tiledb - Interface to the TileDB Storage Manager API

Description

The efficient multi-dimensional array management system 'TileDB' introduces a novel on-disk format that can effectively store reads. It features excellent compression, an efficient parallel I/O system which also scales well, and bindings to multiple languages.

Author(s)

Maintainer: Isaiah Norton isaiah@tiledb.com

Authors:

• TileDB, Inc. [copyright holder]

See Also

Useful links:

• https://github.com/TileDB-Inc/TileDB-R

• https://tiledb-inc.github.io/TileDB-R/

• Report bugs at https://github.com/TileDB-Inc/TileDB-R/issues

libtiledb Information

Description

Get version and install information of the core libtiledb install

Usage

.core_info()

.core_hash()

Value

.core_info(): A named character vector with the following entries:

• “version”: libtiledb version

• “libtype”: type of libtiledb install; will be one of “vendored”, “system”, or “unknown”

.core_hash(): The MD5 hash of the core info

Checking the libtiledb information in downstream packages

These functions are designed to make it easy to test if the core libtiledb install has changed. This is accomplished by adding a build-time constant to cache the version of libtiledb was built with. For example, in zzz.R, put the following line to cache the libtiledb information during package build

.built_with <- list(libtiledb = tiledb::.core_hash())

Then, in the load hook, add the following check

.onLoad <- function(libname, pkgname) {
  if (.built_with$libtiledb != tiledb::.core_hash()) {
    warning("Core libtiledb has changed, please reinstall ", pkgname)
  }
}

This will throw a warning if tiledb, and therefore libtiledb, has changed between downstream package install and load

Examples

.core_info()

.core_hash()

Compiler Arguments for Using libtiledb

Description

Get compiler flags for using the core libtiledb install used by tiledb

Usage

.pkg_config(opt = c("PKG_CXX_FLAGS", "PKG_CXX_LIBS"))

Arguments

Value

A single string containing either the include directories or linking directories for libtiledb

Examples

.pkg_config()
.pkg_config("PKG_CXX_LIBS")

Sets a tiledb array value or value range

Description

This function assigns a right-hand side object, typically a data.frame or something that can be coerced to a data.frame, to a tiledb array.

Usage

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

Arguments

Details

For sparse matrices, row and column indices can either be supplied as part of the left-hand side object, or as part of the data.frame provided approrpiate column names.

This function may still still change; the current implementation should be considered as an initial draft.

Value

The modified object

Examples

## Not run: 
uri <- "quickstart_sparse" ## as created by the other example
arr <- tiledb_array(uri) ## open array
df <- arr[] ## read current content
## First approach: matching data.frame with appriate row and column
newdf <- data.frame(rows = c(1, 2, 2), cols = c(1, 3, 4), a = df$a + 100)
## Second approach: supply indices explicitly
arr[c(1, 2), c(1, 3)] <- c(42, 43) ## two values
arr[2, 4] <- 88 ## or just one

## End(Not run)

Sets a config parameter value

Description

Sets a config parameter value

Usage

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

Arguments

Value

updated tiledb_config object

Examples

cfg <- tiledb_config()
cfg["sm.tile_cache_size"]

# set tile cache size to custom value
cfg["sm.tile_cache_size"] <- 100
cfg["sm.tile_cache_size"]

Returns a TileDB array, allowing for specific subset ranges.

Description

Heterogenous domains are supported, including timestamps and characters.

Usage

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

Arguments

Details

This function may still still change; the current implementation should be considered as an initial draft.

Value

The resulting elements in the selected format

Gets a config parameter value

Description

Gets a config parameter value

Usage

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

Arguments

Value

a config string value if parameter exists, else NA

Examples

cfg <- tiledb_config()
cfg["sm.tile_cache_size"]
cfg["does_not_exist"]

Returns the filter at given index

Description

Returns the filter at given index

Usage

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

Arguments

Value

object tiledb_filter

Examples

flt <- tiledb_filter("ZSTD")
tiledb_filter_set_option(flt, "COMPRESSION_LEVEL", 5)
filter_list <- tiledb_filter_list(c(flt))
filter_list[0]

Returns logical value whether the array schema allows duplicate values or not. This is only valid for sparse arrays.

Description

Returns logical value whether the array schema allows duplicate values or not. This is only valid for sparse arrays.

Usage

allows_dups(x)

## S4 method for signature 'tiledb_array_schema'
allows_dups(x)

tiledb_array_schema_get_allows_dups(x)

Arguments

Value

A logical value.

Sets toggle whether the array schema allows duplicate values or not. This is only valid for sparse arrays.

Description

Sets toggle whether the array schema allows duplicate values or not. This is only valid for sparse arrays.

Usage

allows_dups(x) <- value

## S4 replacement method for signature 'tiledb_array_schema'
allows_dups(x) <- value

tiledb_array_schema_set_allows_dups(x, value)

Arguments

Value

An object of class tiledb_array_schema.

Consolidate fragments of a TileDB Array

Description

This function invokes a consolidation operation. Parameters affecting the operation can be set via an optional configuration object. Start and end timestamps can also be set directly.

Usage

array_consolidate(
  uri,
  cfg = NULL,
  start_time,
  end_time,
  ctx = tiledb_get_context()
)

Arguments

Value

NULL is returned invisibly

After consolidation, remove consolidated fragments of a TileDB Array

Description

This function can remove fragments following a consolidation step. Note that vacuuming should not be run if one intends to use the TileDB time-traveling feature of opening arrays at particular timestamps.

Usage

array_vacuum(uri, cfg = NULL, start_time, end_time, ctx = tiledb_get_context())

Arguments

Details

Parameters affecting the operation can be set via an optional configuration object. Start and end timestamps can also be set directly.

Value

NULL is returned invisibly

Convert a tiledb_config object to a R data.frame

Description

Convert a tiledb_config object to a R data.frame

Usage

## S3 method for class 'tiledb_config'
as.data.frame(x, ...)

Arguments

Value

a data.frame wth parameter, value columns

Examples

cfg <- tiledb_config()
as.data.frame(cfg)

Convert a tiledb_config object to a R vector

Description

Convert a tiledb_config object to a R vector

Usage

## S3 method for class 'tiledb_config'
as.vector(x, mode = "any")

Arguments

Value

a character vector of config parameter names, values

Examples

cfg <- tiledb_config()
as.vector(cfg)

Selects attributes for the given TileDB array

Description

Selects attributes for the given TileDB array

Usage

## S4 replacement method for signature 'tiledb_array'
attrs(x) <- value

Arguments

Value

The modified tiledb_array object

Retrieve attributes from tiledb_array object

Description

By default, all attributes will be selected. But if a subset of attribute names is assigned to the internal slot attrs, then only those attributes#' will be queried. This methods accesses the slot.

Usage

## S4 method for signature 'tiledb_array,ANY'
attrs(object)

Arguments

Value

An empty character vector if no attributes have been selected or else a vector with attributes; NA means no attributes will be returned.

Returns a list of all tiledb_attr objects associated with the tiledb_array_schema

Description

Returns a list of all tiledb_attr objects associated with the tiledb_array_schema

Usage

## S4 method for signature 'tiledb_array_schema,ANY'
attrs(object, idx, ...)

Arguments

Value

A list of tiledb_attr objects

Examples

dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 10L), type = "INT32")))
sch <- tiledb_array_schema(dom, attrs = c(
  tiledb_attr("a1", type = "INT32"),
  tiledb_attr("a2", type = "FLOAT64")
))
attrs(sch)

lapply(attrs(sch), datatype)

Returns a tiledb_attr object associated with the tiledb_array_schema with a given name.

Description

Returns a tiledb_attr object associated with the tiledb_array_schema with a given name.

Usage

## S4 method for signature 'tiledb_array_schema,character'
attrs(object, idx, ...)

Arguments

Value

A tiledb_attr object

Examples

dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 10L), type = "INT32")))
sch <- tiledb_array_schema(dom, attrs = c(
  tiledb_attr("a1", type = "INT32"),
  tiledb_attr("a2", type = "FLOAT64")
))
attrs(sch, "a2")

Returns a tiledb_attr object associated with the tiledb_array_schema with a given index

Description

The attribute index is defined by the order the attributes were defined in the schema

Usage

## S4 method for signature 'tiledb_array_schema,numeric'
attrs(object, idx, ...)

Arguments

Value

A tiledb_attr object

Examples

dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 10L), type = "INT32")))
sch <- tiledb_array_schema(dom, attrs = c(
  tiledb_attr("a1", type = "INT32"),
  tiledb_attr("a2", type = "FLOAT64")
))
attrs(sch, 2)

Retrieve schema capacity (for sparse fragments)

Description

Returns the tiledb_array schema tile capacity for sparse fragments.

Usage

capacity(object)

## S4 method for signature 'tiledb_array_schema'
capacity(object)

tiledb_array_schema_get_capacity(object)

Arguments

Value

The tile capacity value

Sets the schema capacity (for sparse fragments)

Description

Sets the tiledb_array schema tile capacity for sparse fragments.

Usage

capacity(x) <- value

## S4 replacement method for signature 'tiledb_array_schema'
capacity(x) <- value

tiledb_array_schema_set_capacity(x, value)

Arguments

Value

The modified tiledb_array_schema object.

Returns the cell layout string associated with the tiledb_array_schema

Description

Returns the cell layout string associated with the tiledb_array_schema

Usage

## S4 method for signature 'tiledb_array_schema'
cell_order(object)

Arguments

Value

A character string with cell's layout, e.g., "COL_MAJOR".

Return the number of scalar values per attribute cell

Description

Return the number of scalar values per attribute cell

Usage

cell_val_num(object)

## S4 method for signature 'tiledb_attr'
cell_val_num(object)

tiledb_attribute_get_cell_val_num(object)

Arguments

Value

integer number of cells

Examples

a1 <- tiledb_attr("a1", type = "FLOAT64", ncells = 1)
cell_val_num(a1)

Set the number of scalar values per attribute cell

Description

Set the number of scalar values per attribute cell

Usage

cell_val_num(x) <- value

## S4 replacement method for signature 'tiledb_attr'
cell_val_num(x) <- value

tiledb_attribute_set_cell_val_num(x, value)

Arguments

Value

The modified attribute is returned

Return the number of scalar values per dimension cell

Description

Return the number of scalar values per dimension cell

Usage

## S4 method for signature 'tiledb_dim'
cell_val_num(object)

tiledb_dim_get_cell_val_num(object)

Arguments

Value

integer number of cells

Check ‘batched’ query for completion

Description

Batched queries return an initial result set even when it is incomplete. Where the normal retrieval process will loop in place to complete a (potentially large) result set, this function will return a result (which may be part of a larger result set) allowing the user to assemble all part.

Usage

completedBatched(obj)

Arguments

Value

A logical value to indicated if the query completed

Retrieve the tiledb_config object from the tiledb_ctx

Description

Retrieve the tiledb_config object from the tiledb_ctx

Usage

## S4 method for signature 'tiledb_ctx'
config(object = tiledb_get_context())

Arguments

Value

tiledb_config object associated with the tiledb_ctx instance

Examples

ctx <- tiledb_ctx(c("sm.tile_cache_size" = "10"))
cfg <- config(ctx)
cfg["sm.tile_cache_size"]

Create a ‘batched’ query object

Description

Batched queries return an initial result set even when it is incomplete. Where the normal retrieval process will loop in place to complete a (potentially large) result set, this function will return a result (which may be part of a larger result set) allowing the user to assemble all part.

Usage

createBatched(x)

Arguments

Details

The tiledb_array object can be parameterised as usual.

Value

A batchedquery object, that is a list containing an external pointer to a TileDB Query object along with other support variables used by fetchBatched

Return the tiledb_attr datatype

Description

Return the tiledb_attr datatype

Usage

## S4 method for signature 'tiledb_attr'
datatype(object)

Arguments

Value

tiledb datatype string

Examples

a1 <- tiledb_attr("a1", type = "INT32")
datatype(a1)

a2 <- tiledb_attr("a1", type = "FLOAT64")
datatype(a2)

Return the tiledb_dim datatype

Description

Return the tiledb_dim datatype

Usage

## S4 method for signature 'tiledb_dim'
datatype(object)

Arguments

Value

A character string with tiledb's datatype.

