Package {dbMatrix}

Title:	Database-Backed Matrix Classes and Operations
Version:	0.1.0
Description:	Provides S4 classes and methods for storing dense and sparse matrices in 'DuckDB' databases. The package supports constructing database-backed matrices from base R and 'Matrix' objects, extracting slices and summaries, performing arithmetic and selected linear algebra operations, and materializing results for larger-than-memory workflows. It integrates with 'dbProject' to keep database paths, live connections, and lazy matrix tables synchronized across interactive analyses.
License:	GPL-3
Encoding:	UTF-8
URL:	https://github.com/dbverse-org/dbmatrix-r, https://dbverse-org.github.io/dbmatrix-r/
BugReports:	https://github.com/dbverse-org/dbmatrix-r/issues
RoxygenNote:	7.3.3
Depends:	R (≥ 4.1.0)
Imports:	Matrix (≥ 1.6-5), MatrixGenerics (≥ 1.12.3), methods, DBI, dplyr, dbplyr, duckdb (≥ 1.4.0), data.table (≥ 1.12.2), glue, bit64, cli, Rcpp, arrow, nanoarrow, dbProject, rlang
LinkingTo:	Rcpp, RcppEigen, RSpectra, nanoarrow
Suggests:	knitr, rmarkdown, testthat (≥ 3.0.0), irlba, crayon, R.utils, checkmate, reticulate, sparseMatrixStats, RSpectra
VignetteBuilder:	knitr
Config/testthat/edition:	3
NeedsCompilation:	yes
Packaged:	2026-05-14 02:35:49 UTC; ecruiz
Author:	Edward C. Ruiz [aut, cre], Jiaji George Chen [aut], Ruben Dries [aut]
Maintainer:	Edward C. Ruiz <ecr7407@gmail.com>
Repository:	CRAN
Date/Publication:	2026-05-19 08:30:02 UTC

Value Matching

Description

Implements the %in% operator for dbMatrix objects. This operator checks if elements from the left operand are contained in the right operand, returning a logical vector.

Usage

## S4 method for signature 'dbDenseMatrix,ANY'
x %in% table

## S4 method for signature 'ANY,dbDenseMatrix'
x %in% table

## S4 method for signature 'dbSparseMatrix,ANY'
x %in% table

Arguments

Details

This is a method for the standard %in% operator for dbMatrix objects. It follows R's standard behavior for the %in% operator:

• When x is a dbDenseMatrix, it returns a logical vector with the same length as the total number of elements in the matrix.

• When table is a dbDenseMatrix, it allows checking if elements in x are in the matrix.

• For dbSparseMatrix objects, it throws an error to match the behavior of dgCMatrix.

Value

A logical vector of the same length as x, indicating which elements of x are in table.

Examples

con <- DBI::dbConnect(duckdb::duckdb(), ":memory:")
mat <- matrix(1:9, nrow = 3, ncol = 3)
dbmat <- dbMatrix(
  value = mat,
  con = con,
  name = "example_matrix",
  class = "dbDenseMatrix",
  overwrite = TRUE
)

dbmat %in% c(1, 3, 5, 7, 9)

c(1, 3, 5, 7, 9) %in% dbmat
DBI::dbDisconnect(con, shutdown = TRUE)

Input validation for data arg

Description

Input validation for data arg

Usage

.check_value(value)

Arguments

Value

No return value. Called for input validation and throws an error if value is invalid.

Evaluate if a dbSparseMatrix should be densified

Description

Evaluate if a dbSparseMatrix should be densified

Usage

.eval_op_densify(generic_char, vec_matrix)

Arguments

Details

Evaluates if a dbSparseMatrix should be densified for ⁠[Arith]⁠ operations and specific scalar values for operations in the order of dbSparseMatrix, vector

Value

TRUE if the operation should densify the sparse matrix before evaluation, otherwise FALSE.

Join a dbSparseMatrix with a dbMatrix object

Description

Join a dbSparseMatrix with a dbMatrix object

Usage

.join_dbm_vect(dbm, vec_matrix, op, swap_arith_order = FALSE)

Arguments

Value

A dbMatrix object containing the result of applying op between dbm and vec_matrix.

Convert a dbSparseMatrix to dbDenseMatrix

Description

Internal function to convert a dbSparseMatrix to dbDenseMatrix.

