-of-Core Lists of Vectors | $,matter_list-method $<-,matter_list-method as.list,matter_list-method as.vector,matter_list-method c,matter_list-method class:matter_list combine,matter_list,ANY-method dim,matter_list-method fetch,matter_list-method flash,matter_list-method length,matter_list-method lengths,matter_list-method matter_list matter_list-class [,matter_list,ANY,ANY,ANY-method [,matter_list-method [<-,matter_list,ANY,ANY,ANY-method [<-,matter_list-method [[,matter_list,ANY,ANY-method [[,matter_list-method [[<-,matter_list,ANY,ANY-method [[<-,matter_list-method |
| Out-of-Core Strings | as.character,matter_str-method as.vector,matter_str-method c,matter_str-method class:matter_str combine,matter_str,ANY-method dim,matter_str-method Encoding,matter_str-method Encoding<-,matter_str-method fetch,matter_str-method flash,matter_str-method length,matter_str-method lengths,matter_str-method matter_str matter_str-class [,matter_str,ANY,ANY,ANY-method [,matter_str-method [<-,matter_str,ANY,ANY,ANY-method [<-,matter_str-method |
| Vectors, Matrices, and Arrays Stored in Virtual Memory | adata adata,matter-method aindex aindex,matter-method as.data.frame,atoms-method as.list,atoms-method as.matter as.shared atomdata atomdata,matter-method atomdata<- atomdata<-,matter-method atomindex atomindex,matter-method atomindex<- atoms atoms-class c,atoms-method c,matter-method cbind2,atoms,ANY-method class:atoms class:matter combine,atoms,ANY-method dim,atoms-method dim,matter-method dim<-,matter-method dimnames,matter-method dimnames<-,matter,ANY-method dims,atoms-method is.matter is.shared length,atoms-method length,matter-method length<-,matter-method lengths,atoms-method matter matter-class names,matter-method names<-,matter-method path path,atoms-method path,matter_-method path<- path<-,atoms-method path<-,matter_-method rbind2,atoms,ANY-method readonly readonly,atoms-method readonly,matter_-method readonly<- readonly<-,atoms-method readonly<-,matter_-method type type,array-method type,atoms-method type,matter-method type,vector-method type<- type<-,atoms-method type<-,matter-method [,atoms,ANY,ANY,ANY-method [,atoms-method [[,atoms,ANY,ANY-method [[,atoms-method |
| Options for ``matter'' Objects | matter-options matter_defaults |
| Data Types for ``matter'' Objects | matter-types types |
| Monitor Memory Use | mem memcl memtime |
| Multiple Instance Learning | mi_learn |
| Nonnegative Matrix Factorization | nndsvd nnmf nnmf_als nnmf_mult predict.nnmf |
| Nearest Shrunken Centroids | fitted.nscentroids logLik.nscentroids nscentroids predict.nscentroids |
| Peak Summarization | peakareas peakheights peakwidths |
| Pseudoinverse of a Matrix | pinv |
| Plot a Signal or Image | plot_image plot_signal |
| Plotting Graphical Marks | plot,vizi_bars,ANY-method plot,vizi_boxplot,ANY-method plot,vizi_image,ANY-method plot,vizi_intervals,ANY-method plot,vizi_lines,ANY-method plot,vizi_peaks,ANY-method plot,vizi_pixels,ANY-method plot,vizi_points,ANY-method plot,vizi_rules,ANY-method plot,vizi_text,ANY-method plot,vizi_voxels,ANY-method plot.vizi_bars plot.vizi_boxplot plot.vizi_image plot.vizi_intervals plot.vizi_lines plot.vizi_peaks plot.vizi_pixels plot.vizi_points plot.vizi_rules plot.vizi_text plot.vizi_voxels vizi_bars vizi_boxplot vizi_image vizi_intervals vizi_lines vizi_peaks vizi_pixels vizi_points vizi_rules vizi_text vizi_voxels |
| Partial Least Squares | coef.opls fitted.opls fitted.pls opls opls_nipals pls pls_kernel pls_nipals pls_simpls predict.opls predict.pls residuals.opls vip |
| Principal Components Analysis for ``matter'' Matrices | prcomp prcomp,matter_mat-method prcomp,sparse_mat-method prcomp_lanczos |
| Score predictive performance | predscore |
| Signal Normalization | rescale rescale_iqr rescale_range rescale_ref rescale_rms rescale_sum |
| Parallel RNG Streams | getRNGStream RNGStreams setRNGStream |
| Compute area under ROC curve | rocscore |
| Rolling Summaries of a Vector | roll rollvec |