Examples

d1 <- tiledb_dim("d1", domain = c(5L, 10L), tile = 2L, type = "INT32")
datatype(d1)

Returns the tiledb_domain TileDB type string

Description

Returns the tiledb_domain TileDB type string

Usage

## S4 method for signature 'tiledb_domain'
datatype(object)

Arguments

Value

tiledb_domain type string

Examples

dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 100L), type = "INT32")))
datatype(dom)
dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(0.5, 100.0), type = "FLOAT64")))
datatype(dom)

Retrieve datetimes_as_int64 toggle

Description

A tiledb_array object may contain date and datetime objects. While their internal representation is generally shielded from the user, it can useful to access them as the ‘native’ format which is an integer64. This function retrieves the current value of the selection variable, which has a default of FALSE.

Usage

datetimes_as_int64(object)

## S4 method for signature 'tiledb_array'
datetimes_as_int64(object)

Arguments

Value

A logical value indicating whether datetimes_as_int64 is selected

Set datetimes_as_int64 toggle

Description

A tiledb_array object may contain date and datetime objects. While their internal representation is generally shielded from the user, it can useful to access them as the ‘native’ format which is an integer64. This function set the current value of the selection variable, which has a default of FALSE.

Usage

datetimes_as_int64(x) <- value

## S4 replacement method for signature 'tiledb_array'
datetimes_as_int64(x) <- value

Arguments

Value

The modified tiledb_array array object

Describe a TileDB array schema via code to create it

Description

Note that this function is an unexported internal function that can be called using the colons as in tiledb:::describe(arr).

Usage

describe(arr)

Arguments

Value

Nothing is returned as the function is invoked for the side effect of printing the schema via a sequence of R instructions to re-create it.

Retrieve the dimension (domain extent) of the domain

Description

Only valid for integral (integer) domains

Usage

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

Arguments

Value

a dimension vector

Examples

dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 10L), type = "INT32")))
sch <- tiledb_array_schema(dom, attrs = c(
  tiledb_attr("a1", type = "INT32"),
  tiledb_attr("a2", type = "FLOAT64")
))
dim(sch)

Retrieves the dimension of the tiledb_dim domain

Description

Retrieves the dimension of the tiledb_dim domain

Usage

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

Arguments

Value

A vector of the tile_dim domain type, of the dim domain dimension (extent)

Examples

d1 <- tiledb_dim("d1", c(1L, 10L), 5L)
dim(d1)

Retrieve the dimension (domain extent) of the domain

Description

Only valid for integral (integer) domains

Usage

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

Arguments

Value

dimension vector

Examples

dom <- tiledb_domain(dims = c(
  tiledb_dim("d1", c(1L, 100L), type = "INT32"),
  tiledb_dim("d2", c(1L, 100L), type = "INT32")
))
dim(dom)

Returns a list of tiledb_dim objects associated with the tiledb_array_schema

Description

Returns a list of tiledb_dim objects associated with the tiledb_array_schema

Usage

## S4 method for signature 'tiledb_array_schema'
dimensions(object)

Arguments

Value

A list of tiledb_dim objects

Examples

dom <- tiledb_domain(dims = c(
  tiledb_dim("d1", c(1L, 100L), type = "INT32"),
  tiledb_dim("d2", c(1L, 50L), type = "INT32")
))
sch <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a1", type = "INT32")))
dimensions(dom)

lapply(dimensions(dom), name)

Returns a list of the tiledb_domain dimension objects

Description

Returns a list of the tiledb_domain dimension objects

Usage

## S4 method for signature 'tiledb_domain'
dimensions(object)

Arguments

Value

a list of tiledb_dim

Examples

dom <- tiledb_domain(dims = c(
  tiledb_dim("d1", c(1L, 100L), type = "INT32"),
  tiledb_dim("d2", c(1L, 50L), type = "INT32")
))
dimensions(dom)

lapply(dimensions(dom), name)

Returns the tiledb_domain object associated with a given tiledb_array_schema

Description

Returns the tiledb_domain object associated with a given tiledb_array_schema

Usage

## S4 method for signature 'tiledb_array_schema'
domain(object)

Arguments

Value

A tiledb_domain object

Examples

dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 10L), type = "INT32")))
sch <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a1", type = "INT32")))
domain(sch)

Return the tiledb_dim domain

Description

Return the tiledb_dim domain

Usage

## S4 method for signature 'tiledb_dim'
domain(object)

Arguments

Value

a vector of (lb, ub) inclusive domain of the dimension

Examples

d1 <- tiledb_dim("d1", domain = c(5L, 10L))
domain(d1)

Retrieve data.frame extended returns columns toggle

Description

A tiledb_array object can be returned as data.frame. This methods returns the selection value for ‘extended’ format including row (and column, if present) indices.

Usage

extended(object)

## S4 method for signature 'tiledb_array'
extended(object)

Arguments

Value

A logical value indicating whether an extended return is selected

Set data.frame extended return columns toggle

Description

A tiledb_array object can be returned as data.frame. This methods set the selection value for ‘extended’ format including row (and column, if present) indices.

Usage

extended(x) <- value

## S4 replacement method for signature 'tiledb_array'
extended(x) <- value

Arguments

Value

The modified tiledb_array array object

Run a ‘batched’ query

Description

Batched queries return an initial result set even when it is incomplete. Where the normal retrieval process will loop in place to complete a (potentially large) result set, this function will return a result (which may be part of a larger result set) allowing the user to assemble all part.

Usage

fetchBatched(x, obj)

Arguments

Details

The tiledb_array object can be parameterised as usual.

Value

A data.frame object with the (potentially partial) result of a batched query

Sets the TileDB Filter List for the TileDB Attribute object

Description

Sets the TileDB Filter List for the TileDB Attribute object

Usage

## S4 replacement method for signature 'tiledb_attr'
filter_list(x) <- value

Arguments

Value

The modified TileDB Attribute object

Sets the TileDB Filter List for the TileDB Dimension object

Description

Sets the TileDB Filter List for the TileDB Dimension object

Usage

## S4 replacement method for signature 'tiledb_dim'
filter_list(x) <- value

Arguments

Value

The modified TileDB Dimension object

Returns the offsets and coordinate filter_lists associated with the tiledb_array_schema

Description

Returns the offsets and coordinate filter_lists associated with the tiledb_array_schema

Usage

## S4 method for signature 'tiledb_array_schema'
filter_list(object)

Arguments

Value

A list of tiledb_filter_list objects

Returns the TileDB Filter List object associated with the given TileDB Attribute

Description

Returns the TileDB Filter List object associated with the given TileDB Attribute

Usage

## S4 method for signature 'tiledb_attr'
filter_list(object)

Arguments

Value

a tiledb_filter_list object

Examples

attr <- tiledb_attr(
  type = "INT32",
  filter_list = tiledb_filter_list(list(tiledb_filter("ZSTD")))
)
filter_list(attr)

Returns the TileDB Filter List object associated with the given TileDB Dimension

Description

Returns the TileDB Filter List object associated with the given TileDB Dimension

Usage

## S4 method for signature 'tiledb_dim'
filter_list(object)

Arguments

Value

A tiledb_filter_list object

Create a TileDB dense or sparse array from a given data.frame Object

Description

The supplied data.frame object is (currently) limited to integer, numeric, or character. In addition, three datetime columns are supported with the R representations of Date, POSIXct and nanotime.

Usage

fromDataFrame(
  obj,
  uri,
  col_index = NULL,
  sparse = TRUE,
  allows_dups = sparse,
  cell_order = "COL_MAJOR",
  tile_order = "COL_MAJOR",
  filter = "ZSTD",
  capacity = 10000L,
  tile_domain = NULL,
  tile_extent = NULL,
  mode = c("ingest", "schema_only", "append"),
  filter_list = NULL,
  coords_filters = "ZSTD",
  offsets_filters = "ZSTD",
  validity_filters = "RLE",
  debug = FALSE,
  timestamps = as.POSIXct(double(), origin = "1970-01-01")
)

Arguments

Details

The created (dense or sparse) array will have as many attributes as there are columns in the data.frame. Each attribute will be a single column. For a sparse array, one or more columns have to be designated as dimensions.

At present, factor variable are converted to character.

Value

Null, invisibly.

Examples

uri <- tempfile()
fromDataFrame(iris, uri)
arr <- tiledb_array(uri, return_as="data.frame", extended=FALSE)
newdf <- arr[]
all.equal(iris, newdf, check.attributes=FALSE)  # extra attribute on query in newdf
all.equal(as.matrix(iris), as.matrix(newdf))	# also strips attribute

Create a TileDB array from an R matrix, or return an R matrix

Description

The functions fromMatrix and toMatrix help in storing (and retrieving) matrices using a TileDB backend. In particular they help for matrices with explicit rownames.

Usage

fromMatrix(obj, uri, filter = "ZSTD", capacity = 10000L)

toMatrix(uri)

Arguments

Value

Null, invisibly.

Create (or return) a TileDB sparse array

Description

The functions fromSparseMatrix and toSparseMatrix help in storing (and retrieving) sparse matrices using a TileDB backend.

Usage

fromSparseMatrix(
  obj,
  uri,
  cell_order = "ROW_MAJOR",
  tile_order = "ROW_MAJOR",
  filter = "ZSTD",
  capacity = 10000L
)

toSparseMatrix(uri)

Arguments

Value

Null, invisibly.

Examples

## Not run: 
if (requireNamespace("Matrix", quietly=TRUE)) {
  library(Matrix)
  set.seed(123)      # just to fix it
  mat <- matrix(0, nrow=20, ncol=10)
  mat[sample(seq_len(200), 20)] <- seq(1, 20)
  spmat <- as(mat, "dgTMatrix")  # sparse matrix in dgTMatrix format
  uri <- "sparse_matrix"
  fromSparseMatrix(spmat, uri)   # now written
  chk <- toSparseMatrix(uri)     # and re-read
  print(chk)
  all.equal(spmat, chk)
}

## End(Not run)

Generic Methods

Description

Definition of generic methods

Usage

schema(object, ...)

return.data.frame(object, ...)

return.data.frame(x) <- value

attrs(x) <- value

raw_dump(object, ...)

domain(object, ...)

dimensions(object, ...)

attrs(object, idx, ...)

cell_order(object, ...)

tile_order(object, ...)

filter_list(object, ...)

filter_list(x) <- value

is.sparse(object, ...)

tiledb_ndim(object, ...)

name(object)

datatype(object)

config(object, ...)

tile(object)

is.integral(object)

nfilters(object)

tdb_filter(x, ...)

tdb_select(x, ...)

tdb_collect(x, ...)

Arguments

Check a schema for a given attribute name

Description

Check a schema for a given attribute name

Usage

has_attribute(schema, attr)

Arguments

Value

A boolean value indicating if the attribute exists in the schema

Returns TRUE if the tiledb_dim is anonymous

Description

A TileDB attribute is anonymous if no name/label is defined

Usage

is.anonymous(object)

## S3 method for class 'tiledb_attr'
is.anonymous(object)

Arguments

Value

TRUE or FALSE

Examples

a1 <- tiledb_attr("a1", type = "FLOAT64")
is.anonymous(a1)

a2 <- tiledb_attr("", type = "FLOAT64")
is.anonymous(a2)

Returns TRUE if the tiledb_dim is anonymous

Description

A TileDB dimension is anonymous if no name/label is defined

Usage

## S3 method for class 'tiledb_dim'
is.anonymous(object)

Arguments

Value

TRUE or FALSE

Examples

d1 <- tiledb_dim("d1", c(1L, 10L), 10L)
is.anonymous(d1)

d2 <- tiledb_dim("", c(1L, 10L), 10L)
is.anonymous(d2)

Returns TRUE is tiledb_domain is an integral (integer) domain

Description

Returns TRUE is tiledb_domain is an integral (integer) domain

Usage

## S4 method for signature 'tiledb_domain'
is.integral(object)

Arguments

Value

TRUE if the domain is an integral domain, else FALSE

Examples

dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 100L), type = "INT32")))
is.integral(dom)
dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(0.5, 100.0), type = "FLOAT64")))
is.integral(dom)

Returns TRUE if the tiledb_array_schema is sparse, else FALSE

Description

Returns TRUE if the tiledb_array_schema is sparse, else FALSE

Usage

## S4 method for signature 'tiledb_array_schema'
is.sparse(object)

Arguments

Value

TRUE if tiledb_array_schema object is sparse

Limit TileDB core use to a given number of cores

Description

By default, TileDB will use all available cores on a given machine. In multi-user or multi-process settings, one may want to reduce the number of core. This function will take a given number, or default to smaller of the ‘Ncpus’ options value or the ‘"OMP_THREAD_LIMIT"’ enviroment variable (or two as hard fallback).