Usage

.to_db_dense(x, chunk_size = NULL)

Arguments

Value

A dbDenseMatrix object

Arith dbMatrix, e2

Description

See methods::Arith for more details.

See methods::Arith for more details.

See methods::Arith for more details.

See methods::Ops for more details.

See methods::Ops for more details.

See methods::Ops for more details.

Usage

## S4 method for signature 'dbMatrix,ANY'
Arith(e1, e2)

## S4 method for signature 'ANY,dbMatrix'
Arith(e1, e2)

## S4 method for signature 'dbMatrix,dbMatrix'
Arith(e1, e2)

## S4 method for signature 'dbMatrix,ANY'
Ops(e1, e2)

## S4 method for signature 'ANY,dbMatrix'
Ops(e1, e2)

## S4 method for signature 'dbMatrix,dbMatrix'
Ops(e1, e2)

## S4 method for signature 'DBIConnection'
dbLoad(conn, name, class)

## S4 method for signature 'dbMatrix'
writeMM(obj, file, ...)

Arguments

Value

• Arithmetic and logical group methods return a dbMatrix object of the appropriate dense or sparse subclass, with the same dimensions as the input and transformed values stored in DuckDB.

• dbLoad() returns a dbDenseMatrix or dbSparseMatrix pointing to an existing DuckDB table.

• writeMM() writes a Matrix Market file to file and returns invisible(TRUE) on success.

Math Operations for dbMatrix Objects

Description

Implements the Math S4groupGeneric functions for dbMatrix objects. This includes various mathematical operations such as logarithms, exponentials, trigonometric functions, and other transformations.

Usage

## S4 method for signature 'dbMatrix'
Math(x)

Arguments

Details

This method provides implementations for the following Math functions:

Arithmetic and rounding:

• abs(), sign(), sqrt(), ceiling(), floor(), trunc()

Cumulative operations:

• cummax(), cummin(), cumprod(), cumsum()

• Note: cumprod() is not supported

Logarithmic:

• log(), log10(), log2(), log1p()

DuckDB Log Function Mappings:

Sparsity-Preserving Log: For dbSparseMatrix with pending operations, log(x + 1) operations preserve sparsity since log(0 + 1) = 0. The multiplicative component is applied first, then the log transformation is applied to sparse values only.

Trigonometric:

• cos(), sin(), tan(), acos(), asin(), atan()

• cosh(), sinh(), tanh(), acosh(), asinh(), atanh()

• cospi(), sinpi(), tanpi()

• Note: acosh() asinh() atanh() are not supported

Exponential:

• exp(), expm1()

• Note: expm1() is not supported

Special functions:

• gamma(), lgamma(), digamma(), trigamma()

• Note: digamma() trigamma() are not supported

The function applies the specified mathematical operation to each element of the dbMatrix object.

Value

A dbMatrix object with the mathematical operation applied to each element.

Examples

mat <- matrix(1, nrow = 3, ncol = 3)
dbmat <- as.dbMatrix(mat)
log(dbmat)
sqrt(dbmat)
sin(dbmat)

Summary Methods for dbMatrix Objects

Description

Implements the S4groupGeneric group generic functions for dbMatrix objects.

Usage

## S4 method for signature 'dbMatrix'
Summary(x, ..., na.rm = TRUE)

Arguments

Details

This method provides implementations for the following S4groupGeneric functions:

• max(): Maximum value

• min(): Minimum value

• range(): Not supported

• prod(): Product of all values

• sum(): Sum of all values

• any(): Returns TRUE if any value is TRUE

• all(): Returns TRUE if all values are TRUE

Value

The result of applying the respective summary function to the dbMatrix object. The type of the return value depends on the specific function called.

Examples

mat <- matrix(1, nrow = 3, ncol = 3)
dbmat <- as.dbMatrix(mat)
max(dbmat)
min(dbmat)
prod(dbmat)
sum(dbmat)
any(dbmat > 0)
all(dbmat > 0)

Extract or replace values in database-backed matrices

Description

Methods for subsetting and replacing values in dbMatrix objects.

