# Out-of-memory dense and sparse signal arrays

## Documentation for package ‘matter’ version 2.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F H I K L M N O P R S T U V W misc

## -- A --

adata | Vectors, Matrices, and Arrays Stored in Virtual Memory
adata-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
add_alpha | Color Palettes
add_facets | A Simple Grammar of Base Graphics
add_mark | A Simple Grammar of Base Graphics
aindex | Sparse Vectors and Matrices
aindex-method | Sparse Vectors and Matrices
all-method | Summary Statistics for "matter" Objects
any-method | Summary Statistics for "matter" Objects
approx1 | Resampling in 1D with Interpolation
approx2 | Resampling in 2D with Interpolation
Arith | Deferred Operations on "matter" Objects
Arith-method | Deferred Operations on "matter" Objects
as.array-method | Out-of-Memory Arrays
as.array-method | Sparse Vectors and Matrices
as.character-method | Out-of-Memory Strings
as.data.frame-method | Delta Run Length Encoding
as.data.frame-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
as.data.frame-method | Streaming Summary Statistics
as.factor-method | Delta Run Length Encoding
as.factor-method | Out-of-Memory Factors
as.integer-method | Delta Run Length Encoding
as.integer-method | Out-of-Memory Arrays
as.list-method | Delta Run Length Encoding
as.list-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
as.list-method | Out-of-Memory Lists of Vectors
as.logical-method | Out-of-Memory Arrays
as.matrix-method | Out-of-Memory Arrays
as.matrix-method | Sparse Vectors and Matrices
as.matter | Vectors, Matrices, and Arrays Stored in Virtual Memory
as.numeric-method | Delta Run Length Encoding
as.numeric-method | Out-of-Memory Arrays
as.raw-method | Out-of-Memory Arrays
as.sparse | Sparse Vectors and Matrices
as.vector-method | Delta Run Length Encoding
as.vector-method | Out-of-Memory Arrays
as.vector-method | Out-of-Memory Strings
asearch | Approximate Key-Value Search
atomdata | Vectors, Matrices, and Arrays Stored in Virtual Memory
atomdata-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
atomdata-method | Sparse Vectors and Matrices
atomdata<- | Vectors, Matrices, and Arrays Stored in Virtual Memory
atomdata<--method | Vectors, Matrices, and Arrays Stored in Virtual Memory
atomindex | Sparse Vectors and Matrices
atomindex-method | Sparse Vectors and Matrices
atomindex<- | Sparse Vectors and Matrices
atomindex<--method | Sparse Vectors and Matrices
atoms | Vectors, Matrices, and Arrays Stored in Virtual Memory
atoms-class | Vectors, Matrices, and Arrays Stored in Virtual Memory

## -- B --

bigglm | Linear Regression for "matter" Matrices
bigglm-method | Linear Regression for "matter" Matrices
binpeaks | Peak Processing
binvec | Binned Summaries of a Vector
bsearch | Binary Search with Approximate Matching