Usage

limitTileDBCores(ncores, verbose = FALSE)

Arguments

Details

As this function returns a config object, its intended use is as argument to the context creating functions: ctx <- tiledb_ctx(limitTileDBCores()). To check that the values are set (or at a later point, still set) the config object should be retrieved via the corresponding method and this ctx object: cfg <- config(ctx).

Value

The modified configuration object is returned invisibly.

Returns the filter_list's max_chunk_size

Description

Returns the filter_list's max_chunk_size

Usage

max_chunk_size(object)

## S4 method for signature 'tiledb_filter_list'
max_chunk_size(object)

tiledb_filter_list_get_max_chunk_size(object)

Arguments

Value

integer max_chunk_size

Examples

flt <- tiledb_filter("ZSTD")
tiledb_filter_set_option(flt, "COMPRESSION_LEVEL", 5)
filter_list <- tiledb_filter_list(c(flt))
max_chunk_size(filter_list)

Return the tiledb_attr name

Description

Return the tiledb_attr name

Usage

## S4 method for signature 'tiledb_attr'
name(object)

Arguments

Value

string name, empty string if the attribute is anonymous

Examples

a1 <- tiledb_attr("a1", type = "INT32")
name(a1)

a2 <- tiledb_attr(type = "INT32")
name(a2)

Return the tiledb_dim name

Description

Return the tiledb_dim name

Usage

## S4 method for signature 'tiledb_dim'
name(object)

Arguments

Value

string name, empty string if the dimension is anonymous

Examples

d1 <- tiledb_dim("d1", c(1L, 10L))
name(d1)

d2 <- tiledb_dim("", c(1L, 10L))
name(d2)

Returns the filter_list's number of filters

Description

Returns the filter_list's number of filters

Usage

## S4 method for signature 'tiledb_filter_list'
nfilters(object)

Arguments

Value

integer number of filters

Examples

flt <- tiledb_filter("ZSTD")
tiledb_filter_set_option(flt, "COMPRESSION_LEVEL", 5)
filter_list <- tiledb_filter_list(c(flt))
nfilters(filter_list)

Create a 'tiledb_query_condition' object from an expression

Description

The grammar for query conditions is at present constraint to eight operators (">", ">=", "<", "<=", "==", "!=", "%in%", "%nin%"), and three boolean operators ("&&", also as "&", ("||", also as "|", and "!" for negation. Note that we locally define "%nin%" as Negate() call around %in%) which extends R a little for this use case.

Usage

parse_query_condition(
  expr,
  ta = NULL,
  debug = FALSE,
  strict = TRUE,
  use_int64 = FALSE
)

Arguments

Details

Expressions are parsed locally by this function. The debug=TRUE option may help if an issue has to be diagnosed. In most cases of an errroneous parse, it generally helps to supply the tiledb_array providing schema information. One example are numeric and integer columns where the data type is difficult to guess. Also, when using the "%in%" or "%nin%" operators, the argument is mandatory.

Value

A tiledb_query_condition object

Examples

## Not run: 
uri <- "mem://airquality" # change to on-disk for persistence
fromDataFrame(airquality, uri, col_index = c("Month", "Day")) # dense array
## query condition on dense array requires extended=FALSE
tiledb_array(uri,
  return_as = "data.frame", extended = FALSE,
  query_condition = parse_query_condition(Temp > 90)
)[]

## End(Not run)

Print a TileDB Array Metadata object

Description

Print a TileDB Array Metadata object

Usage

## S3 method for class 'tiledb_metadata'
print(x, width = NULL, ...)

Arguments

Value

The array object, invisibly

Retrieve query_condition value for the array

Description

A tiledb_array object can have a corresponding query condition object. This methods returns it.

Usage

query_condition(object)

## S4 method for signature 'tiledb_array'
query_condition(object)

Arguments

Value

A tiledb_query_condition object

Set query_condition object for the array

Description

A tiledb_array object can have an associated query condition object to set conditions on the read queries. This methods sets the ‘query_condition’ object.

Usage

query_condition(x) <- value

## S4 replacement method for signature 'tiledb_array'
query_condition(x) <- value

Arguments

Value

The modified tiledb_array array object

Retrieve query_layout values for the array

Description

A tiledb_array object can have a corresponding query with a given layout given layout. This methods returns the selection value for ‘query_layout’ as a character value.

Usage

query_layout(object)

## S4 method for signature 'tiledb_array'
query_layout(object)

Arguments

Value

A character value describing the query layout

Set query_layout return values for the array

Description

A tiledb_array object can have an associated query with a specific layout. This methods sets the selection value for ‘query_layout’ from a character value.

Usage

query_layout(x) <- value

## S4 replacement method for signature 'tiledb_array'
query_layout(x) <- value

Arguments

Value

The modified tiledb_array array object

Retrieve query_statistics toggle

Description

A tiledb_array object can, if requested, return query statistics as a JSON string in an attribute ‘query_statistics’ attached to the return object. The default value of the logical switch is ‘FALSE’. This method returns the current value.

Usage

query_statistics(object, ...)

## S4 method for signature 'tiledb_array'
query_statistics(object)

Arguments

Value

A logical value indicating whether query statistics are returned.

Set query_statistics toggle

Description

A tiledb_array object can, if requested, return query statistics as a JSON string in an attribute ‘query_statistics’ attached to the return object. The default value of the logical switch is ‘FALSE’. This method sets the value.

Usage

query_statistics(x) <- value

## S4 replacement method for signature 'tiledb_array'
query_statistics(x) <- value

Arguments

Value

The modified tiledb_array array object

Look up TileDB type corresponding to the type of an R object

Description

Look up TileDB type corresponding to the type of an R object

Usage

r_to_tiledb_type(x)

Arguments

Value

single character, e.g. INT32

Raw display of an array schema object

Description

This method used the display method provided by the underlying library.

Usage

## S4 method for signature 'tiledb_array_schema'
raw_dump(object)

Arguments

Raw display of an attribute object

Description

This method used the display method provided by the underlying library.

Usage

## S4 method for signature 'tiledb_attr'
raw_dump(object)

Arguments

Raw display of a domain object

Description

This method used the display method provided by the underlying library.

Usage

## S4 method for signature 'tiledb_domain'
raw_dump(object)

Arguments

Retrieve array return toggle

Description

A tiledb_array object can be returned as an array (or list of arrays), or, if select, as a data.frame or as a matrix. This methods returns the selection value for the array selection.

Usage

return.array(object, ...)

## S4 method for signature 'tiledb_array'
return.array(object)

Arguments

Value

A logical value indicating whether array return is selected

Set array return toggle

Description

A tiledb_array object can be returned as an array (or list of arrays), or, if select, as a data.frame or a matrix. This methods sets the selection value for a array.

Usage

return.array(x) <- value

## S4 replacement method for signature 'tiledb_array'
return.array(x) <- value

Arguments

Value

The modified tiledb_array array object

Set data.frame return toggle

Description

A tiledb_array object can be returned as an array (or list of arrays), or, if select, as a data.frame. This methods sets the selection value.

Usage

## S4 replacement method for signature 'tiledb_array'
return.data.frame(x) <- value

Arguments

Value

The modified tiledb_array array object

Retrieve data.frame return toggle

Description

A tiledb_array object can be returned as an array (or list of arrays), or, if select, as a data.frame. This methods returns the selection value.

Usage

## S4 method for signature 'tiledb_array'
return.data.frame(object)

Arguments

Value

A logical value indicating whether data.frame return is selected

Retrieve matrix return toggle

Description

A tiledb_array object can be returned as an array (or list of arrays), or, if select, as a data.frame or as a matrix. This methods returns the selection value for the matrix selection.

Usage

return.matrix(object, ...)

## S4 method for signature 'tiledb_array'
return.matrix(object)

Arguments

Value

A logical value indicating whether matrix return is selected

Set matrix return toggle

Description

A tiledb_array object can be returned as an array (or list of arrays), or, if select, as a data.frame or a matrix. This methods sets the selection value for a matrix.

Usage

return.matrix(x) <- value

## S4 replacement method for signature 'tiledb_array'
return.matrix(x) <- value

Arguments

Value

The modified tiledb_array array object

Retrieve return_as conversion preference

Description

A tiledb_array object can be returned as a ‘list’ (default), ‘array’, ‘matrix’, ‘data.frame’, ‘data.table’ or ‘tibble’. This method permits to select a preference for the returned object. The default value of ‘asis’ means that no conversion is performed.

Usage

return_as(object, ...)

## S4 method for signature 'tiledb_array'
return_as(object)

Arguments

Value

A character value indicating the preferred conversion where the value is one of ‘asis’ (the default), ‘array’, ‘matrix’,‘data.frame’, ‘data.table’, or ‘tibble’.

Retrieve return_as conversion preference

Description

A tiledb_array object can be returned as a ‘list’ (default), ‘array’, ‘matrix’, ‘data.frame’, ‘data.table’ or ‘tibble’. This method This methods permits to set a preference of returning a list, array, matrix, data.frame, a data.table, or a tibble. The default value of “asis” means that no conversion is performed and a list is returned.

Usage

return_as(x) <- value

## S4 replacement method for signature 'tiledb_array'
return_as(x) <- value

Arguments

Value

The modified tiledb_array array object

Store allocation size preference

Description

Save (or load) allocation size default preference in an optional config file

Usage

save_allocation_size_preference(value)

load_allocation_size_preference()

get_allocation_size_preference()

set_allocation_size_preference(value)

Arguments

Details

When retrieving data from sparse arrays, allocation sizes cannot be determined ex ante as the degree of sparsity is unknown. A configuration value can aide in providing an allocation size value. These functions let the user store such a value for retrieval by their package or script code. The preference will be encoded in a configuration file as R (version 4.0.0 or later) allows a user- and package specific configuration files. These helper functions sets and retrieve the value, respectively, or retrieve the cached value from the package environment where is it set at package load.

The value will be stored as a character value and reparsed so ‘1e6’ and ‘1000000’ are equivalent, and the fixed (but adjustable) number of digits for numerical precision use for formatting will impact the writing. This should have no effect on standard allocation sizes.

The value is used as a limit per column so total memory use per query will a multiple of this value, and increasing in dimension and attribute count.

A fallback value of 10 mb is used if no user value is set.

Value

For the setter, TRUE is returned invisibly but the function is invoked for the side effect of storing the value. For the getters, the value as a numeric.

Note

This function requires R version 4.0.0 or later to utilise the per-user config directory accessor function. For older R versions, a fallback from the TileDB configuration object is used.

Store object conversion preference

Description

Save (or load) ‘return_as’ conversion preference in an optional config file

Usage

save_return_as_preference(
  value = c("asis", "array", "matrix", "data.frame", "data.table", "tibble")
)

load_return_as_preference()

get_return_as_preference()

set_return_as_preference(
  value = c("asis", "array", "matrix", "data.frame", "data.table", "tibble")
)

Arguments

Details

The tiledb_array object can set a preference for conversion for each retrieved object. This preference can also be encoded in a configuration file as R (version 4.0.0 or later) allows a user- and package specific configuration files. These helper functions set and retrieve the value, respectively, or retrieve the cached value from the package environment where it is set at package load.

Note that the value must be one of ‘asis’ (the default), ‘array’, ‘matrix’‘data.frame’, ‘data.table’ or ‘tibble’. The latter two require the corresponding package to be installed.

Value

For the setter, TRUE is returned invisibly but the function is invoked for the side effect of storing the value. For either getter, the character value.

Note

This function requires R version 4.0.0 or later to utilise the per-user config directory accessor function. For older R versions, please set the attribute directly when creating the tiledb_array object, or via the return_as() method.

Return a schema from a URI character value

Description

Return a schema from a URI character value

Usage

## S4 method for signature 'character'
schema(object, ...)

Arguments

Value

The scheme for the object

Return a schema from a tiledb_array object

Description

Return a schema from a tiledb_array object

Usage

## S4 method for signature 'tiledb_array'
schema(object, ...)

Arguments

Value

The scheme for the object

Check the schema for correctness

Description

Returns the tiledb_array schema for correctness

Usage

schema_check(object)

## S4 method for signature 'tiledb_array_schema'
schema_check(object)

check(object)

## S4 method for signature 'tiledb_array_schema'
check(object)

tiledb_array_schema_check(object)

Arguments

Value

The boolean value TRUE is returned for a correct schema; for an incorrect schema an error condition is triggered.

