Ctx

tiledb_ctx-class

An S4 class for a TileDB context

tiledb_ctx()

Creates a tiledb_ctx object

tiledb_ctx_set_default_tags()

Sets default context tags

tiledb_ctx_set_tag()

Sets a string:string "tag" on the Ctx

tiledb_is_supported_fs()

Query if a TileDB backend is supported

tiledb_get_context()

Retrieve a TileDB context object from the package cache

tiledb_set_context()

Store a TileDB context object in the package cache

config(<tiledb_ctx>)

Retrieve the tiledb_config object from the tiledb_ctx

Config

tiledb_config-class

An S4 class for a TileDB configuration

tiledb_config()

Creates a tiledb_config object

tiledb_config_load()

Load a saved tiledb_config file from disk

tiledb_config_save()

Save a tiledb_config object ot a local text file

tiledb_config_unset()

Unset a TileDB Config parameter to its default value

as.vector(<tiledb_config>)

Convert a tiledb_config object to a R vector

as.data.frame(<tiledb_config>)

Convert a tiledb_config object to a R data.frame

show(<tiledb_config>)

Prints the config object to STDOUT

`[`(<tiledb_config>,<ANY>)

Gets a config parameter value

`[<-`(<tiledb_config>,<ANY>,<ANY>,<ANY>)

Sets a config parameter value

Array

tiledb_array_create()

Creates a new TileDB array given an input schema.

tiledb_dense-class

An S4 class for a TileDB dense array

tiledb_dense()

Constructs a tiledb_dense object backed by a persisted tiledb array uri

tiledb_sparse-class

An S4 class for a TileDB sparse array

tiledb_sparse()

Constructs a tiledb_sparse object backed by a persisted tiledb array uri

`attrs<-`(<tiledb_array>)

Selects attributes for the given TileDB array

attrs(<tiledb_array>,<ANY>)

Retrieve attributes from tiledb_array object

attrs(<tiledb_array_schema>,<ANY>)

Returns a list of all tiledb_attr objects associated with the tiledb_array_schema

attrs(<tiledb_array_schema>,<character>)

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

attrs(<tiledb_array_schema>,<numeric>)

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

cell_order(<tiledb_array_schema>)

Returns the cell layout string associated with the tiledb_array_schema

`datetimes_as_int64<-`()

Set datetimes_as_int64 toggle

datetimes_as_int64()

Retrieve datetimes_as_int64 toggle

dim(<tiledb_array_schema>)

Retrieve the dimension (domain extent) of the domain

dimensions(<tiledb_array_schema>)

Returns a list of tiledb_dim objects associated with the tiledb_array_schema

domain(<tiledb_array_schema>)

Returns the tiledb_domain object associated with a given tiledb_array_schema

`extended<-`()

Set data.frame extended return columns toggle

extended()

Retrieve data.frame extended returns columns toggle

filter_list(<tiledb_array_schema>)

Returns the offsets and coordinate filter_lists associated with the tiledb_array_schema

is.sparse(<tiledb_array_schema>)

Returns TRUE if the tiledb_array_schema is sparse, else FALSE

`query_layout<-`()

Set query_layout return values for the array

query_layout()

Retrieve query_layout values for the array

`return.data.frame<-`(<tiledb_array>)

Set data.frame return toggle

return.data.frame(<tiledb_array>)

Retrieve data.frame return toggle

schema(<tiledb_array>)

Return a schema from a tiledb_array object

`selected_ranges<-`()

Set selected_ranges return values for the array

selected_ranges()

Retrieve selected_ranges values for the array

show(<tiledb_array>)

Prints a tiledb_array object

show(<tiledb_array_schema>)

Prints an array schema object

`[`(<tiledb_array>,<ANY>)

Returns a TileDB array, allowing for specific subset ranges.

`[<-`(<tiledb_array>,<ANY>,<ANY>,<ANY>)

Sets a tiledb array value or value range

tile_order(<tiledb_array_schema>)

Returns the tile layout string associated with the tiledb_array_schema

tiledb_array-class

An S4 class for a TileDB Array

tiledb_array()

Constructs a tiledb_array object backed by a persisted tiledb array uri

tiledb_array_close()

Close a TileDB Array

tiledb_array_get_non_empty_domain_from_index()

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

tiledb_array_get_non_empty_domain_from_name()

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

tiledb_array_is_heterogeneous()

Check for Heterogeneous Domain

tiledb_array_is_homogeneous()

Check for Homogeneous Domain

tiledb_array_open()

Open a TileDB Array

tiledb_array_open_at()