## -- C --

c-method | Delta Run Length Encoding
c-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
c-method | Out-of-Memory Arrays
c-method | Out-of-Memory Lists of Vectors
c-method | Out-of-Memory Strings
cbind2-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
cbind2-method | Out-of-Memory Arrays
cbind2-method | Sparse Vectors and Matrices
checksum | Calculate Checksums and Cryptographic Hashes
checksum-method | Calculate Checksums and Cryptographic Hashes
chunkApply | Apply Functions Over Chunks of a List, Vector, or Matrix
chunkLapply | Apply Functions Over Chunks of a List, Vector, or Matrix
chunkMapply | Apply Functions Over Chunks of a List, Vector, or Matrix
chunk_apply | Apply Functions Over Chunks of a List, Vector, or Matrix
chunk_colapply | Apply Functions Over Chunks of a List, Vector, or Matrix
chunk_lapply | Apply Functions Over Chunks of a List, Vector, or Matrix
chunk_mapply | Apply Functions Over Chunks of a List, Vector, or Matrix
chunk_rowapply | Apply Functions Over Chunks of a List, Vector, or Matrix
class:atoms | Vectors, Matrices, and Arrays Stored in Virtual Memory
class:drle | Delta Run Length Encoding
class:drle_fct | Delta Run Length Encoding
class:matter | Vectors, Matrices, and Arrays Stored in Virtual Memory
class:matter_arr | Out-of-Memory Arrays
class:matter_fct | Out-of-Memory Factors
class:matter_list | Out-of-Memory Lists of Vectors
class:matter_mat | Out-of-Memory Arrays
class:matter_str | Out-of-Memory Strings
class:matter_vec | Out-of-Memory Arrays
class:sparse_arr | Sparse Vectors and Matrices
class:sparse_mat | Sparse Vectors and Matrices
class:sparse_vec | Sparse Vectors and Matrices
coldist | Compute Distances between Rows or Columns of a Matrix
colDistFun | FastMap Projection
colDists | Compute Distances between Rows or Columns of a Matrix
colDists-method | Compute Distances between Rows or Columns of a Matrix
coldist_at | Compute Distances between Rows or Columns of a Matrix
colMeans | Summary Statistics for "matter" Objects
colMeans-method | Summary Statistics for "matter" Objects
colscale | Scaling and Centering by Row or Column Based on Grouping
colscale-method | Scaling and Centering by Row or Column Based on Grouping
colStats | Row and Column Summary Statistics Based on Grouping
colStats-method | Row and Column Summary Statistics Based on Grouping
colSums | Summary Statistics for "matter" Objects
colSums-method | Summary Statistics for "matter" Objects
colsweep | Sweep out Matrix Summaries Based on Grouping
colsweep-method | Sweep out Matrix Summaries Based on Grouping
combine-method | Delta Run Length Encoding
combine-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
combine-method | Out-of-Memory Arrays
combine-method | Out-of-Memory Factors
combine-method | Out-of-Memory Lists of Vectors
combine-method | Out-of-Memory Strings
combine-method | Streaming Summary Statistics
Compare | Deferred Operations on "matter" Objects
convolve_at | Convolution at Arbitrary Indices
cpal | Color Palettes
crossprod-method | Out-of-Memory Arrays
crossprod-method | Sparse Vectors and Matrices
cwt | CWT-based Peak Detection

## -- D --

dim-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
dim-method | Out-of-Memory Arrays
dim-method | Out-of-Memory Lists of Vectors
dim-method | Out-of-Memory Strings
dim-method | Sparse Vectors and Matrices
dim<--method | Vectors, Matrices, and Arrays Stored in Virtual Memory
dim<--method | Out-of-Memory Arrays
dimnames-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
dimnames<--method | Vectors, Matrices, and Arrays Stored in Virtual Memory
dims-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
domain | Sparse Vectors and Matrices
domain-method | Sparse Vectors and Matrices
domain<- | Sparse Vectors and Matrices
domain<--method | Sparse Vectors and Matrices
downsample | Downsample a Signal
dpal | Color Palettes
drle | Delta Run Length Encoding
drle-class | Delta Run Length Encoding
drle_fct | Delta Run Length Encoding
drle_fct-class | Delta Run Length Encoding

## -- E --

Encoding-method | Out-of-Memory Strings
Encoding<--method | Out-of-Memory Strings
enhance | Contrast Enhancement
enhance_adapt | Contrast Enhancement
enhance_hist | Contrast Enhancement
estbase | Continuum Estimation
estbase_hull | Continuum Estimation
estbase_loc | Continuum Estimation
estbase_med | Continuum Estimation
estbase_snip | Continuum Estimation
estdim | Estimate Raster Dimensions
estnoise | Local Noise Estimation
estnoise_diff | Local Noise Estimation
estnoise_filt | Local Noise Estimation
estnoise_mad | Local Noise Estimation
estnoise_quant | Local Noise Estimation
estnoise_sd | Local Noise Estimation
estres | Estimate Signal Resolution

