Bracket

Description

tableList method, passes data.table bracket functionality to the table attribute. Usage is the same as in data.table[] and data.table[] <-. Assigning works only for tab part and only i and j from data.table is used.

Bracket

Usage

## S3 method for class 'tableList'
x[...]

## S3 replacement method for class 'tableList'
x[i, j] <- value

Arguments

Value

tableList or vector.

Examples

data(images8By8)

# Create tableList from images8By8[,1:3]
TL <- tableList(images8By8[,1:3])

# Apply data.table bracket on a tableList object
TL[direction=="both"]


TL[2,1] <- "aaa"

# setting row
TL[2,] <- list("aaa", 1000, 1000)

# setting column
TL[,2] <- 1

Bracket

Description

tableMatrix method, passes data.table bracket functionality to the table attribute. Assigning works only for tab part and only i and j from data.table is used. If j is numeric, it corresponds to first attribute after tmName names.

Bracket

Usage

## S3 method for class 'tableMatrix'
x[...]

## S3 replacement method for class 'tableMatrix'
x[i, j] <- value

Arguments

Value

tableMatrix or vector.

Examples

data(images8By8)

# Create tableMatrix from images8By8
TM <- tableMatrix(images8By8, 1:3, 4:ncol(images8By8))


TM[2,1] <- "aaa"

TM[1,"dimX"] <- 1000

# setting row
TM[2,] <- list("aaa", 1000, 1000)

# setting column
TM[,2] <- 1

Double bracket

Description

tableList method, passes double bracket functionality to the table attribute.

Usage

## S3 method for class 'tableList'
x[[...]]

Arguments

Value

vector

S3 tableMatrix generic to get or set aid attribute

Description

S3 tableMatrix generic to get or set aid attribute

Usage

aid(obj, ...)

aid(obj) <- value

Arguments

Value

User aid data.

Get or set aid attribute

Description

tableList method to get or set aid attribute.

Usage

## S3 method for class 'tableList'
aid(obj, ...)

## S3 replacement method for class 'tableList'
aid(obj) <- value

Arguments

Value

Aid part.

Column binding

Description

Column binding

Column binding of tab part of tableMatrix or tableList object.

Usage

## S3 method for class 'tableList'
cbind(x, y, ...)

## S3 method for class 'tableMatrix'
cbind(x, y, ...)

Arguments

Value

Matrix object.

Copy

Description

Copy of a tableList object.

Usage

## S3 method for class 'tableList'
copy(obj)

Arguments

Value

tableList object.

Copy

Description

Copy of a tableMatrix object.

Usage

## S3 method for class 'tableMatrix'
copy(obj)

Arguments

Value

tableMatrix object.

S3 tableMatrix generic to get or set dataType attribute

Description

S3 tableMatrix generic to get or set dataType attribute

Usage

dataType(obj, ...)

dataType(obj) <- value

Arguments

Value

List.

Get or set dataType attribute

Description

tableList and tableMarix method to get or set dataType attribute.

Usage

## S3 method for class 'tableList'
dataType(obj, ...)

## S3 replacement method for class 'tableList'
dataType(obj) <- value

## S3 method for class 'tableMatrix'
dataType(obj, ...)

## S3 replacement method for class 'tableMatrix'
dataType(obj) <- value

Arguments

Value

List of datatypes.

Dimensions

Description

tableList method, returns dimensions of the table attribute.

Usage

## S3 method for class 'tableList'
dim(x)

Arguments

Value

Dimensions of the table part.

Dimension names

Description

tableList method, returns dimension names of the table attribute.

Usage

## S3 method for class 'tableList'
dimnames(x)

Arguments

Value

Column and row names of the table part.

S3 tableMatrix generic to get or set row from matrix attribute

Description

S3 tableMatrix generic to get or set row from matrix attribute

Usage

getRow(...)

setRow(...)

Arguments

Value

numeric vector.

Get or set row from the matrix attribute

Description

tableMatrix method to get or set a row from the matrix attribute.