Usage

## S4 method for signature 'dbMatrix,dbIndex,missing,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'dbMatrix,missing,dbIndex,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'dbMatrix,dbIndex,dbIndex,ANY'
x[i, j, ..., drop = FALSE]

## S4 method for signature 'dbMatrix,dbMatrix,missing,ANY'
x[i, j, ..., drop = TRUE]

## S4 replacement method for signature 'dbMatrix,dbMatrix,missing,ANY'
x[i, j] <- value

## S4 method for signature 'dbMatrix,dbDenseMatrix,missing,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'dbMatrix,missing,dbDenseMatrix,ANY'
x[i, j, ..., drop = FALSE]

## S4 method for signature 'dbMatrix,dbDenseMatrix,dbDenseMatrix,ANY'
x[i, j, ..., drop = FALSE]

Arguments

Value

A subsetted or modified dbMatrix, or an extracted vector for matrix-style indexing.

Convert Matrix::Matrix to dbMatrix

Description

Converts in-memory matrix, Matrix::dgeMatrix, or Matrix::dgCMatrix into a dbMatrix object.

Generic function to convert in-memory objects to dbMatrix objects.

Usage

as.dbMatrix(x, con = NULL, name = "dbMatrix", overwrite = FALSE, ...)

as.dbMatrix(x, con = NULL, name = "dbMatrix", overwrite = FALSE, ...)

Arguments

Details

If no con is provided, a temporary in-memory database connection is created. If no name is provided, a unique table name is generated.

Value

A dbDenseMatrix for dense matrix inputs or a dbSparseMatrix for sparse matrix inputs. The returned object keeps the input dimensions and dimnames while storing matrix values in DuckDB.

Convert dbMatrix to in-memory matrix

Description

Converts a dbMatrix object into an in-memory matrix or sparse matrix.

Usage

## S3 method for class 'dbMatrix'
as.matrix(x, ..., sparse = FALSE, names = TRUE)

Arguments

Details

This method converts a dbMatrix object into an in-memory Matrix::dgCMatrix (sparse = TRUE) or matrix() (default, sparse = FALSE).

Warning: This function can cause memory issues for large dbMatrix objects.

Set sparse = TRUE to convert to a sparse matrix. Set names = TRUE to keep dimnames.

Value

A Matrix::dgCMatrix or matrix

Coerce dbMatrix to dgCMatrix

Description

Coercion methods to convert dbMatrix objects to in-memory dgCMatrix objects. Respects dbMatrix.max_mem_convert option to prevent OOM errors.

Value

A Matrix::dgCMatrix object containing the collected matrix values. Dense inputs are converted to sparse Matrix format after collection.

Coerce dbMatrix to matrix

Description

Coercion methods to convert dbMatrix objects to in-memory matrix objects. Respects dbMatrix.max_mem_convert option to prevent OOM errors.

Value

A base R matrix containing the collected matrix values with the same dimensions and dimnames as the source object.

Coerce matrix to dbMatrix

Description

Coercion methods to convert in-memory matrix objects to dbMatrix objects. Creates a new in-memory DuckDB connection.

Value

A database-backed matrix object. Dense inputs return a dbDenseMatrix, while sparse Matrix::dgCMatrix inputs return a dbSparseMatrix.

Row (column) standard deviations for dbMatrix objects

Description

Calculates the standard deviation for each row (column) of a matrix-like object.

Usage

## S4 method for signature 'dbDenseMatrix'
colSds(
  x,
  rows = NULL,
  cols = NULL,
  na.rm = FALSE,
  center = NULL,
  ...,
  useNames = TRUE
)

## S4 method for signature 'dbSparseMatrix'
colSds(
  x,
  rows = NULL,
  cols = NULL,
  na.rm = FALSE,
  center = NULL,
  ...,
  useNames = TRUE
)

## S4 method for signature 'dbDenseMatrix'
rowSds(
  x,
  rows = NULL,
  cols = NULL,
  na.rm = TRUE,
  center = NULL,
  ...,
  useNames = TRUE
)

## S4 method for signature 'dbSparseMatrix'
rowSds(
  x,
  rows = NULL,
  cols = NULL,
  na.rm = TRUE,
  center = NULL,
  ...,
  useNames = TRUE
)

Arguments

Value

A named numeric vector containing one sample standard deviation per row or column of x.