## -- F --

fastmap | FastMap Projection
filt1 | Smoothing Filters in 1D
filt1_adapt | Smoothing Filters in 1D
filt1_bi | Smoothing Filters in 1D
filt1_conv | Smoothing Filters in 1D
filt1_diff | Smoothing Filters in 1D
filt1_gauss | Smoothing Filters in 1D
filt1_guide | Smoothing Filters in 1D
filt1_ma | Smoothing Filters in 1D
filt1_pag | Smoothing Filters in 1D
filt1_sg | Smoothing Filters in 1D
filt2 | Smoothing Filters in 2D
filt2_adapt | Smoothing Filters in 2D
filt2_bi | Smoothing Filters in 2D
filt2_conv | Smoothing Filters in 2D
filt2_diff | Smoothing Filters in 2D
filt2_gauss | Smoothing Filters in 2D
filt2_guide | Smoothing Filters in 2D
filt2_ma | Smoothing Filters in 2D
findbins | Downsample a Signal
findpeaks | Peak Detection
findpeaks_cwt | CWT-based Peak Detection
findridges | CWT-based Peak Detection

## -- H --

hex2raw | Universally Unique Identifiers

## -- I --

icor | Warping to Align 1D Signals
image | Display a Color Image from a Formula
image-method | Display a Color Image from a Formula
inpoly | Point in polygon
is.drle | Delta Run Length Encoding
is.matter | Vectors, Matrices, and Arrays Stored in Virtual Memory
is.sparse | Sparse Vectors and Matrices
is_gridded | Rasterize a Scattered 2D or 3D Signal

## -- K --

kdsearch | K-Dimensional Nearest Neighbor Search
kdtree | K-Dimensional Nearest Neighbor Search
knnsearch | K-Dimensional Nearest Neighbor Search

## -- L --

length-method | Delta Run Length Encoding
length-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
length-method | Out-of-Memory Lists of Vectors
length-method | Out-of-Memory Strings
length-method | Sparse Vectors and Matrices
length<--method | Vectors, Matrices, and Arrays Stored in Virtual Memory
lengths-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
lengths-method | Out-of-Memory Lists of Vectors
lengths-method | Out-of-Memory Strings
lengths-method | Sparse Vectors and Matrices
levels-method | Delta Run Length Encoding
levels-method | Out-of-Memory Factors
levels<--method | Delta Run Length Encoding
levels<--method | Out-of-Memory Factors
locmax | Peak Detection
locmin | Peak Detection
Logic | Deferred Operations on "matter" Objects

## -- M --

matter | Vectors, Matrices, and Arrays Stored in Virtual Memory
matter-class | Vectors, Matrices, and Arrays Stored in Virtual Memory
matter-options | Options for "matter" Objects
matter-types | Data Types for "matter" Objects
matter_arr | Out-of-Memory Arrays
matter_arr-class | Out-of-Memory Arrays
matter_fct | Out-of-Memory Factors
matter_fct-class | Out-of-Memory Factors
matter_list | Out-of-Memory Lists of Vectors
matter_list-class | Out-of-Memory Lists of Vectors
matter_mat | Out-of-Memory Arrays
matter_mat-class | Out-of-Memory Arrays
matter_str | Out-of-Memory Strings
matter_str-class | Out-of-Memory Strings
matter_vec | Out-of-Memory Arrays
matter_vec-class | Out-of-Memory Arrays
max-method | Summary Statistics for "matter" Objects
mean-method | Summary Statistics for "matter" Objects
mem | Check Memory Use
memtime | Check Memory Use
mergepeaks | Peak Processing
mi | Warping to Align 2D Signals
min-method | Summary Statistics for "matter" Objects

## -- N --

names-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
names<--method | Vectors, Matrices, and Arrays Stored in Virtual Memory
nndsvd | Nonnegative Matrix Factorization
nnmf | Nonnegative Matrix Factorization
nnmf_als | Nonnegative Matrix Factorization
nnmf_mult | Nonnegative Matrix Factorization
nnpairs | K-Dimensional Nearest Neighbor Search
nnzero-method | Sparse Vectors and Matrices

