Scientific computing for out-of-memory signals and images


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Documentation for package ‘matter’ version 2.6.2

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A B C D E F G 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
as_facets A Simple Grammar of Base Graphics
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
c-method A Simple Grammar of Base Graphics
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
chunkify 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
chunk_writer 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
coef.opls Partial Least Squares
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
combine-method A Simple Grammar of Base Graphics
Compare Deferred Operations on "matter" Objects
convolve_at Convolution at Arbitrary Indices
coscore Colocalization Coefficients
cpal Color Palettes
crossprod-method Out-of-Memory Arrays
crossprod-method Sparse Vectors and Matrices
cv_do Perform Cross Validation
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
droplevels-method 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
fitted.cv Perform Cross Validation
fitted.nscentroids Nearest Shrunken Centroids
fitted.opls Partial Least Squares
fitted.pls Partial Least Squares
fitted.sgmix Spatial Gaussian Mixture Model

-- G --

getRNGStream Parallel RNG Streams

-- H --

hex2raw Universally Unique Identifiers

-- I --

icor Warping to Align 1D Signals
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
logLik.nscentroids Nearest Shrunken Centroids
logLik.sgmix Spatial Gaussian Mixture Model
logLik.sgmixn Spatial Gaussian Mixture Model

-- 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
mi_learn Multiple Instance Learning

-- 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
nscentroids Nearest Shrunken Centroids

-- 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
peakheights Peak Summarization
peakwidths Peak Summarization
plot-method A Simple Grammar of Base Graphics
plot-method Plotting Graphical Marks
plot.vizi_bars Plotting Graphical Marks
plot.vizi_boxplot Plotting Graphical Marks
plot.vizi_image Plotting Graphical Marks
plot.vizi_intervals Plotting Graphical Marks
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_rules Plotting Graphical Marks
plot.vizi_text Plotting Graphical Marks
plot.vizi_voxels Plotting Graphical Marks
plot_image Plot a Signal or Image
plot_signal Plot a Signal or Image
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.nscentroids Nearest Shrunken Centroids
predict.opls Partial Least Squares
predict.pls Partial Least Squares
predscore Score predictive performance
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
rescale Signal Normalization
rescale_iqr Signal Normalization
rescale_range Signal Normalization
rescale_ref Signal Normalization
rescale_rms Signal Normalization
rescale_sum Signal Normalization
residuals.opls Partial Least Squares
ricker CWT-based Peak Detection
RNGStreams Parallel RNG Streams
rocscore Compute area under ROC curve
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
setRNGStream Parallel RNG Streams
set_channel A Simple Grammar of Base Graphics
set_coord A Simple Grammar of Base Graphics
set_engine A Simple Grammar of Base Graphics
set_par A Simple Grammar of Base Graphics
set_title A Simple Grammar of Base Graphics
sgmix Spatial Gaussian Mixture Model
sgmixn Spatial Gaussian Mixture Model
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_bars Plotting Graphical Marks
vizi_boxplot Plotting Graphical Marks
vizi_engine Set Graphical Parameters
vizi_image Plotting Graphical Marks
vizi_intervals Plotting Graphical Marks
vizi_lines Plotting Graphical Marks
vizi_par Set Graphical Parameters
vizi_peaks Plotting Graphical Marks
vizi_pixels Plotting Graphical Marks
vizi_points Plotting Graphical Marks
vizi_rules Plotting Graphical Marks
vizi_style Set Graphical Parameters
vizi_text Plotting Graphical Marks
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