Scientific computing for out-of-memory signals and images

Documentation for package ‘matter’ version 2.6.1

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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