| Compute Distances between Rows or Columns of a Matrix | .colDists .rowDists coldist colDists colDists,ANY,missing-method colDists,matrix,matrix-method colDists,matrix,matter_mat-method colDists,matrix,sparse_mat-method colDists,matter_mat,matrix-method colDists,sparse_mat,matrix-method coldist_at rowdist rowDists rowDists,ANY,missing-method rowDists,matrix,matrix-method rowDists,matrix,matter_mat-method rowDists,matrix,sparse_mat-method rowDists,matter_mat,matrix-method rowDists,sparse_mat,matrix-method rowdist_at |
| Relative Sequence Generation | seq_rel |
| Spatial Gaussian Mixture Model | fitted.sgmix logLik.sgmix sgmix |
| Cleveland-Style Shingles | shingles |
| Simple Logging | class:simple_logger matter_logger path,simple_logger-method path<-,simple_logger-method simple_logger simple_logger-class |
| Simulate Spectra | simspec simspec1 |
| Fast Simple Network of Workstations (SNOW)-style Parallel Backend | bpislocal bplocalized bpstart,SnowfastParam-method bpstop,SnowfastParam-method bptrystart bptrystop class:SnowfastParam SnowfastParam SnowfastParam-class |
| Sparse Vectors and Matrices | %*%,matrix,sparse_mat-method %*%,sparse_mat,matrix-method %*%,sparse_mat,vector-method %*%,vector,sparse_mat-method aindex,sparse_arr-method as.array,sparse_arr-method as.integer,sparse_arr-method as.logical,sparse_arr-method as.matrix,sparse_arr-method as.numeric,sparse_arr-method as.raw,sparse_arr-method as.sparse as.vector,sparse_arr-method atomdata,sparse_arr-method atomindex,sparse_arr-method atomindex<-,sparse_arr-method cbind2,sparse_mat,sparse_mat-method class:sparse_arr class:sparse_mat class:sparse_vec crossprod,ANY,sparse_mat-method crossprod,sparse_mat,ANY-method dim,sparse_vec-method domain domain,array-method domain,sparse_arr-method domain,vector-method domain<- domain<-,array-method domain<-,sparse_arr-method domain<-,vector-method exp,sparse_arr-method fetch,sparse_arr-method flash,sparse_arr-method is.sparse length,sparse_arr-method lengths,sparse_arr-method log,sparse_arr-method log10,sparse_arr-method log1p,sparse_arr-method log2,sparse_arr-method nnzero,sparse_arr-method pointers pointers,sparse_arr-method pointers<- pointers<-,sparse_arr-method rbind2,sparse_mat,sparse_mat-method rowMaj,sparse_arr-method sampler sampler,sparse_arr-method sampler<- sampler<-,sparse_arr-method sparse_arr sparse_arr-class sparse_mat sparse_mat-class sparse_vec sparse_vec-class t,sparse_arr-method t,sparse_vec-method tcrossprod,ANY,sparse_mat-method tcrossprod,sparse_mat,ANY-method tolerance,sparse_arr-method tolerance<- tolerance<-,sparse_arr-method [,sparse_arr,ANY,ANY,ANY-method [<-,sparse_arr,ANY,ANY,ANY-method [<-,sparse_arr-method |
| Streaming Summary Statistics | as.data.frame,stream_stat-method combine,stream_stat,ANY-method stat_c stream_stat s_all s_any s_colstats s_max s_mean s_min s_nnzero s_prod s_range s_rowstats s_sd s_stat s_sum s_var |
| C-Style Structs Stored in Virtual Memory | struct |
| Summary Statistics for ``matter'' Objects | all,matter_arr-method any,matter_arr-method colMeans colMeans,matter_mat-method colMeans,sparse_mat-method colSums colSums,matter_mat-method colSums,sparse_mat-method max,matter_arr-method mean,matter_arr-method min,matter_arr-method prod,matter_arr-method range,matter_arr-method rowMeans rowMeans,matter_mat-method rowMeans,sparse_mat-method rowSums rowSums,matter_mat-method rowSums,sparse_mat-method sd,matter_arr-method sum,matter_arr-method Summary var,matter_arr-method |
| Rasterize a Scattered 2D or 3D Signal | is_gridded to_raster to_raster3 |
| 2D Spatial Transformation | trans2d |
| Universally Unique Identifiers | hex2raw raw2hex tempmem uuid |
| A Simple Grammar of Base Graphics | add_facets add_mark as_facets as_layers c,vizi_facets-method c,vizi_plot-method combine,vizi_facets,vizi_facets-method combine,vizi_plot,vizi_plot-method plot,vizi_colorkey,ANY-method plot,vizi_facets,ANY-method plot,vizi_key,ANY-method plot,vizi_plot,ANY-method preplot,vizi_facets-method preplot,vizi_plot-method print,vizi_facets,ANY-method print,vizi_plot,ANY-method set_channel set_coord set_engine set_par set_title vizi |
| Set Graphical Parameters | vizi_engine vizi_par vizi_style |
| Warping to Align 1D Signals | icor warp1 warp1_cow warp1_dtw warp1_loc |
| Warping to Align 2D Signals | mi warp2 warp2_trans |