Force computation of a dbMatrix

Description

Explicitly compute a dbMatrix and save it to a table in the database. This overrides the default dplyr::compute to use a direct ⁠CREATE TABLE AS⁠ statement, which is more robust for large tables in DuckDB.

Usage

## S3 method for class 'dbMatrix'
compute(
  x,
  name = NULL,
  temporary = TRUE,
  dimnames = TRUE,
  overwrite = FALSE,
  ...
)

Arguments

Value

A dbMatrix object pointing to the new table.

S4 Class for dbDenseMatrix

Description

Representation of dense matrices using an on-disk database. Inherits from dbMatrix.

Value

Objects of class dbDenseMatrix store all matrix entries explicitly in DuckDB. They are typically returned by dbMatrix() or as.dbMatrix() for dense inputs.

S4 virtual class for dbMatrix

Description

Representation of sparse and dense matrices in a database. Each object is used as a connection to a single table that exists within the database. Inherits from dbData.

Create an S4 dbMatrix object in sparse or dense triplet vector format.

Usage

dbMatrix(
  value,
  class = NULL,
  con = NULL,
  overwrite = FALSE,
  name = "dbMatrix",
  dims = NULL,
  dim_names = NULL,
  mtx_rowname_file_path,
  mtx_rowname_col_idx = 1,
  mtx_colname_file_path,
  mtx_colname_col_idx = 1,
  ...
)

dbMatrix(
  value,
  class = NULL,
  con = NULL,
  overwrite = FALSE,
  name = "dbMatrix",
  dims = NULL,
  dim_names = NULL,
  mtx_rowname_file_path,
  mtx_rowname_col_idx = 1,
  mtx_colname_file_path,
  mtx_colname_col_idx = 1,
  ...
)

Arguments

Details

This function reads in data into a pre-existing DuckDB database. Supported value data types:

• Matrix::dgCMatrix In-memory sparse matrix from the Matrix::Matrix package

• Matrix::dgTMatrix In-memory triplet vector or COO matrix

• matrix In-memory dense matrix from base R

• .mtx Path to .mtx file

• .csv Path to .csv file

• tbl_duckdb_connection Table in duckdb::duckdb database in ijx format from existing dbMatrix object. dims and dim_names must be specified if value is tbl_duckdb_connection.

Value

dbMatrix() returns an initialized dbDenseMatrix or dbSparseMatrix S4 object that points to matrix data stored in DuckDB.

A dbDenseMatrix or dbSparseMatrix object, depending on class, pointing to matrix data stored in DuckDB. The object records the matrix dimensions and dimension names.

Slots

dim_names

row (1) and col (2) names

dims

dimensions of the matrix

init

logical. Whether the object is fully initialized

Examples

dgc <- readRDS(system.file("extdata", "dgc.rds", package = "dbMatrix"))
con <- DBI::dbConnect(duckdb::duckdb(), ":memory:")
dbSparse <- dbMatrix(
  value = dgc,
  con = con,
  name = "sparse_matrix",
  class = "dbSparseMatrix",
  overwrite = TRUE
)
dbSparse

dbMatrix_from_tbl

Description

Constructs a dbSparseMatrix object from a tbl_duckdb_connection object.

Usage

dbMatrix_from_tbl(
  tbl,
  rownames_colName,
  colnames_colName,
  value_colName = NULL,
  name = "dbMatrix",
  overwrite = FALSE,
  row_names = NULL,
  col_names = NULL,
  i_col = NULL,
  j_col = NULL
)

Arguments

Details

The tbl_duckdb_connection object must contain dimension names as columns in long format.

If value_colName is provided, the function uses pre-aggregated counts from that column. This is useful when the input table already contains aggregated counts (e.g., from a GROUP BY + SUM operation). If value_colName is NULL (default), the function counts occurrences of each row-column pair.

When row_names and/or col_names are provided, the function uses these directly instead of querying distinct values from the table. This can significantly improve performance when the input table is a complex lazy query (e.g., result of spatial joins).

When i_col and j_col are provided, the function uses these pre-computed integer indices directly, skipping expensive string-to-index encoding. This is the fastest path.

Value

dbMatrix object

dbMatrix Package Global Options

Description

The following global options can be modified to control the behavior of the dbMatrix package.

Details

Use options() to set the below options.

Value

No return value. This documentation page describes package options.

