Out-of-memory dense and sparse signal arrays

---

Documentation for package ‘matter’ version 2.4.1

• 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