Open a TileDB Array at Timestamp

tiledb_array_schema-class

An S4 class for the TileDB array schema

tiledb_array_schema()

Constructs a tiledb_array_schema object

check() tiledb_array_schema_check()

Check the schema for correctness

allows_dups() tiledb_array_schema_get_allows_dups()

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

capacity() tiledb_array_schema_get_capacity()

Retrieve schema capacity (for sparse fragments)

`allows_dups<-`() tiledb_array_schema_set_allows_dups()

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

`capacity<-`() tiledb_array_schema_set_capacity()

Sets the schema capacity (for sparse fragments)

tiledb_array_schema_set_coords_filter_list()

Set a Filter List for Coordinate of a TileDB Schema

tiledb_array_schema_set_offsets_filter_list()

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

tiledb_ndim(<tiledb_array_schema>)

Return the number of dimensions associated with the tiledb_array_schema

`attrs<-`()

Selects attributes for the given TileDB array

attrs(<tiledb_dense>,<ANY>)

Retrieve attributes from tiledb_dense object

is.sparse(<tiledb_dense>)

Returns true is if the array or array_schema is sparse

`return.data.frame<-`()

Set data.frame return toggle

return.data.frame()

Retrieve data.frame return toggle

schema(<tiledb_dense>)

Returns the tiledb_dense array tiledb_schema object

show(<tiledb_dense>)

Prints a tiledb_dense array object

`[`(<tiledb_dense>,<ANY>)

Gets a dense array value

`[<-`(<tiledb_dense>,<ANY>,<ANY>,<ANY>)

Sets a dense array value

`attrs<-`(<tiledb_sparse>)

Selects attributes for the given TileDB array

attrs(<tiledb_sparse>,<ANY>)

Retrieve attributes from tiledb_sparse object

is.sparse(<tiledb_sparse>)

Check if object is sparse

`return.data.frame<-`(<tiledb_sparse>)

Set data.frame return toggle

return.data.frame(<tiledb_sparse>)

Retrieve data.frame return toggle

schema(<tiledb_sparse>)

Return a schema from a sparse array

show(<tiledb_sparse>)

Prints a tiledb_sparse array object

`[`(<tiledb_sparse>,<ANY>)

Gets a sparse array value

`[<-`(<tiledb_sparse>,<ANY>,<ANY>,<ANY>)

Sets a sparse array value

tiledb_subarray()

Query a array using a subarray vector

ArraySchema

tiledb_array_schema-class

An S4 class for the TileDB array schema

tiledb_array_schema()

Constructs a tiledb_array_schema object

check() tiledb_array_schema_check()

Check the schema for correctness

allows_dups() tiledb_array_schema_get_allows_dups()

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

capacity() tiledb_array_schema_get_capacity()

Retrieve schema capacity (for sparse fragments)

`allows_dups<-`() tiledb_array_schema_set_allows_dups()

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

`capacity<-`() tiledb_array_schema_set_capacity()

Sets the schema capacity (for sparse fragments)

tiledb_array_schema_set_coords_filter_list()

Set a Filter List for Coordinate of a TileDB Schema

tiledb_array_schema_set_offsets_filter_list()

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

r_to_tiledb_type()

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

tiledb_schema_get_names()

Get all Dimension and Attribute Names

tiledb_schema_get_types()

Get all Dimension and Attribute Types

attrs(<tiledb_array_schema>,<character>)

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

schema(<character>)

Return a schema from a URI character value

Attribute

tiledb_attr-class

An S4 class for a TileDB attribute

tiledb_attr()

Contructs a tiledb_attr object

tiledb_attribute_get_cell_size()

Get the TileDB Attribute cell size

cell_val_num() tiledb_attribute_get_cell_val_num()

Return the number of scalar values per attribute cell

tiledb_attribute_get_fill_value()

Get the fill value for a TileDB Attribute

tiledb_attribute_get_nullable()

Get the TileDB Attribute Nullable flag value

tiledb_attribute_is_variable_sized()

Check whether TileDB Attribute is variable-sized

`cell_val_num<-`() tiledb_attribute_set_cell_val_num()

Set the number of scalar values per attribute cell

tiledb_attribute_set_fill_value()

Set the fill value for a TileDB Attribute

tiledb_attribute_set_nullable()

Set the TileDB Attribute Nullable flags

`attrs<-`(<tiledb_array>)

Selects attributes for the given TileDB array

`attrs<-`()

Selects attributes for the given TileDB array

`attrs<-`(<tiledb_sparse>)