Retrieve selected_points values for the array

Description

A tiledb_array object can have a range selection for each dimension attribute. This methods returns the selection value for ‘selected_points’ and returns a list (with one element per dimension) of vectors where each row describes one selected points. Alternatively, the list can be named with the names providing the match to the corresponding dimension.

Usage

selected_points(object)

## S4 method for signature 'tiledb_array'
selected_points(object)

Arguments

Value

A list which can contain a vector for each dimension

Set selected_points return values for the array

Description

A tiledb_array object can have a range selection for each dimension attribute. This methods sets the selection value for ‘selected_points’ which is a list (with one element per dimension) of two-column matrices where each row describes one pair of minimum and maximum values. Alternatively, the list can be named with the names providing the match to the corresponding dimension.

Usage

selected_points(x) <- value

## S4 replacement method for signature 'tiledb_array'
selected_points(x) <- value

Arguments

Value

The modified tiledb_array array object

Retrieve selected_ranges values for the array

Description

A tiledb_array object can have a range selection for each dimension attribute. This methods returns the selection value for ‘selected_ranges’ and returns a list (with one element per dimension) of two-column matrices where each row describes one pair of minimum and maximum values. Alternatively, the list can be named with the names providing the match to the corresponding dimension.

Usage

selected_ranges(object)

## S4 method for signature 'tiledb_array'
selected_ranges(object)

Arguments

Value

A list which can contain a matrix for each dimension

Set selected_ranges return values for the array

Description

A tiledb_array object can have a range selection for each dimension attribute. This methods sets the selection value for ‘selected_ranges’ which is a list (with one element per dimension) of two-column matrices where each row describes one pair of minimum and maximum values. Alternatively, the list can be named with the names providing the match to the corresponding dimension.

Usage

selected_ranges(x) <- value

## S4 replacement method for signature 'tiledb_array'
selected_ranges(x) <- value

Arguments

Value

The modified tiledb_array array object

Set the filter_list's max_chunk_size

Description

Set the filter_list's max_chunk_size

Usage

set_max_chunk_size(object, value)

## S4 method for signature 'tiledb_filter_list,numeric'
set_max_chunk_size(object, value)

tiledb_filter_list_set_max_chunk_size(object, value)

Arguments

Examples

flt <- tiledb_filter("ZSTD")
tiledb_filter_set_option(flt, "COMPRESSION_LEVEL", 5)
filter_list <- tiledb_filter_list(c(flt))
set_max_chunk_size(filter_list, 10)

Prints a tiledb_array object

Description

Prints a tiledb_array object

Usage

## S4 method for signature 'tiledb_array'
show(object)

Arguments

Prints an array schema object

Description

Prints an array schema object

Usage

## S4 method for signature 'tiledb_array_schema'
show(object)

Arguments

Prints an attribute object

Description

Prints an attribute object

Usage

## S4 method for signature 'tiledb_attr'
show(object)

Arguments

Prints the config object to STDOUT

Description

Prints the config object to STDOUT

Usage

## S4 method for signature 'tiledb_config'
show(object)

Arguments

Examples

cfg <- tiledb_config()
show(cfg)

Prints a dimension object

Description

Prints a dimension object

Usage

## S4 method for signature 'tiledb_dim'
show(object)

Arguments

Prints a domain object

Description

Prints a domain object

Usage

## S4 method for signature 'tiledb_domain'
show(object)

Arguments

Prints a filter object

Description

Prints a filter object

Usage

## S4 method for signature 'tiledb_filter'
show(object)

Arguments

Prints a filter_list object

Description

Prints a filter_list object

Usage

## S4 method for signature 'tiledb_filter_list'
show(object)

Arguments

Display the TileDB Group object to STDOUT

Description

Display the TileDB Group object to STDOUT

Usage

## S4 method for signature 'tiledb_group'
show(object)

Arguments

Return ‘batched’ status

Description

Batched queries return an initial result set even when it is incomplete. Where the normal retrieval process will loop in place to complete a (potentially large) result set, this function will return a result (which may be part of a larger result set) allowing the user to assemble all part.

Usage

statusBatched(obj)

Arguments

Value

The Query status as a character variable

Retrieve strings_as_factors conversion toggle

Description

A tiledb_array object containing character column can have those converted to factors variables. This methods returns the selection value for ‘strings_as_factors’.

Usage

strings_as_factors(object)

## S4 method for signature 'tiledb_array'
strings_as_factors(object)

Arguments

Value

A logical value indicating whether an strings_as_factors return is selected

Set strings_as_factors return toggle

Description

A tiledb_array object containing character column can have those converted to factors variables. This methods sets the selection value for ‘strings_as_factors’.

Usage

strings_as_factors(x) <- value

## S4 replacement method for signature 'tiledb_array'
strings_as_factors(x) <- value

Arguments

Value

The modified tiledb_array array object

Collect the query results to finalize piped expression

Description

Collect the query results to finalize piped expression

Usage

## S4 method for signature 'tiledb_array'
tdb_collect(x, ...)

Arguments

Value

The object returning from a tiledb_array query (the type of which can be set via the return preference mechanism, see the help for "[" accessor)

Filter from array for query via logical conditions

Description

Filter from array for query via logical conditions

Usage

## S4 method for signature 'tiledb_array'
tdb_filter(x, ..., strict = TRUE)

Arguments

Value

The tiledb_array object, permitting piping

Select attributes from array for query

Description

Select attributes from array for query

Usage

## S4 method for signature 'tiledb_array'
tdb_select(x, ...)

Arguments

Value

The tiledb_array object, permitting piping

Return the tiledb_dim tile extent

Description

Return the tiledb_dim tile extent

Usage

## S4 method for signature 'tiledb_dim'
tile(object)

Arguments

Value

A scalar tile extent

Examples

d1 <- tiledb_dim("d1", domain = c(5L, 10L), tile = 2L)
tile(d1)

Returns the tile layout string associated with the tiledb_array_schema

Description

Returns the tile layout string associated with the tiledb_array_schema

Usage

## S4 method for signature 'tiledb_array_schema'
tile_order(object)

Arguments

Value

A character string with tile's layout, e.g., "COL_MAJOR".

Constructs a tiledb_array object backed by a persisted tiledb array uri

Description

tiledb_array returns a new object. This class is experimental.

Usage

tiledb_array(
  uri,
  query_type = c("READ", "WRITE"),
  is.sparse = NA,
  attrs = character(),
  extended = TRUE,
  selected_ranges = list(),
  selected_points = list(),
  query_layout = character(),
  datetimes_as_int64 = FALSE,
  encryption_key = character(),
  query_condition = new("tiledb_query_condition"),
  timestamp_start = as.POSIXct(double(), origin = "1970-01-01"),
  timestamp_end = as.POSIXct(double(), origin = "1970-01-01"),
  return_as = get_return_as_preference(),
  query_statistics = FALSE,
  strings_as_factors = getOption("stringsAsFactors", FALSE),
  keep_open = FALSE,
  sil = list(),
  dumpbuffers = character(),
  buffers = list(),
  ctx = tiledb_get_context(),
  as.data.frame = FALSE
)

tiledb_dense(...)

tiledb_sparse(...)

Arguments

Value

tiledb_array object

An S4 class for a TileDB Array

Description

This class replaces the earlier (and now removed) tiledb_dense and tiledb_sparse and provides equivalent functionality based on a refactored implementation utilising newer TileDB features.

Slots

ctx

A TileDB context object

uri

A character despription with the array URI

is.sparse

A logical value whether the array is sparse or not

attrs

A character vector to select particular column ‘attributes’; default is an empty character vector implying ‘all’ columns, the special value NA_character_ has the opposite effect and selects ‘none’.

extended

A logical value, defaults to TRUE, indicating whether index columns are returned as well.

selected_ranges

An optional list with matrices where each matrix i describes the (min,max) pair of ranges for dimension i

selected_points

An optional list with vectors where each vector i describes the selected points for dimension i

query_layout

An optional character value

datetimes_as_int64

A logical value

encryption_key

A character value

query_condition

A Query Condition object

timestamp_start

A POSIXct datetime variable for the inclusive interval start

timestamp_end

A POSIXct datetime variable for the inclusive interval start

return_as

A character value with the desired tiledb_array conversion, permitted values are ‘asis’ (default, returning a list of columns), ‘array’, ‘matrix’,‘data.frame’, ‘data.table’ ‘tibble’, ‘arrow_table’ or ‘arrow’ (where the last two are synomyms); note that ‘data.table’, ‘tibble’ and ‘arrow’ require the respective packages to be installed.

query_statistics

A logical value, defaults to ‘FALSE’; if ‘TRUE’ the query statistics are returned (as a JSON string) via the attribute ‘query_statistics’ of the return object.

sil

An optional and internal list object with schema information, used for parsing queries.

dumpbuffers

An optional character variable with a directory name (relative to /dev/shm) for writing out results buffers (for internal use / testing)

buffers

An optional list with full pathnames of shared memory buffers to read data from

strings_as_factors

An optional logical to convert character columns to factor type

keep_open

An optional logical to not close after read or write

ptr

External pointer to the underlying implementation

Run an aggregate query on the given (sparse) array and attribute

Description

For dense arrays, use tiledb_query_apply_aggregate after setting an appropriate subarray.

Usage

tiledb_array_apply_aggregate(
  array,
  attrname,
  operation = c("Count", "NullCount", "Min", "Max", "Mean", "Sum"),
  nullable = TRUE
)

Arguments

Value

The value of the aggregation

Close a TileDB Array

Description

Close a TileDB Array

Usage

tiledb_array_close(arr)

Arguments

Value

The TileDB Array object but closed

Creates a new TileDB array given an input schema.

Description

Creates a new TileDB array given an input schema.

Usage

tiledb_array_create(uri, schema, encryption_key)

Arguments

Examples

## Not run: 
pth <- tempdir()
dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 10L), type = "INT32")))
sch <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a1", type = "INT32")))
tiledb_array_create(pth, sch)
tiledb_object_type(pth)

## End(Not run)

Delete fragments written between the start and end times given

Description

Delete fragments written between the start and end times given

Usage

tiledb_array_delete_fragments(
  arr,
  ts_start,
  ts_end,
  ctx = tiledb_get_context()
)

Arguments

Value

A boolean indicating success

Delete fragments written given by their URIs

Description

Delete fragments written given by their URIs

Usage

tiledb_array_delete_fragments_list(arr, fragments, ctx = tiledb_get_context())

Arguments

Value

A boolean indicating success

Get the non-empty domain from a TileDB Array by index

Description

This functions works for both fixed- and variable-sized dimensions and switches internally.

Usage

tiledb_array_get_non_empty_domain_from_index(arr, idx)

Arguments

Value

A two-element object is returned describing the domain of selected dimension; it will either be a numeric vector in case of a fixed-size fixed-sized dimensions, or a character vector for a variable-sized one.

Get the non-empty domain from a TileDB Array by name

Description

This functions works for both fixed- and variable-sized dimensions and switches internally.

Usage

tiledb_array_get_non_empty_domain_from_name(arr, name)

Arguments

Value

A two-element object is returned describing the domain of selected dimension; it will either be a numeric vector in case of a fixed-size fixed-sized dimensions, or a character vector for a variable-sized one.

Check for Enumeration (aka Factor aka Dictionary)

Description

Check for Enumeration (aka Factor aka Dictionary)

Usage

tiledb_array_has_enumeration(arr)

Arguments

Value

A boolean indicating if the array has homogeneous domains

Check for Heterogeneous Domain

Description

Check for Heterogeneous Domain

Usage

tiledb_array_is_heterogeneous(arr)

Arguments

Value

A boolean indicating if the array has heterogenous domains

Check for Homogeneous Domain

Description

Check for Homogeneous Domain

Usage

tiledb_array_is_homogeneous(arr)

Arguments

Value

A boolean indicating if the array has homogeneous domains

Test if TileDB Array is open

Description

Test if TileDB Array is open

Usage

tiledb_array_is_open(arr)

Arguments

Value

A boolean indicating whether the TileDB Array object is open

Test if TileDB Array is open for reading

Description

Test if TileDB Array is open for reading

Usage

tiledb_array_is_open_for_reading(arr)

Arguments

Value

A boolean indicating whether the TileDB Array object is open, and the mode is "READ".

Test if TileDB Array is open for writing

Description

Test if TileDB Array is open for writing

Usage

tiledb_array_is_open_for_writing(arr)

Arguments

Value

A boolean indicating whether the TileDB Array object is open, and the mode is "WRITE".