Options

• dbMatrix.digits: integer. Number of digits to round to in the show function of dbMatrix objects. Default is 7.

• dbMatrix.max_mem_convert: numeric. Maximum size (in bytes) allowed for implicit conversion of dbMatrix to in-memory matrix. Default is 8 * 1024^3 (8GB).

• dbMatrix.chunk_size: integer. Number of columns to process per chunk during densification (.to_db_dense). Smaller chunks reduce memory usage but may increase execution time. Default is NULL (automatically calculated based on dbMatrix.max_mem_convert).

• dbMatrix.max_chunks: integer. Maximum number of chunks allowed during densification. This prevents query parser errors caused by excessive ⁠UNION ALL⁠ branches. Default is 10000.

• dbMatrix.verbose: logical. If TRUE (default), prints informative messages during implicit coercion.

• dbMatrix.precomp_db: character. Path to an external DuckDB file containing precomputed table(s). If set, dbMatrix will automatically attach this database (read-only) and look for a suitable precomputed table to speed up densification.

• dbMatrix.allow_densify: logical. If FALSE (default), automatic sparse-to-dense conversion is disabled. This prevents unexpected disk spilling and memory issues when operations would require densification (e.g., division by zero, scalar addition to sparse matrix). Set to TRUE to enable on-disk dense conversion. Warning: Dense conversion can cause massive disk usage for large matrices.

S4 Class for dbSparseMatrix

Description

Representation of sparse matrices using an on-disk database. Inherits from dbMatrix.

Value

Objects of class dbSparseMatrix store only non-zero matrix entries in DuckDB. They are typically returned by dbMatrix() or as.dbMatrix() for sparse inputs.

Perform Streaming SVD on a dbMatrix

Description

Perform Streaming SVD on a dbMatrix

Usage

db_svd(
  dbm,
  k = 10,
  center = TRUE,
  scale = FALSE,
  center_rows = NULL,
  memory_limit = getOption("dbMatrix.svd_memory", 8 * 1024^3),
  return_format = c("svd", "pca")
)

Arguments

Value

List with SVD or PCA components

Dimensions of an Object

Description

Retrieve the dimension of an object.

Usage

## S4 method for signature 'dbMatrix'
dim(x)

Arguments

Value

An integer vector of length 2 giving the number of rows and columns in x.

get_MM_dim

Description

Internal function to read dimensions of a .mtx file

Usage

get_MM_dim(mtx_file_path)

Arguments

Details

Scans for the header of an mtx file (starting with %) and takes one more line representing the dimensions and number of nonzero values.

Note: the header size can vary depending on the .mtx file.

Value

integer vector of dimensions

get_MM_dimnames

Description

Internal function to read row and column names of a .mtx file

Usage

get_MM_dimnames(
  mtx_file_path,
  mtx_rowname_file_path,
  mtx_rowname_col_idx = 1,
  mtx_colname_file_path,
  mtx_colname_col_idx = 1,
  ...
)

Arguments

Details

Can be used to read row and column names from .mtx files. Note: these files must not contain a header (colnames).

The mtx_rowname_col_idx and mtx_colname_col_idx can be used to specify the column index of the row and column name files, respectively. By default, the first column is used for both.

TODO: Support for reading in only rownames or colnames.

Value

list of row and column name character vectors

get_con

Description

get_con

Usage

get_con(dbMatrix)

Arguments

Value

A live DBI connection associated with the database-backed object.

get_dbdir

Description

get_dbdir

Usage

get_dbdir(dbMatrix)

Arguments

Value

A character scalar giving the DuckDB database directory used by the object.

get_tblName

Description

get_tblName

Usage

get_tblName(dbMatrix)

Arguments

Value

A character scalar giving the DuckDB table name associated with the object.

Return the First or Last Parts of an Object

Description

Returns the first or last parts of a vector, matrix, array, table, data frame or function. Since head() and tail() are generic functions, they have been extended to other classes, including "ts" from stats.

Usage

## S4 method for signature 'dbMatrix'
head(x, n = 6L, ...)

## S4 method for signature 'dbMatrix'
tail(x, n = 6L, ...)

Arguments

Value

A dbMatrix object containing the first or last n rows of x, with updated dimensions and row names.

Element-wise is.na for dbMatrix

Description

Returns a dbMatrix with numeric values indicating NA positions (1 = NA, 0 = not NA).