## -- O --

opls | Partial Least Squares
opls_nipals | Partial Least Squares
Ops | Deferred Operations on "matter" Objects

## -- P --

path | Vectors, Matrices, and Arrays Stored in Virtual Memory
path-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
path<- | Vectors, Matrices, and Arrays Stored in Virtual Memory
path<--method | Vectors, Matrices, and Arrays Stored in Virtual Memory
peakareas | Peak Summarization
peakwidths | Peak Summarization
plot-method | Plotting Graphical Marks
plot-method | A Simple Grammar of Base Graphics
plot.vizi_lines | Plotting Graphical Marks
plot.vizi_peaks | Plotting Graphical Marks
plot.vizi_pixels | Plotting Graphical Marks
plot.vizi_points | Plotting Graphical Marks
plot.vizi_voxels | Plotting Graphical Marks
plot_facets | A Simple Grammar of Base Graphics
pls | Partial Least Squares
pls_kernel | Partial Least Squares
pls_nipals | Partial Least Squares
pls_simpls | Partial Least Squares
pointers | Sparse Vectors and Matrices
pointers-method | Sparse Vectors and Matrices
pointers<- | Sparse Vectors and Matrices
pointers<--method | Sparse Vectors and Matrices
prcomp | Principal Components Analysis for "matter" Matrices
prcomp-method | Principal Components Analysis for "matter" Matrices
prcomp_lanczos | Principal Components Analysis for "matter" Matrices
predict.fastmap | FastMap Projection
predict.nnmf | Nonnegative Matrix Factorization
predict.opls | Partial Least Squares
predict.pls | Partial Least Squares
preplot-method | A Simple Grammar of Base Graphics
print-method | A Simple Grammar of Base Graphics
prod-method | Summary Statistics for "matter" Objects
profmem | Check Memory Use

## -- R --

range-method | Summary Statistics for "matter" Objects
raw2hex | Universally Unique Identifiers
rbind2-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
rbind2-method | Out-of-Memory Arrays
rbind2-method | Sparse Vectors and Matrices
readonly | Vectors, Matrices, and Arrays Stored in Virtual Memory
readonly-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
readonly<- | Vectors, Matrices, and Arrays Stored in Virtual Memory
readonly<--method | Vectors, Matrices, and Arrays Stored in Virtual Memory
reldiff | Binary Search with Approximate Matching
ricker | CWT-based Peak Detection
rollvec | Rolling Summaries of a Vector
rowdist | Compute Distances between Rows or Columns of a Matrix
rowDistFun | FastMap Projection
rowDists | Compute Distances between Rows or Columns of a Matrix
rowDists-method | Compute Distances between Rows or Columns of a Matrix
rowdist_at | Compute Distances between Rows or Columns of a Matrix
rowMaj | Out-of-Memory Arrays
rowMaj-method | Out-of-Memory Arrays
rowMaj-method | Sparse Vectors and Matrices
rowMeans | Summary Statistics for "matter" Objects
rowMeans-method | Summary Statistics for "matter" Objects
rowscale | Scaling and Centering by Row or Column Based on Grouping
rowscale-method | Scaling and Centering by Row or Column Based on Grouping
rowStats | Row and Column Summary Statistics Based on Grouping
rowStats-method | Row and Column Summary Statistics Based on Grouping
rowSums | Summary Statistics for "matter" Objects
rowSums-method | Summary Statistics for "matter" Objects
rowsweep | Sweep out Matrix Summaries Based on Grouping
rowsweep-method | Sweep out Matrix Summaries Based on Grouping