Usage

## S3 method for class 'tableMatrix'
getRow(obj, i = NULL, repo = NULL, ...)

## S3 method for class 'tableMatrix'
setRow(obj, value, i = NULL, repo = NULL, ...)

Arguments

Value

Row from the matrix part.

Examples

data(images8By8)
data(images10By10)

# Create tableMatrix from images8By8 and images10By10
TM <- tableMatrix(list(images8By8, images10By10), list(1:3, 1:3),
list(4:ncol(images8By8),4:ncol(images10By10)))

# Row 91 in tab(TM) corresponds to second matrix, first row 
row <- getRow(TM, 91)

# Row 91 in tab(TM) corresponds to second matrix, first row 
getRow(TM, repo=c(2,1))

# Change matrix row corresponding to row 91 in tab(TM) 
TM <- setRow(TM, rep(2,length(row)), 91)
getRow(TM, 91)

S3 tableMatrix generic to get row dim

Description

S3 tableMatrix generic to get row dim

Usage

getRowDim(...)

Arguments

Value

integer vector.

Get row dimensions

Description

tableMatrix method to get row dimensions from matDim attribute.

Usage

## S3 method for class 'tableMatrix'
getRowDim(obj, i = NULL, repo = NULL, ...)

Arguments

Value

Dimensions corresponding to the row.

Examples

data(images8By8)
data(images10By10)

# Create tableMatrix from images8By8 and images10By10
TM <- tableMatrix(list(images8By8, images10By10), 
list(r=c(1,3), r=c(1,3)),
list(r=c(4,ncol(images8By8)),r=c(4,ncol(images10By10))),list(c(8,8),c(10,10)),
dimNames =c("dimX", "dimY"))
matDim(TM)
tab(TM) 

# Dimensions corresponding to row 1 in tab(TM)
getRowDim(TM, 1)

# Dimensions corresponding to row 91 in tab(TM)
getRowDim(TM, 91)

# Dimensions corresponding to row 1 in second matrix in mat(TM)
getRowDim(TM, repo=c(2,1))

S3 tableMatrix generic to get row repo for matrix attribute

Description

S3 tableMatrix generic to get row repo for matrix attribute

Usage

getRowRepo(...)

Arguments

Value

numeric vector.

Get row repo

Description

tableMatrix method to get row repo (vector of matN and matRow) for the matrix attribute

Usage

## S3 method for class 'tableMatrix'
getRowRepo(obj, i = NULL, repo = NULL, ...)

Arguments

Value

Vector of matN and matRow.

Examples

data(images8By8)
data(images10By10)

# Create tableMatrix from images8By8 and images10By10
TM <- tableMatrix(list(images8By8, images10By10), list(1:3, 1:3),
list(c(4:ncol(images8By8)),c(4:ncol(images10By10))))
tab(TM)

# Row 2 in tab(TM) corresponds to first matrix, second row 
getRowRepo(TM, 2)

# Row 91 in tab(TM) corresponds to second matrix, first row 
getRowRepo(TM, 91)

Images of distributions

Description

Dataset containing samples of multivariate normal distributions. Each row in the dataset represents a generated matrix. Dimensions are stored in dimX and dimY columns. Directions "up" and "down" correspond to different covariance matrices. Direction "both" was created as a combination of "up" and "down".

Usage

images10By10

Format

Data frame with 90 rows and 103 variables:

• direction direction of diagonal, factor "up", "down", "both"

• dimX dimension x of image, in pixels

• dimY dimension y of image, in pixels

• pixel1:pixel100 pixel of image, in number

Images of distributions

Description

Dataset containing samples of multivariate normal distributions. Each row in the dataset represents a generated matrix. Dimensions are stored in dimX and dimY columns. Directions "up" and "down" correspond to different covariance matrices. Direction "both" was created as a combination of "up" and "down".