Usage

## S4 method for signature 'dbMatrix'
is.na(x)

Arguments

Value

A dbMatrix with same dimensions, containing 1 where the original value was NA and 0 otherwise.

Examples

mat <- matrix(c(1, NA, 3, NA), nrow = 2)
dbmat <- as.dbMatrix(mat)
is.na(dbmat)

Length of a dbMatrix Object

Description

Get or set the length of vectors (including lists) and factors, and of any other R object for which a method has been defined.

Usage

## S4 method for signature 'dbMatrix'
length(x)

Arguments

Value

A length-one integer giving the number of stored elements in x.

Map dimnames to i,j indices

Description

Map dimnames to i,j indices

Usage

map_ijx_dimnames(dbMatrix, colName_i, colName_j)

Arguments

Details

Constructs a table in a database that contains the accompanying dimnames for a dbMatrix. The resulting columns in the table:

• i (row index)

• colName_i (rownames),

• j (col index)

• j_names (colnames)

• x (counts of i,j occcurences)

Value

A lazy tbl_dbi with i, j, x, and the mapped row/column name columns.

Arithmetic Mean for dbMatrix objects

Description

Generic function for the (trimmed) arithmetic mean.

Usage

## S4 method for signature 'dbDenseMatrix'
mean(x, ...)

## S4 method for signature 'dbSparseMatrix'
mean(x, ...)

Arguments

Value

A length-one numeric vector giving the arithmetic mean of all entries in x.

The names of a dbMatrix Object

Description

The names of a dbMatrix Object

Usage

## S4 method for signature 'dbDenseMatrix'
names(x)

Arguments

Value

A character vector of the names of the 1D dbMatrix object (1D matrices only)

The Number of Rows/Columns of a dbMatrix Object

Description

nrow and ncol return the number of rows or columns present in x.

Usage

nrow.dbMatrix(x)

ncol.dbMatrix(x)

Arguments

Value

A length-one integer giving the number of rows or columns in x.

Compute a dense COO table in a database connection

Description

Precomputes a COO list table in a specificied database connection in column- major order. This can speed up operations that involve breaking sparsity of a dbSparseMatrix, such as in cases when performing + or - arithmetic operations.

Usage

precompute(conn, m, n, verbose = FALSE)

Arguments

Details

The m and n parameters must exceed the maximum row and column indices of the dbMatrix in order to be used for densifying any dbMatrix. If these params are less than the maximum row and column indices, a new precomputed table will be automatically generated with the name 'precomp_mXn'.

In such cases, run this function again with a larger n_rows and num_cols, or to manually remove the precomputed table set options(dbMatrix.precomp = NULL) in the R console.

Value

A tbl_dbi object referencing the newly created precomputed lookup table in DuckDB.

Generate array for pretty printing of matrix values

Description

Generate array for pretty printing of matrix values

Usage

print_array(
  i = NULL,
  j = NULL,
  x = NULL,
  dims,
  rownames = rep("", dims[1]),
  class = c("sparse", "dense"),
  fill = ".",
  digits = 5L
)

Arguments

Value

No return value. Called for its side effect of printing a formatted matrix preview to the console.

Row (column) means for dbMatrix objects

Description

Calculates the mean for each row (column) of a matrix-like object.

Usage

## S4 method for signature 'dbMatrix'
rowMeans(x, na.rm = FALSE, dims = 1, ...)

## S4 method for signature 'dbMatrix'
colMeans(x, na.rm = FALSE, dims = 1, ...)

Arguments

Value

A named numeric vector containing one mean per row or column of x.

Row (column) sums for dbMatrix objects

Description

Calculates the sum for each row (column) of a matrix-like object.

Usage

## S4 method for signature 'dbDenseMatrix'
rowSums(x, na.rm = FALSE, dims = 1, ..., memory = FALSE)

## S4 method for signature 'dbSparseMatrix'
rowSums(x, na.rm = FALSE, dims = 1, ...)

## S4 method for signature 'dbDenseMatrix'
colSums(x, na.rm = FALSE, dims = 1, ...)

## S4 method for signature 'dbSparseMatrix'
colSums(x, na.rm = FALSE, dims = 1, ...)

Arguments

Value

A named numeric vector containing one sum per row or column of x.

