SFBM-class {bigsparser}

Class SFBM

Description

A reference class for storing and accessing sparse matrix-like data stored in files on disk.

Convert a 'dgCMatrix' or 'dsCMatrix' to an SFBM.

Usage

as_SFBM(spmat, backingfile = tempfile(), compact = FALSE)

Arguments

spmat

A 'dgCMatrix' (non-symmetric sparse matrix of type 'double') or 'dsCMatrix' (symmetric sparse matrix of type 'double').

backingfile

Path to file where to store data. Extension .sbk is automatically added.

compact

Whether to use a compact format? Default is FALSE. This is useful when non-zero values in columns are contiguous (or almost).

Details

An object of class SFBM has many fields:

• ⁠$address⁠: address of the external pointer containing the underlying C++ object to be used as a ⁠XPtr<SFBM>⁠ in C++ code

• ⁠$extptr⁠: (internal) use ⁠$address⁠ instead

• ⁠$nrow⁠: number of rows

• ⁠$ncol⁠: number of columns

• ⁠$nval⁠: number of non-zero values

• ⁠$p⁠: vector of column positions

• ⁠$backingfile⁠ or ⁠$sbk⁠: File with extension 'sbk' that stores the data of the SFBM

• ⁠$rds⁠: 'rds' file (that may not exist) corresponding to the 'sbk' file

• ⁠$is_saved⁠: whether this object is stored in ⁠$rds⁠?

And some methods:

• ⁠$save()⁠: Save the SFBM object in ⁠$rds⁠. Returns the SFBM.

• ⁠$add_columns()⁠: Add new columns from a 'dgCMatrix' or a 'dsCMatrix'.

• ⁠$dense_acc()⁠: Equivalent to as.matrix(.[ind_row, ind_col]). Use with caution; ind_row and ind_col must be positive indices within range.

Value

The new SFBM.

Examples

spmat2 <- Matrix::Diagonal(4, 0:3)
spmat2[4, 2] <- 5
spmat2[1, 4] <- 6
spmat2[3, 4] <- 7
spmat2

# Stores all (i, x) for x != 0
(X2 <- as_SFBM(spmat2))
matrix(readBin(X2$sbk, what = double(), n = 100), 2)

# Stores only x, but all (even the zero ones) from first to last being not 0
(X3 <- as_SFBM(spmat2, compact = TRUE))
X3$first_i
readBin(X3$sbk, what = double(), n = 100)