Selects attributes for the given TileDB array

attrs(<tiledb_array>,<ANY>)

Retrieve attributes from tiledb_array object

attrs(<tiledb_array_schema>,<ANY>)

Returns a list of all tiledb_attr objects associated with the tiledb_array_schema

attrs(<tiledb_array_schema>,<character>)

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

attrs(<tiledb_array_schema>,<numeric>)

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

attrs(<tiledb_dense>,<ANY>)

Retrieve attributes from tiledb_dense object

attrs(<tiledb_sparse>,<ANY>)

Retrieve attributes from tiledb_sparse object

domain() dimensions() attrs() cell_order() tile_order() filter_list() `filter_list<-`() is.sparse() tiledb_ndim() name() datatype() config() schema() tile() is.integral() nfilters()

Generic Methods

datatype(<tiledb_attr>)

Return the tiledb_attr datatype

`filter_list<-`(<tiledb_attr>)

Sets the TileDB Filter List for the TileDB Attribute object

filter_list(<tiledb_attr>)

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

name(<tiledb_attr>)

Return the tiledb_attr name

show(<tiledb_attr>)

Prints an attribute object

has_attribute()

Check a schema for a given attribute name

Filter

tiledb_filter-class

An S4 class for a TileDB filter

tiledb_filter()

Constructs a tiledb_filter object

tiledb_filter_get_option()

Returns the filter's option

tiledb_filter_list-class

An S4 class for a TileDB filter list

tiledb_filter_list()

Constructs a tiledb_filter_list object

max_chunk_size() tiledb_filter_list_get_max_chunk_size()

Returns the filter_list's max_chunk_size

set_max_chunk_size() tiledb_filter_list_set_max_chunk_size()

Set the filter_list's max_chunk_size

tiledb_filter_set_option()

Set the filter's option

tiledb_filter_type()

Returns the type of the filter used

`filter_list<-`(<tiledb_attr>)

Sets the TileDB Filter List for the TileDB Attribute object

`filter_list<-`(<tiledb_dim>)

Sets the TileDB Filter List for the TileDB Dimension object

filter_list(<tiledb_array_schema>)

Returns the offsets and coordinate filter_lists associated with the tiledb_array_schema

filter_list(<tiledb_attr>)

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

filter_list(<tiledb_dim>)

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

domain() dimensions() attrs() cell_order() tile_order() filter_list() `filter_list<-`() is.sparse() tiledb_ndim() name() datatype() config() schema() tile() is.integral() nfilters()

Generic Methods

FilterList

nfilters(<tiledb_filter_list>)

Returns the filter_list's number of filters

`[`(<tiledb_filter_list>,<ANY>)

Returns the filter at given index

tiledb_filter_list-class

An S4 class for a TileDB filter list

tiledb_filter_list()

Constructs a tiledb_filter_list object

max_chunk_size() tiledb_filter_list_get_max_chunk_size()

Returns the filter_list's max_chunk_size

set_max_chunk_size() tiledb_filter_list_set_max_chunk_size()

Set the filter_list's max_chunk_size

`filter_list<-`(<tiledb_attr>)

Sets the TileDB Filter List for the TileDB Attribute object

`filter_list<-`(<tiledb_dim>)

Sets the TileDB Filter List for the TileDB Dimension object

filter_list(<tiledb_array_schema>)

Returns the offsets and coordinate filter_lists associated with the tiledb_array_schema

filter_list(<tiledb_attr>)

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

filter_list(<tiledb_dim>)

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

domain() dimensions() attrs() cell_order() tile_order() filter_list() `filter_list<-`() is.sparse() tiledb_ndim() name() datatype() config() schema() tile() is.integral() nfilters()

Generic Methods

Domain

tiledb_domain-class

An S4 class for a TileDB domain

tiledb_domain()

Constructs a tiledb_domain object

tiledb_domain_get_dimension_from_index()

Returns a Dimension indicated by index for the given TileDB Domain

tiledb_domain_get_dimension_from_name()

Returns a Dimension indicated by name for the given TileDB Domain

tiledb_domain_has_dimension()

Check a domain for a given dimension name

domain() dimensions() attrs() cell_order() tile_order() filter_list() `filter_list<-`() is.sparse() tiledb_ndim() name() datatype() config() schema() tile() is.integral() nfilters()

Generic Methods

tiledb_ndim(<tiledb_array_schema>)

Return the number of dimensions associated with the tiledb_array_schema

tiledb_ndim(<tiledb_dim>)

Returns the number of dimensions for a tiledb domain object

tiledb_ndim(<tiledb_domain>)