Open a TileDB Array

Description

Open a TileDB Array

Usage

tiledb_array_open(
  arr,
  type = if (tiledb_version(TRUE) >= "2.12.0") {
     c("READ", "WRITE", "DELETE",
    "MODIFY_EXCLUSIVE")
 } else {
     c("READ", "WRITE")
 }
)

Arguments

Value

The TileDB Array object but opened for reading or writing

Open a TileDB Array at Timestamp

Description

Open a TileDB Array at Timestamp

Usage

tiledb_array_open_at(arr, type = c("READ", "WRITE"), timestamp)

Arguments

Value

The TileDB Array object but opened for reading or writing

Constructs a tiledb_array_schema object

Description

Constructs a tiledb_array_schema object

Usage

tiledb_array_schema(
  domain,
  attrs,
  cell_order = "COL_MAJOR",
  tile_order = "COL_MAJOR",
  sparse = FALSE,
  coords_filter_list = NULL,
  offsets_filter_list = NULL,
  validity_filter_list = NULL,
  capacity = 10000L,
  allows_dups = FALSE,
  enumerations = NULL,
  ctx = tiledb_get_context()
)

Arguments

Value

An object of class tiledb_array_schema.

Examples

schema <- tiledb_array_schema(
  dom = tiledb_domain(
    dims = c(
      tiledb_dim("rows", c(1L, 4L), 4L, "INT32"),
      tiledb_dim("cols", c(1L, 4L), 4L, "INT32")
    )
  ),
  attrs = c(tiledb_attr("a", type = "INT32")),
  cell_order = "COL_MAJOR",
  tile_order = "COL_MAJOR",
  sparse = FALSE
)
schema

An S4 class for the TileDB array schema

Description

An S4 class for the TileDB array schema

Slots

ptr

An external pointer to the underlying implementation

arrptr

An optional external pointer to the underlying array, or NULL if missing

Creates a 'tiledb_array_schema_evolution' object

Description

Creates a 'tiledb_array_schema_evolution' object

Usage

tiledb_array_schema_evolution(ctx = tiledb_get_context())

Arguments

Value

A 'array_schema_evolution' object

An S4 class for a TileDB ArraySchemaEvolution object

Description

An S4 class for a TileDB ArraySchemaEvolution object

Slots

ptr

An external pointer to the underlying implementation

Add an Attribute to a TileDB Array Schema Evolution object

Description

Add an Attribute to a TileDB Array Schema Evolution object

Usage

tiledb_array_schema_evolution_add_attribute(object, attr)

Arguments

Value

The modified 'array_schema_evolution' object, invisibly

Add an Enumeration to a TileDB Array Schema Evolution object

Description

Add an Enumeration to a TileDB Array Schema Evolution object

Usage

tiledb_array_schema_evolution_add_enumeration(
  object,
  name,
  enums,
  ordered = FALSE,
  ctx = tiledb_get_context()
)

Arguments

Value

The modified 'array_schema_evolution' object, invisibly

Evolve an Array Schema by adding an empty Enumeration

Description

Evolve an Array Schema by adding an empty Enumeration

Usage

tiledb_array_schema_evolution_add_enumeration_empty(
  ase,
  enum_name,
  type_str = "ASCII",
  cell_val_num = NA_integer_,
  ordered = FALSE,
  ctx = tiledb_get_context()
)

Arguments

Evolve an Array Schema

Description

Evolve an Array Schema

Usage

tiledb_array_schema_evolution_array_evolve(object, uri)

Arguments

Value

The modified 'array_schema_evolution' object, invisibly

Drop an attribute given by name from a TileDB Array Schema Evolution object

Description

Drop an attribute given by name from a TileDB Array Schema Evolution object

Usage

tiledb_array_schema_evolution_drop_attribute(object, attrname)

Arguments

Value

The modified 'array_schema_evolution' object, invisibly

Drop an Enumeration given by name from a TileDB Array Schema Evolution object

Description

Drop an Enumeration given by name from a TileDB Array Schema Evolution object

Usage

tiledb_array_schema_evolution_drop_enumeration(object, attrname)

Arguments

Value

The modified 'array_schema_evolution' object, invisibly

Expand an the Current Domain of an Array via Array Schema Evolution

Description

Expand an the Current Domain of an Array via Array Schema Evolution

Usage

tiledb_array_schema_evolution_expand_current_domain(ase, cd)

Arguments

Value

The modified ArraySchemaEvolution object

Extend an Evolution via Array Schema Evolution

Description

Extend an Evolution via Array Schema Evolution

Usage

tiledb_array_schema_evolution_extend_enumeration(
  ase,
  array,
  enum_name,
  new_values,
  nullable = FALSE,
  ordered = FALSE,
  ctx = tiledb_get_context()
)

Arguments

Value

The modified ArraySchemaEvolution object

Get the Current Domain of an Array Schema

Description

Note that tiledb_current_domain object may be empty.

Usage

tiledb_array_schema_get_current_domain(schema, ctx = tiledb_get_context())

Arguments

Value

An object of class tiledb_current_domain.

Set a Filter List for Coordinate of a TileDB Schema

Description

Set a Filter List for Coordinate of a TileDB Schema

Usage

tiledb_array_schema_set_coords_filter_list(sch, fl)

Arguments

Value

The modified tiledb_array_schema object.

Set a Current Domain of an Array Schema

Description

Set a Current Domain of an Array Schema

Usage

tiledb_array_schema_set_current_domain(schema, cd, ctx = tiledb_get_context())

Arguments

Value

Nothing is returned from this function (but an error, should it occur is reported)

Add an empty Enumeration to a Schema

Description

Add an empty Enumeration to a Schema

Usage

tiledb_array_schema_set_enumeration_empty(
  schema,
  attr,
  enum_name,
  type_str = "ASCII",
  cell_val_num = NA_integer_,
  ordered = FALSE,
  ctx = tiledb_get_context()
)

Arguments

Value

The modified tiledb_array_schema object.

Set a Filter List for Variable-Sized Offsets of a TileDB Schema

Description

Set a Filter List for Variable-Sized Offsets of a TileDB Schema

Usage

tiledb_array_schema_set_offsets_filter_list(sch, fl)

Arguments

Value

The modified tiledb_array_schema object.

Set a Filter List for Validity of a TileDB Schema

Description

Set a Filter List for Validity of a TileDB Schema

Usage

tiledb_array_schema_set_validity_filter_list(sch, fl)

Arguments

Value

The modified tiledb_array_schema object.

Check the version of the array schema

Description

Returns the (internal) version of the tiledb_array schema

Usage

tiledb_array_schema_version(object)

Arguments

Value

An integer value describing the internal schema format version

Upgrade an Array to the current TileDB Array Schema Format

Description

Upgrade an Array to the current TileDB Array Schema Format

Usage

tiledb_array_upgrade_version(array, config = NULL, ctx = tiledb_get_context())

Arguments

Value

Nothing is returned as the function is invoked for its side effect

(Deprecated) Allocate (or Release) Arrow Array and Schema Pointers

Description

These functions allocate (and free) appropriate pointer objects for, respectively, Arrow array and schema objects. These functions are deprecated and will be removed, it is recommended to rely directly on the nanoarrow replacements.

Usage

tiledb_arrow_array_ptr()

tiledb_arrow_schema_ptr()

tiledb_arrow_array_del(ptr)

tiledb_arrow_schema_del(ptr)

Arguments

Value

The allocating functions return the requested pointer

Constructs a tiledb_attr object

Description

Constructs a tiledb_attr object

Usage

tiledb_attr(
  name,
  type,
  filter_list = tiledb_filter_list(),
  ncells = 1,
  nullable = FALSE,
  enumeration = NULL,
  ctx = tiledb_get_context()
)

Arguments

Value

tiledb_dim object

Examples

flt <- tiledb_filter_list(list(tiledb_filter("GZIP")))
attr <- tiledb_attr(
  name = "a1", type = "INT32",
  filter_list = flt
)
attr

An S4 class for a TileDB attribute

Description

An S4 class for a TileDB attribute

Slots

ptr

External pointer to the underlying implementation

Get the TileDB Attribute cell size

Description

Get the TileDB Attribute cell size

Usage

tiledb_attribute_get_cell_size(attr)

Arguments

Value

A numeric value with the cell size

Get the TileDB Attribute Enumeration

Description

Get the TileDB Attribute Enumeration

Usage

tiledb_attribute_get_enumeration(attr, arr, ctx = tiledb_get_context())

tiledb_attribute_get_enumeration_ptr(attr, arrptr, ctx = tiledb_get_context())

Arguments

Value

A character vector with the enumeration (of length zero if none)

Get the fill value for a TileDB Attribute

Description

Get the fill value for a TileDB Attribute

Usage

tiledb_attribute_get_fill_value(attr)

Arguments

Value

The fill value for the attribute

Get the TileDB Attribute Nullable flag value

Description

Get the TileDB Attribute Nullable flag value

Usage

tiledb_attribute_get_nullable(attr)

Arguments

Value

A boolean value with the ‘Nullable’ status

Test if TileDB Attribute has an Enumeration

Description

Test if TileDB Attribute has an Enumeration

Usage

tiledb_attribute_has_enumeration(attr, ctx = tiledb_get_context())

Arguments

Value

A logical value indicating if the attribute has an enumeration

Check if TileDB Attribute Enumeration is Ordered

Description

Check if TileDB Attribute Enumeration is Ordered

Usage

tiledb_attribute_is_ordered_enumeration_ptr(
  attr,
  arrptr,
  ctx = tiledb_get_context()
)

Arguments

Value

A character vector with the enumeration (of length zero if none)

Check whether TileDB Attribute is variable-sized

Description

Check whether TileDB Attribute is variable-sized

Usage

tiledb_attribute_is_variable_sized(attr)

Arguments

Value

A boolean value indicating variable-size or not

Set a TileDB Attribute Enumeration Name

Description

Set a TileDB Attribute Enumeration Name

Usage

tiledb_attribute_set_enumeration_name(
  attr,
  enum_name,
  ctx = tiledb_get_context()
)

Arguments

Value

The modified TileDB Attribute object

Set the fill value for a TileDB Attribute

Description

Set the fill value for a TileDB Attribute

Usage

tiledb_attribute_set_fill_value(attr, value)

Arguments

Value

NULL is returned invisibly

Set the TileDB Attribute Nullable flags

Description

Set the TileDB Attribute Nullable flags

Usage

tiledb_attribute_set_nullable(attr, flag)

Arguments

Value

Nothing is returned

Creates a tiledb_config object

Description

Note that for actually setting persistent values, the (altered) config object needs to used to create (or update) the tiledb_ctx object. Similarly, to check whether values are set, one should use the config method of the of the tiledb_ctx object. Examples for this are ctx <- tiledb_ctx(limitTileDBCores()) to use updated configuration values to create a context object, and cfg <- config(ctx) to retrieve it.