Usage

images8By8

Format

Data frame with 90 rows and 67 variables:

• direction direction of diagonal, factor "up", "down", "both"

• dimX dimension x of image, in pixels

• dimY dimension y of image, in pixels

• pixel1:pixel64 pixel of image, in number

tableList test

Description

Tests if passed object is of class tableList

Usage

is.tableList(obj)

Arguments

Value

logical vector.

tableMatrix test

Description

Tests if passed object is of class tableMatrix

Usage

is.tableMatrix(obj)

Arguments

Value

logical vector.

S3 tableMatrix generic to get or set matrix attribute

Description

S3 tableMatrix generic to get or set matrix attribute

Usage

mat(obj, ...)

mat(obj) <- value

Arguments

Value

List of matrices

Get or set matrix attribute

Description

tableMatrix method to get or set matrix part attribute. Matrix part is a list of matrices.

Usage

## S3 method for class 'tableMatrix'
mat(obj, matN = NULL, ...)

## S3 replacement method for class 'tableMatrix'
mat(obj) <- value

Arguments

Value

Full matrix part of tableMatrix or a matrix.

Examples

data(images8By8)

# Create tableMatrix from images8By8 and images10By10
TM <- tableMatrix(list(images8By8, images10By10), list(1:3, 1:3),
list(4:ncol(images8By8),4:ncol(images10By10)))

# Full matrix part of TM
mat(TM)

# Matrix part of TM corresponding to matrix type 2
mat(TM, 2)

S3 tableMatrix generic to get or set matDim attribute

Description

S3 tableMatrix generic to get or set matDim attribute

Usage

matDim(obj, ...)

matDim(obj) <- value

Arguments

Value

data.table

Get or set matDim attribute

Description

tableMatrix method to get or set matDim attribute.

Usage

## S3 method for class 'tableMatrix'
matDim(obj, matN = NULL, resetN = FALSE, ...)

## S3 replacement method for class 'tableMatrix'
matDim(obj) <- value

Arguments

Value

Full dimensions part of tableMatrix or a subset of dimensions part.

Examples

data(images8By8)
data(images10By10)

# Create tableMatrix from images8By8 and images10By10
TM <- tableMatrix(list(images8By8, images10By10), list(1:3, 1:3),
list(r=c(4,ncol(images8By8)),r=c(4,ncol(images10By10))))

# Dimensions part of TM
matDim(TM)

# Dimensions part of TM corresponding to matrix type 2
matDim(TM, 2)

Merging tableList

Description

Merging tableList

tableMatrix method, merges tableMatrix or tableList objects with data.table, data.frame, tableList or tableMatrix.

Usage

## S3 method for class 'tableList'
merge(x, y, key, ...)

## S3 method for class 'tableMatrix'
merge(x, y, key, ...)

Arguments

Value

tableMatrix object.

Examples

data(images8By8)

# Create tableMatrix from images8By8
TM <- tableMatrix(images8By8, c("direction","dimX","dimY"), 4:ncol(images8By8), c(8,8))

# Merge tableMatrix object with a data.frame
merge(TM, data.frame(direction="down", flag=TRUE), key="direction")

Print

Description

tableList method, prints table attribute.

Usage

## S3 method for class 'tableList'
print(x, ...)

Arguments

Print

Description

tableMatrix method, prints table attribute without tmName columns.

Usage

## S3 method for class 'tableMatrix'
print(x, ...)

Arguments

Combine by rows

Description

tableList method, binds rows of tableList objects.

Usage

## S3 method for class 'tableList'
rbind(..., use.names = TRUE, fill = FALSE)

Arguments

Value

tableList object.

Examples

data(images8By8)
data(images10By10)

# Create tableList objects from images8By8[,1:3] and images10By10[,1:3]
TL1 <- tableList(images8By8[,1:3])
TL2 <- tableList(images10By10[,1:3])

# Bindind rows of two tableList objects
rbind(TL1, TL2)

Combine by rows

Description

tableMatrix method, binds rows of tableMatrix objects. If matrix parts have the same dimensions, it combines rows in table and matrix parts using data.table and matrix rbind methods respectively. In case when dimensions differ it combines rows in table part and adds new matrix to the matrix part.