Returns the number of dimensions of the tiledb_domain

datatype(<tiledb_domain>)

Returns the tiledb_domain TileDB type string

dimensions(<tiledb_domain>)

Returns a list of the tiledb_domain dimension objects

is.integral(<tiledb_domain>)

Returns TRUE is tiledb_domain is an integral (integer) domain

show(<tiledb_domain>)

Prints an domain object

Dim

tiledb_dim-class

An S4 class for a TileDB dimension object

tiledb_dim()

Contructs a tiledb_dim object

dim(<tiledb_array_schema>)

Retrieve the dimension (domain extent) of the domain

dim(<tiledb_dim>)

Retrieves the dimension of the tiledb_dim domain

dim(<tiledb_domain>)

Retrieve the dimension (domain extent) of the domain

dimensions(<tiledb_array_schema>)

Returns a list of tiledb_dim objects associated with the tiledb_array_schema

dimensions(<tiledb_domain>)

Returns a list of the tiledb_domain dimension objects

domain() dimensions() attrs() cell_order() tile_order() filter_list() `filter_list<-`() is.sparse() tiledb_ndim() name() datatype() config() schema() tile() is.integral() nfilters()

Generic Methods

datatype(<tiledb_dim>)

Return the tiledb_dim datatype

domain(<tiledb_dim>)

Return the tiledb_dim domain

`filter_list<-`(<tiledb_dim>)

Sets the TileDB Filter List for the TileDB Dimension object

filter_list(<tiledb_dim>)

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

name(<tiledb_dim>)

Return the tiledb_dim name

tile(<tiledb_dim>)

Return the tiledb_dim tile extent

tiledb_ndim(<tiledb_dim>)

Returns the number of dimensions for a tiledb domain object

is.anonymous(<tiledb_dim>)

Returns TRUE if the tiledb_dim is anonymous

Query

query object functions

tiledb_query-class

An S4 class for a TileDB Query object

tiledb_query()

Creates a 'tiledb_query' object

tiledb_query_add_range()

Set a range for a given query

tiledb_query_add_range_with_type()

Set a range for a given query

tiledb_query_alloc_buffer_ptr_char()

Allocate a Query buffer for reading a character attribute

tiledb_query_alloc_buffer_ptr_char_subarray()

Allocate a Query buffer for reading a character attribute using a subarray

tiledb_query_buffer_alloc_ptr()

Allocate a Query buffer for a given type

tiledb_query_create_buffer_ptr()

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

tiledb_query_create_buffer_ptr_char()

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

tiledb_query_export_buffer()

Export Query Buffer to Pair of Arrow IO Pointers

tiledb_query_finalize()

Finalize TileDB Query

tiledb_query_get_buffer_char()

Retrieve content from a Query character buffer

tiledb_query_get_buffer_ptr()

Retrieve content from a Query buffer

tiledb_query_get_est_result_size()

Retrieve the estimated result size for a query and attribute

tiledb_query_get_est_result_size_var()

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

tiledb_query_get_fragment_num()

Retrieve the Number of Fragments for Query

tiledb_query_get_fragment_timestamp_range()

Retrieve the timestamp range for a given Query Fragment

tiledb_query_get_fragment_uri()

Retrieve the URI for a given Query Fragment

tiledb_query_get_layout()

Get TileDB Query layout

tiledb_query_get_range() tiledb_query_get_range()

Retrieve the query range for a query dimension and range index

tiledb_query_get_range_num()

Retrieve the number of ranges for a query dimension

tiledb_query_import_buffer()

Import to Query Buffer from Pair of Arrow IO Pointers

tiledb_query_result_buffer_elements()

Get TileDB Query result buffer elements

tiledb_query_set_buffer()

Set TileDB Query buffer

tiledb_query_set_buffer_ptr()

Assigns to a Query buffer for a given attribute

tiledb_query_set_buffer_ptr_char()

Assign a buffer to a Query attribute

tiledb_query_set_layout()

Set TileDB Query layout

tiledb_query_set_subarray()

Set subarray for TileDB Query object

tiledb_query_status()

Get TileDB Query status

tiledb_query_submit()

Submit TileDB Query

tiledb_query_submit_async()

Submit TileDB Query asynchronously without a callback returning immediately

tiledb_query_type()

Return TileDB Query type

Group

tiledb_group_create()

Creates a TileDB group object at given uri path

Object

object management functions

tiledb_object_ls()

List TileDB resources at a given root URI path

tiledb_object_mv()

Move a TileDB resource to new uri path

tiledb_object_rm()