Usage

tiledb_config(config = NA_character_)

Arguments

Value

tiledb_config object

Examples

cfg <- tiledb_config()
cfg["sm.tile_cache_size"]

# set tile cache size to custom value
cfg <- tiledb_config(c("sm.tile_cache_size" = "100"))
cfg["sm.tile_cache_size"]

An S4 class for a TileDB configuration

Description

An S4 class for a TileDB configuration

Slots

ptr

An external pointer to the underlying implementation

Return the 'AsBuilt' JSON string

Description

Return the 'AsBuilt' JSON string

Usage

tiledb_config_as_built_json()

Value

The JSON string containing 'AsBuilt' information

Examples

if (tiledb_version(TRUE) > "2.17") {
  txt <- tiledb::tiledb_config_as_built_json()
}
## now eg either one of
##   sapply(jsonlite::fromJSON(txt)$as_built$parameters$storage_backends, \(x) x[[1]])
##   sapply(RcppSimdJson::fparse(txt)$as_built$parameters$storage_backends, \(x) x[[1]])
## will return a named vector such as
##   c(azure = FALSE, gcs = FALSE, hdfs = FALSE, s3 = TRUE)

Display the 'AsBuilt' JSON string

Description

Display the 'AsBuilt' JSON string

Usage

tiledb_config_as_built_show()

Value

Nothing is returned but as a side-effect the 'AsBuilt' string is displayed

Load a saved tiledb_config file from disk

Description

Load a saved tiledb_config file from disk

Usage

tiledb_config_load(path)

Arguments

Examples

tmp <- tempfile()
cfg <- tiledb_config(c("sm.tile_cache_size" = "10"))
pth <- tiledb_config_save(cfg, tmp)
cfg <- tiledb_config_load(pth)
cfg["sm.tile_cache_size"]

Save a tiledb_config object ot a local text file

Description

Save a tiledb_config object ot a local text file

Usage

tiledb_config_save(config, path)

Arguments

Value

path to created config file

Examples

tmp <- tempfile()
cfg <- tiledb_config(c("sm.tile_cache_size" = "10"))
pth <- tiledb_config_save(cfg, tmp)

cat(readLines(pth), sep = "\n")

Unset a TileDB Config parameter to its default value

Description

Unset a TileDB Config parameter to its default value

Usage

tiledb_config_unset(config, param)

Arguments

Value

The modified TileDB Config object

Creates a tiledb_ctx object

Description

Creates a tiledb_ctx object

Usage

tiledb_ctx(config = NULL, cached = TRUE)

Arguments

Value

tiledb_ctx object

Examples

# default configuration
ctx <- tiledb_ctx()

# optionally set config parameters
ctx <- tiledb_ctx(c("sm.tile_cache_size" = "100"))

An S4 class for a TileDB context

Description

An S4 class for a TileDB context

Slots

ptr

An external pointer to the underlying implementation

Sets default context tags

Description

Sets default context tags

Usage

tiledb_ctx_set_default_tags(object)

Arguments

Sets a string:string "tag" on the Ctx

Description

Sets a string:string "tag" on the Ctx

Usage

tiledb_ctx_set_tag(object, key, value)

Arguments

Examples

ctx <- tiledb_ctx(c("sm.tile_cache_size" = "10"))
cfg <- tiledb_ctx_set_tag(ctx, "tag", "value")

Return context statistics as a JSON string

Description

Return context statistics as a JSON string

Usage

tiledb_ctx_stats(object = tiledb_get_context())

Arguments

Value

A JSON-formatted string with context statistics

Creates a tiledb_current_domain object

Description

Creates a tiledb_current_domain object

Usage

tiledb_current_domain(ctx = tiledb_get_context())

Arguments

Value

The tiledb_current_domain object

Examples

if (tiledb_version(TRUE) >= "2.25.0") {
  cd <- tiledb_current_domain()
}

An S4 class for a TileDB CurrentDomain object

Description

An S4 class for a TileDB CurrentDomain object

Slots

ptr

An external pointer to the underlying CurrentDomain object

Get a tiledb_ndrectangle from a tiledb_current_domain object

Description

Get a tiledb_ndrectangle from a tiledb_current_domain object

Usage

tiledb_current_domain_get_ndrectangle(cd)

Arguments

Value

The corresponding TileDB NDRectangle object

Get tiledb_current_domain data type as string

Description

Get tiledb_current_domain data type as string

Usage

tiledb_current_domain_get_type(cd)

Arguments

Value

The datatype (as string) of the tiledb_current_domain object

Test tiledb_current_domain object for being empty

Description

Test tiledb_current_domain object for being empty

Usage

tiledb_current_domain_is_empty(cd)

Arguments

Value

A boolean indicating whether the object is empty or not

Set a tiledb_ndrectangle in a tiledb_current_domain object

Description

Set a tiledb_ndrectangle in a tiledb_current_domain object

Usage

tiledb_current_domain_set_ndrectangle(cd, ndr)

Arguments

Value

The modifiled TileDB CurrendDomain object

Map from TileDB type to R datatype

Description

This function maps from the TileDB types to the (fewer) key datatypes in R. This can be lossy as TileDB integers range from (signed and unsigned) 8 to 64 bit whereas R only has (signed) 32 bit values. Similarly, R only has 64 bit doubles whereas TileDB has 32 and 64 bit floating point types. TileDB also has more character encodings, and the full range of (NumPy) date and time types.

Usage

tiledb_datatype_R_type(datatype)

Arguments

Value

A string describing the closest match for an R datatype

Delete a TileDB Array Metadata object given by key

Description

Delete a TileDB Array Metadata object given by key

Usage

tiledb_delete_metadata(arr, key)

Arguments

Value

A boolean indicating success

Constructs a tiledb_dim object

Description

Constructs a tiledb_dim object

Usage

tiledb_dim(
  name,
  domain,
  tile,
  type,
  filter_list = tiledb_filter_list(),
  ctx = tiledb_get_context()
)

Arguments

Value

A tiledb_dim object

Examples

tiledb_dim(name = "d1", domain = c(1L, 10L), tile = 5L, type = "INT32")

An S4 class for a TileDB dimension object

Description

An S4 class for a TileDB dimension object

Slots

ptr

An external pointer to the underlying implementation

Constructs a tiledb_domain object

Description

All tiledb_dim must be of the same TileDB type.

Usage

tiledb_domain(dims, ctx = tiledb_get_context())

Arguments

Value

tiledb_domain

Examples

dom <- tiledb_domain(dims = c(
  tiledb_dim("d1", c(1L, 100L), type = "INT32"),
  tiledb_dim("d2", c(1L, 50L), type = "INT32")
))

An S4 class for a TileDB domain

Description

An S4 class for a TileDB domain

Slots

ptr

External pointer to the underlying implementation

Returns a Dimension indicated by index for the given TileDB Domain

Description

Returns a Dimension indicated by index for the given TileDB Domain

Usage

tiledb_domain_get_dimension_from_index(domain, idx)

Arguments

Value

TileDB Dimension object

Returns a Dimension indicated by name for the given TileDB Domain

Description

Returns a Dimension indicated by name for the given TileDB Domain

Usage

tiledb_domain_get_dimension_from_name(domain, name)

Arguments

Value

TileDB Dimension object

Check a domain for a given dimension name

Description

Check a domain for a given dimension name

Usage

tiledb_domain_has_dimension(domain, name)

Arguments

Value

A boolean value indicating if the dimension exists in the domain

Return the error message for a given context

Description

Note that this function requires an actual error to have occurred.

Usage

tiledb_error_message(ctx = tiledb_get_context())

Arguments

Value

A character variable with the error message

Export from a TileDB Filestore to a character variable

Description

Export from a TileDB Filestore to a character variable

Usage

tiledb_filestore_buffer_export(
  filestore_uri,
  offset,
  bytes,
  ctx = tiledb_get_context()
)

Arguments

Value

A character variable containing the filestore content (subject to offset and bytes) is returned

Import size bytes from a string into a TileDB Filestore

Description

Import size bytes from a string into a TileDB Filestore

Usage

tiledb_filestore_buffer_import(
  filestore_uri,
  buf,
  bytes,
  ctx = tiledb_get_context()
)

Arguments

Value

A boolean is returned to indicate successful completion

Create an array schema from a given URI with schema

Description

Create an array schema from a given URI with schema

Usage

tiledb_filestore_schema_create(uri = NULL, ctx = tiledb_get_context())

Arguments

Value

An ArraySchema object corresponding to the supplied schema, or a default if missing

Return (uncompressed) TileDB Filestore size

Description

Return (uncompressed) TileDB Filestore size

Usage

tiledb_filestore_size(filestore_uri, ctx = tiledb_get_context())

Arguments

Value

A numeric with the size is returned

Export a file from a TileDB Filestore

Description

Export a file from a TileDB Filestore

Usage

tiledb_filestore_uri_export(
  file_uri,
  filestore_uri,
  ctx = tiledb_get_context()
)

Arguments

Value

A boolean is returned to indicate successful completion

Import a file into a TileDB Filestore

Description

Import a file into a TileDB Filestore

Usage

tiledb_filestore_uri_import(
  filestore_uri,
  file_uri,
  ctx = tiledb_get_context()
)

Arguments

Value

A boolean is returned to indicate successful completion

Constructs a tiledb_filter object

Description

Available filters:

• "NONE"

• "GZIP"

• "ZSTD"

• "LZ4"

• "RLE"

• "BZIP2"

• "DOUBLE_DELTA"

• "BIT_WIDTH_REDUCTION"

• "BITSHUFFLE"

• "BYTESHUFFLE"

• "POSITIVE_DELTA"

• "CHECKSUM_MD5"

• "CHECKSUM_SHA256"

• "DICTIONARY"

• "SCALE_FLOAT" (TileDB 2.11.0 or later)

• "FILTER_XOR" (TileDB 2.12.0 or later)

Usage

tiledb_filter(name = "NONE", ctx = tiledb_get_context())

Arguments

Details

Valid compression options vary depending on the filter used, consult the TileDB docs for more information.

Value

tiledb_filter object

Examples

tiledb_filter("ZSTD")

An S4 class for a TileDB filter

Description

An S4 class for a TileDB filter

Slots

ptr

External pointer to the underlying implementation

Returns the filter's option

Description

Returns the filter's option

Usage

tiledb_filter_get_option(object, option)

Arguments

Value

Integer value

Examples

c <- tiledb_filter("ZSTD")
tiledb_filter_set_option(c, "COMPRESSION_LEVEL", 5)
tiledb_filter_get_option(c, "COMPRESSION_LEVEL")

Constructs a tiledb_filter_list object

Description

Constructs a tiledb_filter_list object

Usage

tiledb_filter_list(filters = c(), ctx = tiledb_get_context())

Arguments

Value

tiledb_filter_list object

Examples

flt <- tiledb_filter("ZSTD")
tiledb_filter_set_option(flt, "COMPRESSION_LEVEL", 5)
filter_list <- tiledb_filter_list(c(flt))
filter_list

An S4 class for a TileDB filter list

Description

An S4 class for a TileDB filter list

Slots

ptr

An external pointer to the underlying implementation

Set the option for a filter

Description

Set the option for a filter

Usage

tiledb_filter_set_option(object, option, value)

Arguments

Value

The modified filter object is returned.

Examples

c <- tiledb_filter("ZSTD")
tiledb_filter_set_option(c, "COMPRESSION_LEVEL", 5)
tiledb_filter_get_option(c, "COMPRESSION_LEVEL")

Returns the type of the filter used

Description

Returns the type of the filter used

Usage

tiledb_filter_type(object)

Arguments

Value

TileDB filter type string

Examples

c <- tiledb_filter("ZSTD")
tiledb_filter_type(c)

Constructs a tiledb_fragment_info object

Description

Constructs a tiledb_fragment_info object

Usage

tiledb_fragment_info(uri, ctx = tiledb_get_context())

Arguments

Value

tiledb_fragment_info object

An S4 class for a TileDB fragment info object

Description

An S4 class for a TileDB fragment info object

Slots

ptr

An external pointer to the underlying implementation

Return if a fragment info index is dense

Description

Return if a fragment info index is dense

Usage

tiledb_fragment_info_dense(object, fid)

Arguments

Value

A logical value indicating if the fragment is dense

Dump the fragment info to console

Description

Dump the fragment info to console

Usage

tiledb_fragment_info_dump(object)

Arguments

Value

Nothing is returned, as a side effect the fragment info is displayed

Return a fragment info number of cells for a given fragment index

Description

Return a fragment info number of cells for a given fragment index

Usage

tiledb_fragment_info_get_cell_num(object, fid)

Arguments

Value

A numeric value with the number of cells

Return a fragment info non-empty domain from index

Description

TODO: Rework with type information

Usage

tiledb_fragment_info_get_non_empty_domain_index(object, fid, did, typestr)

Arguments

Value

A TileDB Domain object

Return a fragment info non-empty domain from name

Description

TODO: Rework with type information

Usage

tiledb_fragment_info_get_non_empty_domain_name(object, fid, dim_name, typestr)

Arguments

Value

A TileDB Domain object

Return a fragment info non-empty domain variable from index

Description

Return a fragment info non-empty domain variable from index

Usage

tiledb_fragment_info_get_non_empty_domain_var_index(object, fid, did)

Arguments

Value

A character vector with two elements

Return a fragment info non-empty domain variable from name

Description

Return a fragment info non-empty domain variable from name

Usage

tiledb_fragment_info_get_non_empty_domain_var_name(object, fid, dim_name)

Arguments

Value

A character vector with two elements

Return a fragment info number of fragments

Description

Return a fragment info number of fragments

Usage

tiledb_fragment_info_get_num(object)

Arguments

Value

A numeric variable with the number of fragments

Return a fragment info fragment size for a given fragment index

Description

Return a fragment info fragment size for a given fragment index

Usage

tiledb_fragment_info_get_size(object, fid)