Usage

## S3 method for class 'tableMatrix'
rbind(..., use.names = TRUE, fill = FALSE)

Arguments

Value

tableMatrix object.

Examples

data(images8By8)
dim(images8By8)

data(images10By10)
dim(images10By10) 

# Create tableMatrix objects from images8By8 and images10By10
TM1 <- tableMatrix(images8By8, 1:3, 4:ncol(images8By8))
TM2 <- tableMatrix(images10By10, 1:3, 4:ncol(images10By10))

# Combining tableMatrix objects with same dimensions
TM <- rbind(TM1, TM1)
# Combined table part
tab(TM)
# One matrix in the matrix part
length(mat(TM))
# One dimension type
matDim(TM)

# Combining tableMatrix objects with different dimensions
TM <- rbind(TM1, TM2)
# Combined table part
tab(TM)
# Two matrices in the matrix part
length(mat(TM))
# Two dimension types
matDim(TM)

S3 tableMatrix generic to get or set table attribute

Description

S3 tableMatrix generic to get or set table attribute

Usage

tab(obj, ...)

tab(obj) <- value

Arguments

Value

data.table

Get or set table attribute

Description

tableList method to get or set table attribute.

Usage

## S3 method for class 'tableList'
tab(obj, ...)

## S3 replacement method for class 'tableList'
tab(obj) <- value

Arguments

Value

Table part.

Get or set table attribute

Description

tableMatrix method to get or set table attribute of tableMatrix object.

Usage

## S3 method for class 'tableMatrix'
tab(obj, matN = NULL, addRow = FALSE, resetN = TRUE,
  ...)

Arguments

Value

Full table part of tableMatrix or a subset of table part.

Examples

data(images8By8)
data(images10By10)

# Create tableMatrix from images8By8 and images10By10
TM <- tableMatrix(list(images8By8, images10By10), list(1:3, 1:3),
list(4:ncol(images8By8),4:ncol(images10By10)))
matDim(TM)

# Table part of TM
tab(TM)

# Table part of TM corresponding to matrix type 2
tab(TM, 2)

# Add row indexes
tab(TM, 2, TRUE)

tableList constructor

Description

tableList constructor, creates tableList object from a data.frame or a data.table and from aid data. The goal is to wrap data.table and any additional data structures together. tableList behaves like a data.table object. Groups of attributes can be stored together via dataType.

Usage

tableList(tabData, aidData = list(), dataType = NULL)

Arguments

Value

A tableList object

See Also

dim.tableList, dimnames.tableList rbind.tableList

Examples

data(chickwts)

# Bundle chickwts data.frame together with a linear model
TL <- tableList(chickwts, lm(weight~feed, chickwts))

# tableList behaves like a data.table  
mean(TL[feed=="casein", weight])

# Aid part of the tableList object carries the linear model
aid(TL)

# dataType support
TL <- tableList(chickwts, lm(weight~feed, chickwts), dataType=list(group1="weight", group2="feed"))

tableMatrix constructor

Description

tableMatrix constructor, creates tableMatrix object from a list of data.frames or data.tables. It is useful for datasets with the following structure: first set of columns of varying types is intended as meta data, second set of columns of the same type is intended as main data. tableMatrix combines strengths of data.table (access via bracket to the meta data part) and matrix (main data). It also stores dimensions of main data, thus allowing to combine rows of varying lengths into one object. As in tableList, tableMatrix can carry any additional aid data and data types groups.