## -- S --

sampler | Sparse Vectors and Matrices
sampler-method | Sparse Vectors and Matrices
sampler<- | Sparse Vectors and Matrices
sampler<--method | Sparse Vectors and Matrices
sd-method | Summary Statistics for "matter" Objects
set_channel | A Simple Grammar of Base Graphics
set_coord | A Simple Grammar of Base Graphics
set_par | A Simple Grammar of Base Graphics
set_title | A Simple Grammar of Base Graphics
simspec | Simulate Spectra
simspec1 | Simulate Spectra
sparse_arr | Sparse Vectors and Matrices
sparse_arr-class | Sparse Vectors and Matrices
sparse_mat | Sparse Vectors and Matrices
sparse_mat-class | Sparse Vectors and Matrices
sparse_vec | Sparse Vectors and Matrices
sparse_vec-class | Sparse Vectors and Matrices
stat_c | Streaming Summary Statistics
stream_stat | Streaming Summary Statistics
struct | C-Style Structs Stored in Virtual Memory
sum-method | Summary Statistics for "matter" Objects
Summary | Summary Statistics for "matter" Objects
s_all | Streaming Summary Statistics
s_any | Streaming Summary Statistics
s_colstats | Streaming Summary Statistics
s_max | Streaming Summary Statistics
s_mean | Streaming Summary Statistics
s_min | Streaming Summary Statistics
s_nnzero | Streaming Summary Statistics
s_prod | Streaming Summary Statistics
s_range | Streaming Summary Statistics
s_rowstats | Streaming Summary Statistics
s_sd | Streaming Summary Statistics
s_sum | Streaming Summary Statistics
s_var | Streaming Summary Statistics

## -- T --

t-method | Out-of-Memory Arrays
t-method | Sparse Vectors and Matrices
tcrossprod-method | Out-of-Memory Arrays
tcrossprod-method | Sparse Vectors and Matrices
tolerance-method | Sparse Vectors and Matrices
tolerance<- | Sparse Vectors and Matrices
tolerance<--method | Sparse Vectors and Matrices
to_raster | Rasterize a Scattered 2D or 3D Signal
to_raster3 | Rasterize a Scattered 2D or 3D Signal
trans2d | 2D Spatial Transformation
type | Vectors, Matrices, and Arrays Stored in Virtual Memory
type-method | Delta Run Length Encoding
type-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
type<- | Vectors, Matrices, and Arrays Stored in Virtual Memory
type<--method | Vectors, Matrices, and Arrays Stored in Virtual Memory
types | Data Types for "matter" Objects

## -- U --

uuid | Universally Unique Identifiers

## -- V --

var-method | Summary Statistics for "matter" Objects
vip | Partial Least Squares
vizi | A Simple Grammar of Base Graphics
vizi_lines | Plotting Graphical Marks
vizi_par | A Simple Grammar of Base Graphics
vizi_peaks | Plotting Graphical Marks
vizi_pixels | Plotting Graphical Marks
vizi_points | Plotting Graphical Marks
vizi_style | A Simple Grammar of Base Graphics
vizi_voxels | Plotting Graphical Marks

## -- W --

warp1 | Warping to Align 1D Signals
warp1_cow | Warping to Align 1D Signals
warp1_dtw | Warping to Align 1D Signals
warp1_loc | Warping to Align 1D Signals
warp2 | Warping to Align 2D Signals
warp2_trans | Warping to Align 2D Signals

## -- misc --

$-method | Out-of-Memory Lists of Vectors
$<--method | Out-of-Memory Lists of Vectors
%*%-method | Out-of-Memory Arrays
%*%-method | Sparse Vectors and Matrices
.colStats | Row and Column Summary Statistics Based on Grouping
.rowStats | Row and Column Summary Statistics Based on Grouping
[-method | Delta Run Length Encoding
[-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
[-method | Out-of-Memory Arrays
[-method | Out-of-Memory Factors
[-method | Out-of-Memory Lists of Vectors
[-method | Out-of-Memory Strings
[-method | Sparse Vectors and Matrices
[<--method | Out-of-Memory Arrays
[<--method | Out-of-Memory Factors
[<--method | Out-of-Memory Lists of Vectors
[<--method | Out-of-Memory Strings
[<--method | Sparse Vectors and Matrices
[[-method | Vectors, Matrices, and Arrays Stored in Virtual Memory
[[-method | Out-of-Memory Lists of Vectors
[[<--method | Out-of-Memory Lists of Vectors