Arguments

Value

A numeric variable with the number of fragments

Return a fragment info timestamp range for a given fragment index

Description

Return a fragment info timestamp range for a given fragment index

Usage

tiledb_fragment_info_get_timestamp_range(object, fid)

Arguments

Value

A Datetime vector with two elements for the range

Return the number of fragment info elements to be vacuumed

Description

Return the number of fragment info elements to be vacuumed

Usage

tiledb_fragment_info_get_to_vacuum_num(object)

Arguments

Value

A numeric value with the number of to be vacuumed fragments

Return fragment info URI of the to be vacuumed index

Description

Return fragment info URI of the to be vacuumed index

Usage

tiledb_fragment_info_get_to_vacuum_uri(object, fid)

Arguments

Value

A character variable with the URI of the be vacuumed index

Return fragment info number of unconsolidated metadata

Description

Return fragment info number of unconsolidated metadata

Usage

tiledb_fragment_info_get_unconsolidated_metadata_num(object)

Arguments

Value

A numeric value with the number of unconsolidated metadata

Return a fragment info version for a given fragment index

Description

Return a fragment info version for a given fragment index

Usage

tiledb_fragment_info_get_version(object, fid)

Arguments

Value

A integer value value with the version

Return if a fragment info index has consolidated metadata

Description

Return if a fragment info index has consolidated metadata

Usage

tiledb_fragment_info_has_consolidated_metadata(object, fid)

Arguments

Value

A logical value indicating consolidated metadata

Return if a fragment info index is sparse

Description

Return if a fragment info index is sparse

Usage

tiledb_fragment_info_sparse(object, fid)

Arguments

Value

A logical value indicating if the fragment is sparse

Return a fragment info URI given its index

Description

Return a fragment info URI given its index

Usage

tiledb_fragment_info_uri(object, fid)

Arguments

Value

A character variable with URI

Return all TileDB Array Metadata objects as a named list

Description

Return all TileDB Array Metadata objects as a named list

Usage

tiledb_get_all_metadata(arr)

Arguments

Value

A named list with all Metadata objects indexed by the given key

Retrieve a TileDB context object from the package cache

Description

Retrieve a TileDB context object from the package cache

Usage

tiledb_get_context()

Value

A TileDB context object

Return a TileDB Array Metadata object given by key

Description

Return a TileDB Array Metadata object given by key

Usage

tiledb_get_metadata(arr, key)

Arguments

Value

A object stored in the Metadata under the given key, or ‘NULL’ if none found.

Retrieve the cached status of the last finalized query

Description

This function accesses the status of the last query without requiring the query object.

Usage

tiledb_get_query_status()

Value

The status of the last query

Retrieve a TileDB VFS object from the package environment and cache

Description

Retrieve a TileDB VFS object from the package environment and cache

Usage

tiledb_get_vfs()

Value

A TileDB VFS object

Creates a 'tiledb_group' object

Description

Creates a 'tiledb_group' object

Usage

tiledb_group(
  uri,
  type = c("READ", "WRITE"),
  ctx = tiledb_get_context(),
  cfg = NULL
)

Arguments

Value

A 'group' object

An S4 class for a TileDB Group object

Description

An S4 class for a TileDB Group object

Slots

ptr

An external pointer to the underlying implementation

Add Member to TileDB Group

Description

Add Member to TileDB Group

Usage

tiledb_group_add_member(grp, uri, relative, name = NULL)

Arguments

Value

The TileDB Group object, invisibly

Close a TileDB Group

Description

Close a TileDB Group

Usage

tiledb_group_close(grp)

Arguments

Value

The TileDB Group object but closed for reading or writing

Create a TileDB Group at the given path

Description

Create a TileDB Group at the given path

Usage

tiledb_group_create(uri, ctx = tiledb_get_context())

Arguments

Value

The uri path, invisibly

Examples

## Not run: 
pth <- tempdir()
tiledb_group_create(pth)
tiledb_object_type(pth)

## End(Not run)

Deletes all written data from a 'tiledb_group' object

Description

The group must be opened in ‘MODIFY_EXCLUSIVE’ mode, otherwise the function will error out.

Usage

tiledb_group_delete(grp, uri, recursive = FALSE)

Arguments

Value

Nothing is returned, the function is invoked for the side-effect of group data removal.

Deletes Metadata from a TileDB Group

Description

Deletes Metadata from a TileDB Group

Usage

tiledb_group_delete_metadata(grp, key)

Arguments

Value

The TileDB Group object, invisibly

Return all Metadata from a TileDB Group

Description

Return all Metadata from a TileDB Group

Usage

tiledb_group_get_all_metadata(grp)

Arguments

Value

A named List with all Metadata objects index

Get a TileDB Config from a TileDB Group

Description

Get a TileDB Config from a TileDB Group

Usage

tiledb_group_get_config(grp)

Arguments

Value

The TileDB Config object of the TileDB Group object

Accesses Metadata from a TileDB Group

Description

Accesses Metadata from a TileDB Group

Usage

tiledb_group_get_metadata(grp, key)

Arguments

Value

The requested object, or NULL is not found

Accesses Metadata by Index from a TileDB Group

Description

Accesses Metadata by Index from a TileDB Group

Usage

tiledb_group_get_metadata_from_index(grp, idx)

Arguments

Value

The requested object, or NULL is not found

Checks for Metadata in a TileDB Group

Description

Checks for Metadata in a TileDB Group

Usage

tiledb_group_has_metadata(grp, key)

Arguments

Value

A boolean value indicating with the object is present

Test if TileDB Group is open

Description

Test if TileDB Group is open

Usage

tiledb_group_is_open(grp)

Arguments

Value

A boolean indicating whether the TileDB Group object is open

Test if a Named Group is Using a Relative URI

Description

Test if a Named Group is Using a Relative URI

Usage

tiledb_group_is_relative(grp, name)

Arguments

Value

A boolean indicating whether the group uses a relative URI or not

Get a Member (Description) by Index from TileDB Group

Description

This function returns a three-element character vector with the member object translated to character, uri, and optional name.

Usage

tiledb_group_member(grp, idx)

Arguments

Value

A character vector with three elements: the member type, its uri, and name (or "" if the member is unnamed).

Get Member Count from TileDB Group

Description

Get Member Count from TileDB Group

Usage

tiledb_group_member_count(grp)

Arguments

Value

The Count of Members in the TileDB Group object

Dump the TileDB Group to String

Description

Dump the TileDB Group to String

Usage

tiledb_group_member_dump(grp, recursive = FALSE)

Arguments

Value

A character string

Returns Number of Metadata Objects a TileDB Group

Description

Returns Number of Metadata Objects a TileDB Group

Usage

tiledb_group_metadata_num(grp)

Arguments

Value

A numeric value with the number of metadata objects

Open a TileDB Group

Description

Open a TileDB Group

Usage

tiledb_group_open(grp, type = c("READ", "WRITE", "MODIFY_EXCLUSIVE"))

Arguments

Value

The TileDB Group object but opened for reading or writing

Write Metadata to a TileDB Group

Description

Write Metadata to a TileDB Group

Usage

tiledb_group_put_metadata(grp, key, val)

Arguments

Value

On success boolean ‘TRUE’ is returned

Return a TileDB Group query type

Description

Return a TileDB Group query type

Usage

tiledb_group_query_type(grp)

Arguments

Value

A character value with the query type i.e. one of “READ” or “WRITE”.

Remove Member from TileDB Group

Description

Remove Member from TileDB Group

Usage

tiledb_group_remove_member(grp, uri)

Arguments

Value

The TileDB Group object, invisibly

Set a TileDB Config for a TileDB Group

Description

Set a TileDB Config for a TileDB Group

Usage

tiledb_group_set_config(grp, cfg)

Arguments

Value

The TileDB Group object with added Config

Return a TileDB Group URI

Description

Return a TileDB Group URI

Usage

tiledb_group_uri(grp)

Arguments

Value

A character value with the URI

Test if TileDB Array has Metadata

Description

Test if TileDB Array has Metadata

Usage

tiledb_has_metadata(arr, key)

Arguments

Value

A logical value indicating if the given key exists in the metdata of the given array

Query if a TileDB backend is supported

Description

The scheme corresponds to the URI scheme for TileDB resouces.

Usage

tiledb_is_supported_fs(scheme, object = tiledb_get_context())

Arguments

Details

Ex:

• ⁠{file}:///path/to/file⁠

• ⁠{hdfs}:///path/to/file⁠

• ⁠{s3}://hostname:port/path/to/file⁠

Value

TRUE if tiledb backend is supported, FALSE otherwise

Examples

tiledb_is_supported_fs("file")
tiledb_is_supported_fs("s3")

Return the number of dimensions associated with the tiledb_array_schema

Description

Return the number of dimensions associated with the tiledb_array_schema

Usage

## S4 method for signature 'tiledb_array_schema'
tiledb_ndim(object)

Arguments

Value

integer number of dimensions

Examples

dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 10L), type = "INT32")))
sch <- tiledb_array_schema(dom, attrs = c(
  tiledb_attr("a1", type = "INT32"),
  tiledb_attr("a2", type = "FLOAT64")
))
tiledb_ndim(sch)

Returns the number of dimensions for a tiledb domain object

Description

Returns the number of dimensions for a tiledb domain object

Usage

## S4 method for signature 'tiledb_dim'
tiledb_ndim(object)

Arguments

Value

An integer with the number of dimensions.

Examples

d1 <- tiledb_dim("d1", c(1L, 10L), 10L)
tiledb_ndim(d1)

Returns the number of dimensions of the tiledb_domain

Description

Returns the number of dimensions of the tiledb_domain

Usage

## S4 method for signature 'tiledb_domain'
tiledb_ndim(object)

Arguments

Value

integer number of dimensions

Examples

dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(0.5, 100.0), type = "FLOAT64")))
tiledb_ndim(dom)
dom <- tiledb_domain(dims = c(
  tiledb_dim("d1", c(0.5, 100.0), type = "FLOAT64"),
  tiledb_dim("d2", c(0.5, 100.0), type = "FLOAT64")
))
tiledb_ndim(dom)

Creates a tiledb_ndrectangle object

Description

Creates a tiledb_ndrectangle object

Usage

tiledb_ndrectangle(dom, ctx = tiledb_get_context())

Arguments

Value

The tiledb_ndrectangle object

Examples

if (tiledb_version(TRUE) >= "2.25.0") {
  dom <- tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32"))
  ndr <- tiledb_ndrectangle(dom)
}

An S4 class for a TileDB NDRectangle object

Description

An S4 class for a TileDB NDRectangle object

Slots

ptr

An external pointer to the underlying NDRectangle object

Get the datatype of a named tiledb_ndrectangle dimension

Description

Get the datatype of a named tiledb_ndrectangle dimension

Usage

tiledb_ndrectangle_datatype(ndr, dimname)

Arguments

Value

The tiledb_ndrectangle dimension datatype as a character

Examples

if (tiledb_version(TRUE) >= "2.26.0") {
  dom <- tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32"))
  ndr <- tiledb_ndrectangle(dom)
  tiledb_ndrectangle_datatype(ndr, "d1")
}

Get the datatype of a tiledb_ndrectangle dimension by index

Description

Get the datatype of a tiledb_ndrectangle dimension by index

Usage

tiledb_ndrectangle_datatype_by_ind(ndr, dim)

Arguments

Value

The tiledb_ndrectangle dimension datatype as a character

Examples

if (tiledb_version(TRUE) >= "2.26.0") {
  dom <- tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32"))
  ndr <- tiledb_ndrectangle(dom)
  tiledb_ndrectangle_datatype_by_ind(ndr, 0)
}

Get the number of dimensions for tiledb_ndrectangle object

Description

Get the number of dimensions for tiledb_ndrectangle object

Usage

tiledb_ndrectangle_dim_num(ndr)

Arguments

Value

The number of dimentiones for the tiledb_ndrectangle

Examples

if (tiledb_version(TRUE) >= "2.26.0") {
  dom <- tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32"))
  ndr <- tiledb_ndrectangle(dom)
  tiledb_ndrectangle_dim_num(ndr)
}

Get a range from a tiledb_ndrectangle object

Description

Get a range from a tiledb_ndrectangle object

Usage

tiledb_ndrectangle_get_range(ndr, dimname)

Arguments

Value

The tiledb_ndrectangle range as a two-element vector

Examples

if (tiledb_version(TRUE) >= "2.26.0") {
  dom <- tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32"))
  ndr <- tiledb_ndrectangle(dom)
  ndr <- tiledb_ndrectangle_set_range(ndr, "d1", 50, 500)
  tiledb_ndrectangle_get_range(ndr, "d1")
}

Set a range on a tiledb_ndrectangle object

Description

Set a range on a tiledb_ndrectangle object

Usage

tiledb_ndrectangle_set_range(ndr, dimname, start, end)

Arguments

Value

The modified tiledb_ndrectangle object

Start and end values have to be of the same data type as the type of the selected dimension. The set of allowed type includes the different integer types as well as string dimensions.