Usage

tableMatrix(dataList, tabCol, matCol, dims = NULL, dimNames = NULL,
  aidData = list(), dataType = NULL)

Arguments

Details

tableMatrix is a S3 class that consists of 4 parts. tab - table part - is used for storing meta data, mat - matrix part - for storing main data and matDim - dimensions part - for dimensions of main data. mat is a list of matrices. tab is a data.table. In tab first column tm.matN is the matrix number in mat, second column tm.matRow is the row in the matrix. matDim is data.table. In matDim for each matrix number tm.matN dimensions can be specified with user defined dimensions. dataType is a list which contains names of groups of attributes and vectors of attributes belonging to it. Default print of tableMatrix is the print of the tab part without tm.matN and tm.matRow columns.

Value

A tableMatrix object

See Also

getRowRepo.tableMatrix, getRowDim.tableMatrix, merge.tableMatrix, rbind.tableMatrix

Examples

data(images8By8)
dim(images8By8)

data(images10By10)
dim(images10By10)
images10By10DT <- data.table::as.data.table(images10By10)

# Generate tableMatrix from data.frame images8By8: use columns 1:3 as meta data and 
# columns 4:ncol(images8By8) as main data 
TM <- tableMatrix(images8By8, 1:3, 4:ncol(images8By8))
matDim(TM) # show matDim
tab(TM) # show meta data part of tableMatrix
head(mat(TM)[[1]]) # show head of main data part

# Generate tableMatrix from data.frame images8By8: use columns "direction" and "dimY"
# as meta data and columns 4:ncol(images8By8) as main data 
tableMatrix(images8By8, c("direction","dimY"), 4:ncol(images8By8))

# User defined dimensions with default names
TM <- tableMatrix(images8By8, c("direction","dimX","dimY"), 4:ncol(images8By8), c(8,8))
matDim(TM)

# User defined dimensions with custom names
dims <- c(8,8)
names(dims) <- c("dimX", "dimY")

TM <- tableMatrix(images8By8, 1:3, 4:ncol(images8By8), dims)
matDim(TM)

# tabCol and matCol list input with "j" option
# Column indices: first 3 columns in tab, rest in mat
tableMatrix(images8By8, list(j=1:3), list(j=4:ncol(images8By8)))
# Column names: columns "direction" and "dimY" in tab, 
# columns "pixel1" and "pixel2" in mat
tableMatrix(images8By8, list(j=c("direction","dimY")), list(j=c("pixel1","pixel2")))

# tabCol and matCol list input with "r" option
# Column indices: first 3 columns in tab, rest in mat
tableMatrix(images8By8, list(r=c(1,3)), list(r=c(4,ncol(images8By8))))
# Same with column names
tableMatrix(images8By8, list(r=c("direction","dimY")), list(r=c("pixel1","pixel100")))

# data.table as the start dataset
tableMatrix(images10By10DT, 1:3, 4:ncol(images10By10DT))

# data.frame and data.table with different main data parts -> two matrices in mat.
# Elements in tabCol and matCol lists correspond to images8By8 and images10By10DT
# respectively
TM <- tableMatrix(list(images8By8, images10By10DT),
list(r=c("direction","dimY"), j=c("direction","dimX","dimY")),
list(4:ncol(images8By8),4:ncol(images10By10DT)))
matDim(TM)
length(mat(TM)) # 2 matrices in mat

# User defined named dimensions
TM <- tableMatrix(list(images8By8, images10By10),
list(r=c("direction","dimY"), j=c("direction","dimX","dimY")),
list(c(4:ncol(images8By8)),c(4:ncol(images10By10))),list(c(8,8),c(10,10)),
dimNames =c("dimX", "dimY"))
matDim(TM)

# Same main data parts -> only one matrix in mat
TM <- tableMatrix(list(images8By8, images8By8), 
list(r=c("direction","dimY"), j=c("direction","dimX","dimY")),
list(j=4:ncol(images8By8),4:ncol(images8By8)))
matDim(TM)
length(mat(TM)) # 1 matrix in mat

# dataType support
TM <- tableMatrix(images10By10, 1:3, 4:ncol(images10By10), 
dataType=list("group1"="direction", "group2"=c("dimX","dimY")))
dataType(TM)