Row (column) variances for dbMatrix objects

Description

Calculates the variance for each row (column) of a matrix-like object.

Usage

## S4 method for signature 'dbDenseMatrix'
rowVars(
  x,
  rows = NULL,
  cols = NULL,
  na.rm = TRUE,
  center = NULL,
  ...,
  useNames = TRUE
)

## S4 method for signature 'dbSparseMatrix'
rowVars(
  x,
  rows = NULL,
  cols = NULL,
  na.rm = TRUE,
  center = NULL,
  ...,
  useNames = TRUE
)

## S4 method for signature 'dbDenseMatrix'
colVars(
  x,
  rows = NULL,
  cols = NULL,
  na.rm = TRUE,
  center = NULL,
  ...,
  useNames = TRUE
)

## S4 method for signature 'dbSparseMatrix'
colVars(
  x,
  rows = NULL,
  cols = NULL,
  na.rm = TRUE,
  center = NULL,
  ...,
  useNames = TRUE
)

Arguments

Value

A named numeric vector containing one sample variance per row or column of x.

Retrieve and Set Row (Column) Dimension Names of dbMatrix Objects

Description

Retrieve and Set Row (Column) Dimension Names of dbMatrix Objects

Usage

rownames.dbMatrix(x, do.NULL = TRUE, prefix = "row")

## S3 replacement method for class 'dbMatrix'
rownames(x) <- value

colnames.dbMatrix(x, do.NULL = TRUE, prefix = "col")

## S3 replacement method for class 'dbMatrix'
colnames(x) <- value

## S4 method for signature 'dbMatrix'
dimnames(x)

## S4 replacement method for signature 'dbMatrix,list'
dimnames(x) <- value

Arguments

Value

rownames() and colnames() return character vectors of dimension names. dimnames() returns a length-2 list containing row and column name vectors. The replacement forms return the modified dbMatrix object.

sim_dgc

Description

Simulate a dbSparseMatrix in memory

Simulate a dbDenseMatrix in memory.

Usage

sim_duckdb(value = datasets::iris, name = "test", con = NULL, memory = TRUE)

sim_dgc(num_rows = 50, num_cols = 50, n_vals = 50)

sim_denseMat(num_rows = 50, num_cols = 50)

sim_ijx_matrix(mat_type = NULL, num_rows = 50, num_cols = 50, seed_num = 42)

sim_dbSparseMatrix(
  num_rows = 50,
  num_cols = 50,
  seed_num = 42,
  name = "sparse_test",
  memory = FALSE
)

sim_dbDenseMatrix(
  num_rows = 50,
  num_cols = 50,
  seed_num = 42,
  name = "dense_test",
  memory = FALSE
)

Arguments

Details

This function generates a simulated sparse matrix (dgCMatrix) with number of rows and columns and sets n_vals random values to a non-zero value.

This function generates a simulated dense matrix object with a specified number of rows and columns.

This function generates an ijx representation of a simulated dgCMatrix object with a specified number of rows and columns and sets 50 random values to a non-zero value.

Value

A dgCMatrix object

Functions

• sim_duckdb(): Simulate a duckdb connection dplyr tbl_Pool in memory

• sim_dgc(): Simulate a dgcMatrix

• sim_denseMat(): Simulate a dense matrix

• sim_ijx_matrix(): Simulate a duckdb connection dplyr tbl_Pool in memory

• sim_dbSparseMatrix(): Simulate a dbSparseMatrix in memory

• sim_dbDenseMatrix(): Simulate a dbDenseMatrix in memory

Matrix Transpose

Description

Given a dbMatrix x, t returns the transpose of x.

Usage

## S4 method for signature 'dbMatrix'
t(x)

Arguments

Value

dbMatrix object

to_ijx_disk

Description

to_ijx_disk

Usage

to_ijx_disk(con, name)

Arguments

Value

remote table in long format unpivoted from wide format matrix

Convert dbMatrix to named ijx table

Description

Converts a dbMatrix to a lazy long table where row and column indices are replaced by dimension names.

Usage

to_named_ijx_tbl(
  x,
  row_col = "row_name",
  col_col = "col_name",
  compute = FALSE
)

Arguments

Value

A lazy tbl with columns: row_col, col_col, x