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  "Title": "Out-of-core statistical computing and signal processing",
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  "Date": "2016-10-11",
  "Author": "Kylie A. Bemis <k.bemis@northeastern.edu>",
  "Maintainer": "Kylie A. Bemis <k.bemis@northeastern.edu>",
  "Description": "Toolbox for larger-than-memory scientific computing and\nvisualization, providing efficient out-of-core data structures\nusing files or shared memory, for dense and sparse vectors,\nmatrices, and arrays, with applications to nonuniformly sampled\nsignals and images.",
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  "Collate": "matterGenerics.R utils.R logger.R resources.R drle.R atoms.R\nops.R matter.R matter_arr.R matter_fct.R matter_list.R\nmatter_str.R search.R sparse_arr.R stream_stat.R chunked.R\napply.R rowDists.R rowStats.R stats.R scale.R signal.R\nsignal2.R nnmf.R fastmap.R prcomp.R pls.R nscentroids.R sgmix.R\ncv.R mi_learn.R altrep.R parallel.R plot.R vizi.R",
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      ]
    },
    {
      "page": "drle-class",
      "title": "Delta Run Length Encoding",
      "topics": [
        "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"
      ]
    },
    {
      "page": "enhance",
      "title": "Contrast Enhancement",
      "topics": [
        "enhance",
        "enhance_adapt",
        "enhance_adj",
        "enhance_hist"
      ]
    },
    {
      "page": "estbase",
      "title": "Continuum Estimation",
      "topics": [
        "estbase",
        "estbase_hull",
        "estbase_loc",
        "estbase_med",
        "estbase_snip"
      ]
    },
    {
      "page": "estdim",
      "title": "Estimate Raster Dimensions",
      "topics": [
        "estdim"
      ]
    },
    {
      "page": "estnoise",
      "title": "Local Noise Estimation",
      "topics": [
        "estnoise",
        "estnoise_diff",
        "estnoise_filt",
        "estnoise_mad",
        "estnoise_quant",
        "estnoise_sd"
      ]
    },
    {
      "page": "estres",
      "title": "Estimate Signal Resolution",
      "topics": [
        "estres"
      ]
    },
    {
      "page": "fastmap",
      "title": "FastMap Projection",
      "topics": [
        "fastmap",
        "predict.fastmap"
      ]
    },
    {
      "page": "fetch",
      "title": "Move Data Between Shared Memory and File Storage",
      "topics": [
        "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"
      ]
    },
    {
      "page": "filt1",
      "title": "Smoothing Filters in 1D",
      "topics": [
        "filt1",
        "filt1_adapt",
        "filt1_bi",
        "filt1_conv",
        "filt1_diff",
        "filt1_gauss",
        "filt1_guide",
        "filt1_ma",
        "filt1_pag",
        "filt1_sg"
      ]
    },
    {
      "page": "filt2",
      "title": "Smoothing Filters in 2D",
      "topics": [
        "filt2",
        "filt2_adapt",
        "filt2_bi",
        "filt2_conv",
        "filt2_diff",
        "filt2_gauss",
        "filt2_guide",
        "filt2_ma"
      ]
    },
    {
      "page": "filtn",
      "title": "Smoothing Filters using K-nearest neighbors",
      "topics": [
        "filtn",
        "filtn_adapt",
        "filtn_bi",
        "filtn_conv",
        "filtn_gauss",
        "filtn_ma"
      ]
    },
    {
      "page": "findpeaks",
      "title": "Peak Detection",
      "topics": [
        "findpeaks",
        "locmax",
        "locmin"
      ]
    },
    {
      "page": "findpeaks_cwt",
      "title": "CWT-based Peak Detection",
      "topics": [
        "cwt",
        "findpeaks_cwt",
        "findridges",
        "ricker"
      ]
    },
    {
      "page": "findpeaks_knn",
      "title": "Peak Detection using K-nearest neighbors",
      "topics": [
        "findpeaks_knn",
        "knnmax",
        "knnmin"
      ]
    },
    {
      "page": "inpoly",
      "title": "Point in polygon",
      "topics": [
        "inpoly"
      ]
    },
    {
      "page": "iQuote",
      "title": "Quote Identifiers",
      "topics": [
        "iQuote"
      ]
    },
    {
      "page": "isofun",
      "title": "Isolate Closures for Serialization",
      "topics": [
        "isoclos",
        "isofun"
      ]
    },
    {
      "page": "knnsearch",
      "title": "K-Dimensional Nearest Neighbor Search",
      "topics": [
        "kdsearch",
        "kdtree",
        "knnsearch"
      ]
    },
    {
      "page": "matter_arr-class",
      "title": "Out-of-Core Arrays",
      "topics": [
        "%*%,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"
      ]
    },
    {
      "page": "matter_fct-class",
      "title": "Out-of-Core Factors",
      "topics": [
        "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"
      ]
    },
    {
      "page": "matter_list-class",
      "title": "Out-of-Core Lists of Vectors",
      "topics": [
        "$,matter_list-method",
        "$<-,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"
      ]
    },
    {
      "page": "matter_str-class",
      "title": "Out-of-Core Strings",
      "topics": [
        "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"
      ]
    },
    {
      "page": "matter-class",
      "title": "Vectors, Matrices, and Arrays Stored in Virtual Memory",
      "topics": [
        "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"