Removes a TileDB resource

tiledb_object_type()

Return the TileDB object type string of a TileDB resource

tiledb_object_walk()

Recursively discover TileDB resources at a given root URI path

is.anonymous()

Returns TRUE if the tiledb_dim is anonymous

is.anonymous(<tiledb_dim>)

Returns TRUE if the tiledb_dim is anonymous

array_consolidate()

Consolidate fragments of a TileDB Array

array_vacuum()

After consolidation, remove consilidated fragments of a TileDB Array

MetaData

arrray metadata functionality

print(<tiledb_metadata>)

Print a TileDB Array Metadata object

tiledb_delete_metadata()

Delete a TileDB Array Metadata object given by key

tiledb_get_all_metadata()

Return a TileDB Array Metadata object given by key

tiledb_get_metadata()

Return a TileDB Array Metadata object given by key

tiledb_has_metadata()

Test if TileDB Array has Metadata

tiledb_num_metadata()

Return count of TileDB Array Metadata objects

tiledb_put_metadata()

Store an object in TileDB Array Metadata under given key

Stats

performance stat collection functions

tiledb_stats_disable()

Disable internal TileDB statistics counters

tiledb_stats_dump()

Dumps internal TileDB statistics to file

tiledb_stats_enable()

Enable internal TileDB statistics counters

tiledb_stats_print()

Print internal TileDB statistics

tiledb_stats_raw_dump()

Dumps internal TileDB statistics as JSON to file

tiledb_stats_raw_get()

Gets internal TileDB statistics as JSON string

tiledb_stats_raw_print()

Print internal TileDB statistics as JSON

tiledb_stats_reset()

Reset internal TileDB statistics counters

VFS

virtual file system functions

tiledb_vfs-class

An S4 class for a TileDB VFS object

tiledb_vfs()

Creates a tiledb_vfs object

tiledb_vfs_close()

Close a TileDB VFS Filehandle

tiledb_vfs_create_bucket()

Create a VFS Bucket

tiledb_vfs_create_dir()

Create a VFS Directory

tiledb_vfs_empty_bucket()

Empty a VFS Bucket

tiledb_vfs_file_size()

Return VFS File Size

tiledb_vfs_is_bucket()

Check for VFS Bucket

tiledb_vfs_is_dir()

Test for VFS Directory

tiledb_vfs_is_empty_bucket()

Check for empty VFS Bucket

tiledb_vfs_is_file()

Test for VFS File

tiledb_vfs_move_dir()

Move (or rename) a VFS Directory

tiledb_vfs_move_file()

Move (or rename) a VFS File

tiledb_vfs_open()

Open a TileDB VFS Filehandle for reading or writing

tiledb_vfs_read()

Read from a TileDB VFS Filehandle

tiledb_vfs_remove_bucket()

Remove a VFS Bucket

tiledb_vfs_remove_dir()

Remove a VFS Directory

tiledb_vfs_remove_file()

Remove a VFS File

tiledb_vfs_sync()

Sync a TileDB VFS Filehandle

tiledb_vfs_touch()

Touch a VFS URI Resource

tiledb_vfs_write()

Write to a TileDB VFS Filehandle

tiledb_get_vfs()

Retrieve a TileDB VFS object from the package environment and cache

tiledb_set_vfs()

Store a TileDB VFS object in the package environment

DataFrame

data.frame functionality functions

as_data_frame()

Construct a data.frame from query results

fromDataFrame()

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

`return.data.frame<-`(<tiledb_array>)

Set data.frame return toggle

`return.data.frame<-`()

Set data.frame return toggle

`return.data.frame<-`(<tiledb_sparse>)

Set data.frame return toggle

return.data.frame(<tiledb_array>)

Retrieve data.frame return toggle

return.data.frame()

Retrieve data.frame return toggle

return.data.frame(<tiledb_sparse>)

Retrieve data.frame return toggle

as.data.frame(<tiledb_config>)

Convert a tiledb_config object to a R data.frame

SparseMatrix

sparse matrices helper functions

fromSparseMatrix() toSparseMatrix()

Create (or return) a TileDB sparse array

Arrow

interface to Arrow in-memory representation

tiledb_arrow_array_ptr() tiledb_arrow_schema_ptr() tiledb_arrow_array_del() tiledb_arrow_schema_del()

Allocate (or Release) Arrow Array and Schema Pointers

Package

package and version information

tiledb_version()

The version of the libtiledb library

tiledb-package

tiledb - Interface to the TileDB Storage Manager API

limitTileDBCores()

Limit TileDB core use to a given number of cores