Examples

if (tiledb_version(TRUE) >= "2.26.0") {
  dom <- tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32"))
  ndr <- tiledb_ndrectangle(dom)
  ndr <- tiledb_ndrectangle_set_range(ndr, "d1", 50, 500)
}

Return count of TileDB Array Metadata objects

Description

Return count of TileDB Array Metadata objects

Usage

tiledb_num_metadata(arr)

Arguments

Value

A integer variable with the number of Metadata objects

List TileDB resources at a given root URI path

Description

List TileDB resources at a given root URI path

Usage

tiledb_object_ls(uri, filter = NULL, ctx = tiledb_get_context())

Arguments

Value

a dataframe with object type, object uri string columns

Move a TileDB resource to new uri path

Description

Raises an error if either uri is invalid, or the old uri resource is not a tiledb object

Usage

tiledb_object_mv(old_uri, new_uri, ctx = tiledb_get_context())

Arguments

Value

new uri of moved tiledb resource

Removes a TileDB resource

Description

Raises an error if the uri is invalid, or the uri resource is not a tiledb object

Usage

tiledb_object_rm(uri, ctx = tiledb_get_context())

Arguments

Value

uri of removed TileDB resource

Return the TileDB object type string of a TileDB resource

Description

Object types:

• "ARRAY", dense or sparse TileDB array

• "GROUP", TileDB group

• '"INVALID"“, not a TileDB resource

Usage

tiledb_object_type(uri, ctx = tiledb_get_context())

Arguments

Value

TileDB object type string

Recursively discover TileDB resources at a given root URI path

Description

Recursively discover TileDB resources at a given root URI path

Usage

tiledb_object_walk(
  uri,
  order = c("PREORDER", "POSTORDER"),
  ctx = tiledb_get_context()
)

Arguments

Value

a dataframe with object type, object uri string columns

Store an object in TileDB Array Metadata under given key

Description

Store an object in TileDB Array Metadata under given key

Usage

tiledb_put_metadata(arr, key, val)

Arguments

Value

A boolean value indicating success

Creates a 'tiledb_query' object

Description

Creates a 'tiledb_query' object

Usage

tiledb_query(
  array,
  type = if (tiledb_version(TRUE) >= "2.12.0") {
     c("READ", "WRITE", "DELETE",
    "MODIFY_EXCLUSIVE")
 } else {
     c("READ", "WRITE")
 },
  ctx = tiledb_get_context()
)

Arguments

Value

'tiledb_query' object

An S4 class for a TileDB Query object

Description

An S4 class for a TileDB Query object

Slots

ptr

An external pointer to the underlying implementation

Set a range for a given query

Description

Set a range for a given query

Usage

tiledb_query_add_range(query, schema, attr, lowval, highval, stride = NULL)

Arguments

Value

The query object, invisibly

Set a range for a given query, also supplying type

Description

Set a range for a given query, also supplying type

Usage

tiledb_query_add_range_with_type(
  query,
  idx,
  datatype,
  lowval,
  highval,
  stride = NULL
)

Arguments

Value

The query object, invisibly

Allocate a Query buffer for reading a character attribute

Description

Allocate a Query buffer for reading a character attribute

Usage

tiledb_query_alloc_buffer_ptr_char(sizeoffsets, sizedata, nullable = FALSE)

Arguments

Value

An external pointer to the allocated buffer object

Run an aggregate oprtation on the given query attribute

Description

Run an aggregate oprtation on the given query attribute

Usage

tiledb_query_apply_aggregate(
  query,
  attrname,
  operation = c("Count", "NullCount", "Min", "Max", "Mean", "Sum"),
  nullable = TRUE
)

Arguments

Value

The value of the aggregation

Allocate a Query buffer for a given type

Description

This function allocates a query buffer for the given data type.

Usage

tiledb_query_buffer_alloc_ptr(
  query,
  datatype,
  ncells,
  nullable = FALSE,
  varnum = 1
)

Arguments

Value

An external pointer to the allocated buffer object

Creates a 'tiledb_query_condition' object

Description

Creates a 'tiledb_query_condition' object

Usage

tiledb_query_condition(ctx = tiledb_get_context())

Arguments

Value

A 'tiledb_query_condition' object

An S4 class for a TileDB QueryCondition object

Description

An S4 class for a TileDB QueryCondition object

Slots

ptr

An external pointer to the underlying implementation

init

A logical variable tracking if the query condition object has been initialized

Combine two 'tiledb_query_condition' objects

Description

Combines two query condition object using a relatiional operator. Support for operator 'AND' is generally available, the 'OR' operator is available if TileDB 2.10 or newer is used.

Usage

tiledb_query_condition_combine(lhs, rhs, op)

Arguments

Value

The combined 'tiledb_query_condition' object

Create a query condition for vector 'IN' and 'NOT_IN' operations

Description

Uses ‘IN’ and ‘NOT_IN’ operators on given attribute

Usage

tiledb_query_condition_create(
  name,
  values,
  op = "IN",
  ctx = tiledb_get_context()
)

Arguments

Value

A query condition object is returned

Initialize a 'tiledb_query_condition' object

Description

Initializes (and possibly allocates) a query condition object using a triplet of attribute name, comparison value, and operator. Six types of conditions are supported, they all take a single scalar comparison argument and attribute to compare against. At present only integer or numeric attribute comparisons are implemented.

Usage

tiledb_query_condition_init(
  attr,
  value,
  dtype,
  op,
  qc = tiledb_query_condition()
)

Arguments

Value

The initialized 'tiledb_query_condition' object

Enable use of enumeration in query condition

Description

Set a boolean toggle to signal use of enumeration in query condtion (TileDB 2.17 or later)

Usage

tiledb_query_condition_set_use_enumeration(
  qc,
  use_enum,
  ctx = tiledb_get_context()
)

Arguments

Value

Nothing is retuned, the function is invoked for the side effect

Allocate and populate a Query buffer for a given object of a given data type.

Description

This function allocates a query buffer for the given data object of the given type and assigns the object content to the buffer.

Usage

tiledb_query_create_buffer_ptr(query, datatype, object)

Arguments

Value

An external pointer to the allocated buffer object

Allocate and populate a Query buffer for writing the given char vector

Description

Allocate and populate a Query buffer for writing the given char vector

Usage

tiledb_query_create_buffer_ptr_char(query, varvec)

Arguments

Value

An external pointer to the allocated buffer object

Return query context object

Description

Return query context object

Usage

tiledb_query_ctx(query)

Arguments

Value

A TileDB Context object retrieved from the query

Export Query Buffer to Pair of Arrow IO Pointers

Description

This function exports the named buffer from a ‘READ’ query to two Arrow C pointers.

Usage

tiledb_query_export_buffer(query, name, ctx = tiledb_get_context())

Arguments

Value

A nanoarrow object (which is an external pointer to an Arrow Array with the Arrow Schema stored as the external pointer tag) classed as an S3 object

Finalize TileDB Query

Description

Finalize TileDB Query

Usage

tiledb_query_finalize(query)

Arguments

Value

A character value, either 'READ' or 'WRITE'

Retrieve content from a Query character buffer

Description

This function uses a query buffer for a character attribute or dimension and returns its content.

Usage

tiledb_query_get_buffer_char(bufptr, sizeoffsets = 0, sizestring = 0)

Arguments

Value

An R object as resulting from the query

Retrieve content from a Query buffer

Description

This function uses a query buffer and returns its content.

Usage

tiledb_query_get_buffer_ptr(bufptr)

Arguments

Value

An R object as resulting from the query

Retrieve the estimated result size for a query and attribute

Description

When reading from sparse arrays, one cannot know beforehand how big the result will be (unless one actually executes the query). This function offers a way to get the estimated result size for the given attribute. As TileDB does not actually execute the query, getting the estimated result is very fast.

Usage

tiledb_query_get_est_result_size(query, name)

Arguments

Value

An estimate of the query result size

Retrieve the estimated result size for a query and variable-sized attribute

Description

When reading variable-length attributes from either dense or sparse arrays, one cannot know beforehand how big the result will be (unless one actually executes the query). This function offers a way to get the estimated result size for the given attribute. As TileDB does not actually execute the query, getting the estimated result is very fast.

Usage

tiledb_query_get_est_result_size_var(query, name)

Arguments

Value

An estimate of the query result size

Retrieve the Number of Fragments for Query

Description

This function is only applicable to ‘WRITE’ queries.

Usage

tiledb_query_get_fragment_num(query)

Arguments

Value

An integer with the number of fragments for the given query

Retrieve the timestamp range for a given Query Fragment

Description

This function is only applicable to ‘WRITE’ queries. The time resolution in TileDB is millseconds since the epoch so an R Datetime vector is returned.

Usage

tiledb_query_get_fragment_timestamp_range(query, idx)

Arguments

Value

A two-element datetime vector with the start and end time of the fragment write.

Retrieve the URI for a given Query Fragment

Description

This function is only applicable to ‘WRITE’ queries.

Usage

tiledb_query_get_fragment_uri(query, idx)

Arguments

Value

An character value with the fragment URI

Get TileDB Query layout

Description

Get TileDB Query layout

Usage

tiledb_query_get_layout(query)

Arguments

Value

The TileDB Query layout as a string

Retrieve the query range for a query dimension and range index

Description

Retrieve the query range for a query dimension and range index

Usage

tiledb_query_get_range(query, dimidx, rngidx)

Arguments

Value

An integer vector with elements start, end and stride for the query range for the given dimension and range index

Retrieve the number of ranges for a query dimension

Description

Retrieve the number of ranges for a query dimension

Usage

tiledb_query_get_range_num(query, idx)

Arguments

Value

An integer with the number of query range for the given dimensions

Retrieve the query range for a variable-sized query dimension and range index

Description

Retrieve the query range for a variable-sized query dimension and range index

Usage

tiledb_query_get_range_var(query, dimidx, rngidx)

Arguments

Value

An string vector with elements start and end for the query range for the given dimension and range index

Import to Query Buffer from Pair of Arrow IO Pointers

Description

This function imports to the named buffer for a ‘WRITE’ query from two Arrow exerternal pointers.

Usage

tiledb_query_import_buffer(
  query,
  name,
  nanoarrowptr,
  ctx = tiledb_get_context()
)

Arguments

Value

The update Query external pointer is returned

Get TileDB Query result buffer element size

Description

The underlying library functions returns a pair of values as a vector of length two. The first number is the number of element offsets for variable size attributes (and always zero for fixed-sized attributes and coordinates). The second is the number of elements in the data buffer. For variable-sized attributes the first number is the number of cells read (and hence the number of offsets), the second number is the number of elements in the data buffer.

Usage

tiledb_query_result_buffer_elements(query, attr)

Arguments

Details

As this function was first made available when only a scalar (corresponding to the second result) was returned, we still return that value.

Value

A integer with the number of elements in the results buffer for the given attribute

See Also

tiledb_query_result_buffer_elements_vec

Get TileDB Query result buffer element size pair as vector

Description

The underlying library functions returns a pair of values as a vector of length two. The first number is the number of element offsets for variable size attributes (and always zero for fixed-sized attributes and coordinates). The second is the number of elements in the data buffer. For variable-sized attributes the first number is the number of cells read (and hence the number of offsets), the second number is the number of elements in the data buffer. In the case of a nullable attribute, a third element is returned with the size of the validity buffer.

Usage

tiledb_query_result_buffer_elements_vec(query, attr, nullable = FALSE)

Arguments

Value

A vector with the number of elements in the offsets buffer (and zero for fixed-size attribute or dimensions), the number elements in the results buffer for the given attribute, and (if nullable) a third element with the validity buffer size.

See Also

tiledb_query_result_buffer_elements

Set TileDB Query buffer

Description

This function allocates query buffers directly from R vectors in case the types match: integer, double, logical. For more general types see tiledb_query_buffer_alloc_ptr and tiledb_query_buffer_assign_ptr

Usage

tiledb_query_set_buffer(query, attr, buffer)

Arguments