      ]
    },
    {
      "page": "matter-options",
      "title": "Options for ``matter'' Objects",
      "topics": [
        "matter-options",
        "matter_defaults"
      ]
    },
    {
      "page": "matter-types",
      "title": "Data Types for ``matter'' Objects",
      "topics": [
        "matter-types",
        "types"
      ]
    },
    {
      "page": "mem",
      "title": "Monitor Memory Use",
      "topics": [
        "mem",
        "memcl",
        "memtime"
      ]
    },
    {
      "page": "mi_learn",
      "title": "Multiple Instance Learning",
      "topics": [
        "mi_learn"
      ]
    },
    {
      "page": "nnmf",
      "title": "Nonnegative Matrix Factorization",
      "topics": [
        "nndsvd",
        "nnmf",
        "nnmf_als",
        "nnmf_mult",
        "predict.nnmf"
      ]
    },
    {
      "page": "nscentroids",
      "title": "Nearest Shrunken Centroids",
      "topics": [
        "fitted.nscentroids",
        "logLik.nscentroids",
        "nscentroids",
        "predict.nscentroids"
      ]
    },
    {
      "page": "peakwidths",
      "title": "Peak Summarization",
      "topics": [
        "peakareas",
        "peakheights",
        "peakwidths"
      ]
    },
    {
      "page": "pinv",
      "title": "Pseudoinverse of a Matrix",
      "topics": [
        "pinv"
      ]
    },
    {
      "page": "plot_signal",
      "title": "Plot a Signal or Image",
      "topics": [
        "plot_image",
        "plot_signal"
      ]
    },
    {
      "page": "vizi-methods",
      "title": "Plotting Graphical Marks",
      "topics": [
        "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"
      ]
    },
    {
      "page": "pls",
      "title": "Partial Least Squares",
      "topics": [
        "coef.opls",
        "fitted.opls",
        "fitted.pls",
        "opls",
        "opls_nipals",
        "pls",
        "pls_kernel",
        "pls_nipals",
        "pls_simpls",
        "predict.opls",
        "predict.pls",
        "residuals.opls",
        "vip"
      ]
    },
    {
      "page": "prcomp",
      "title": "Principal Components Analysis for ``matter'' Matrices",
      "topics": [
        "prcomp",
        "prcomp,matter_mat-method",
        "prcomp,sparse_mat-method",
        "prcomp_lanczos"
      ]
    },
    {
      "page": "predscore",
      "title": "Score predictive performance",
      "topics": [
        "predscore"
      ]
    },
    {
      "page": "rescale",
      "title": "Signal Normalization",
      "topics": [
        "rescale",
        "rescale_iqr",
        "rescale_range",
        "rescale_ref",
        "rescale_rms",
        "rescale_sum"
      ]
    },
    {
      "page": "RNGStreams",
      "title": "Parallel RNG Streams",
      "topics": [
        "getRNGStream",
        "RNGStreams",
        "setRNGStream"
      ]
    },
    {
      "page": "rocscore",
      "title": "Compute area under ROC curve",
      "topics": [
        "rocscore"
      ]
    },
    {
      "page": "rollvec",
      "title": "Rolling Summaries of a Vector",
      "topics": [
        "roll",
        "rollvec"
      ]
    },
    {
      "page": "rowDists",
      "title": "Compute Distances between Rows or Columns of a Matrix",
      "topics": [
        ".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"
      ]
    },
    {
      "page": "seq_rel",
      "title": "Relative Sequence Generation",
      "topics": [
        "seq_rel"
      ]
    },
    {
      "page": "sgmix",
      "title": "Spatial Gaussian Mixture Model",
      "topics": [
        "fitted.sgmix",
        "logLik.sgmix",
        "sgmix"
      ]
    },
    {
      "page": "shingles",
      "title": "Cleveland-Style Shingles",
      "topics": [
        "shingles"
      ]
    },
    {
      "page": "simple_logger-class",
      "title": "Simple Logging",
      "topics": [
        "class:simple_logger",
        "matter_logger",
        "path,simple_logger-method",
        "path<-,simple_logger-method",
        "simple_logger",
        "simple_logger-class"
      ]
    },
    {
      "page": "simspec",
      "title": "Simulate Spectra",
      "topics": [
        "simspec",
        "simspec1"
      ]
    },
    {
      "page": "SnowfastParam-class",
      "title": "Fast Simple Network of Workstations (SNOW)-style Parallel Backend",
      "topics": [
        "bpislocal",
        "bplocalized",
        "bpstart,SnowfastParam-method",
        "bpstop,SnowfastParam-method",
        "bptrystart",
        "bptrystop",
        "class:SnowfastParam",
        "SnowfastParam",
        "SnowfastParam-class"
      ]
    },
    {
      "page": "sparse_arr-class",
      "title": "Sparse Vectors and Matrices",
      "topics": [
        "%*%,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"
      ]
    },
    {
      "page": "stream_stat",
      "title": "Streaming Summary Statistics",
      "topics": [
        "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"
      ]
    },
    {
      "page": "struct",
      "title": "C-Style Structs Stored in Virtual Memory",
      "topics": [
        "struct"
      ]
    },
    {
      "page": "summary-stats",
      "title": "Summary Statistics for ``matter'' Objects",
      "topics": [
        "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",
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