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The TileDB R package offers an R interface to the storage engine of TileDB.

Note that the R interface to TileDB is under development, and the API is subject to change.

Documentation

Documentation is available for the R package as well as for the TileDB API.

Installation

TileDB Embedded needs to be present, and can be installed first (from a package or from source) for the TileDB R package to build and link correctly. Alternatively, if no system installation is found, a precompiled shared library is used during the installation of this R package.

The TileDB R package has been published on CRAN and be installed directly via

> install.packages("tiledb")

as usual.

The most recent released version can be installed from Github using the package remotes.

> if (!requireNamespace("remotes",quietly=TRUE)) install.packages("remotes")
> remotes::install_github("TileDB-Inc/TileDB-R")
...
> library(tiledb)
> tiledb_version()
major minor patch
    2     2     9
> help(package=tiledb)

If the TileDB library is installed in a custom location, you need to pass the explicit path:

> remotes::install_github("TileDB-Inc/TileDB-R",
      args="--configure-args='--with-tiledb=/path/to/tiledb'")

Note that the TileDB R package is developed and tested against the latest stable (v2.2.x) version of TileDB, but should also build against the newest development version.

Quick Links

Copyright

The TileDB R package is Copyright 2018-2021 TileDB, Inc

License

MIT

Copy Link

Version

Install

install.packages('tiledb')

Monthly Downloads

863

Version

0.9.2

License

MIT + file LICENSE

Issues

20

Pull Requests

6

Stars

108

Forks

24

Maintainer

Dirk Eddelbuettel

Last Published

May 20th, 2021

Functions in tiledb (0.9.2)

array_vacuum

After consolidation, remove consilidated fragments of a TileDB Array
attrs<-,tiledb_array-method

Selects attributes for the given TileDB array
attrs<-

Selects attributes for the given TileDB array
as.vector.tiledb_config

Convert a tiledb_config object to a R vector
attrs,tiledb_array_schema,ANY-method

Returns a list of all tiledb_attr objects associated with the tiledb_array_schema
as_data_frame

Construct a data.frame from query results
attrs,tiledb_array,ANY-method

Retrieve attributes from tiledb_array object
array_consolidate

Consolidate fragments of a TileDB Array
attrs,tiledb_array_schema,character-method

Returns a tiledb_attr object associated with the tiledb_array_schema with a given name.
as.data.frame.tiledb_config

Convert a tiledb_config object to a R data.frame
attrs,tiledb_sparse,ANY-method

Retrieve attributes from tiledb_sparse object
filter_list,tiledb_array_schema-method

Returns the offsets and coordinate filter_lists associated with the tiledb_array_schema
attrs,tiledb_dense,ANY-method

Retrieve attributes from tiledb_dense object
filter_list,tiledb_attr-method

Returns the TileDB Filter List object associated with the given TileDB Attribute
cell_order,tiledb_array_schema-method

Returns the cell layout string associated with the tiledb_array_schema
datatype,tiledb_attr-method

Return the tiledb_attr datatype
datatype,tiledb_domain-method

Returns the tiledb_domain TileDB type string
domain,tiledb_array_schema-method

Returns the tiledb_domain object associated with a given tiledb_array_schema
attrs<-,tiledb_sparse-method

Selects attributes for the given TileDB array
datetimes_as_int64<-

Set datetimes_as_int64 toggle
nfilters,tiledb_filter_list-method

Returns the filter_list's number of filters
dim.tiledb_array_schema

Retrieve the dimension (domain extent) of the domain
is.sparse,tiledb_dense-method

Returns true is if the array or array_schema is sparse
datetimes_as_int64

Retrieve datetimes_as_int64 toggle
r_to_tiledb_type

Look up TileDB type corresponding to the type of an R object
is.sparse,tiledb_array_schema-method

Returns TRUE if the tiledb_array_schema is sparse, else FALSE
filter_list,tiledb_dim-method

Returns the TileDB Filter List object associated with the given TileDB Dimension
dimensions,tiledb_array_schema-method

Returns a list of tiledb_dim objects associated with the tiledb_array_schema
attrs,tiledb_array_schema,numeric-method

Returns a tiledb_attr object associated with the tiledb_array_schema with a given index
dimensions,tiledb_domain-method

Returns a list of the tiledb_domain dimension objects
fromDataFrame

Create a TileDB dense or sparse array from a given data.frame Object
datatype,tiledb_dim-method

Return the tiledb_dim datatype
return.data.frame<-,tiledb_array-method

Set data.frame return toggle
return.data.frame<-

Set data.frame return toggle
return.data.frame<-,tiledb_sparse-method

Set data.frame return toggle
print.tiledb_metadata

Print a TileDB Array Metadata object
schema,character-method

Return a schema from a URI character value
[,tiledb_config,ANY-method

Gets a config parameter value
[,tiledb_array,ANY-method

Returns a TileDB array, allowing for specific subset ranges.
return.matrix

Retrieve matrix.frame return toggle
[<-,tiledb_sparse,ANY,ANY,ANY-method

Sets a sparse array value
schema,tiledb_sparse-method

Return a schema from a sparse array
domain,tiledb_dim-method

Return the tiledb_dim domain
config,tiledb_ctx-method

Retrieve the tiledb_config object from the tiledb_ctx
extended

Retrieve data.frame extended returns columns toggle
extended<-

Set data.frame extended return columns toggle
fromSparseMatrix

Create (or return) a TileDB sparse array
return.matrix<-

Set marix return toggle
is.integral,tiledb_domain-method

Returns TRUE is tiledb_domain is an integral (integer) domain
show,tiledb_attr-method

Prints an attribute object
return.data.frame,tiledb_sparse-method

Retrieve data.frame return toggle
is.anonymous.tiledb_dim

Returns TRUE if the tiledb_dim is anonymous
show,tiledb_array_schema-method

Prints an array schema object
has_attribute

Check a schema for a given attribute name
domain

Generic Methods
is.sparse,tiledb_sparse-method

Check if object is sparse
limitTileDBCores

Limit TileDB core use to a given number of cores
query_layout<-

Set query_layout return values for the array
return.data.frame,tiledb_array-method

Retrieve data.frame return toggle
[,tiledb_dense,ANY-method

Gets a dense array value
return.data.frame

Retrieve data.frame return toggle
is.anonymous

Returns TRUE if the tiledb_dim is anonymous
[,tiledb_filter_list,ANY-method

Returns the filter at given index
selected_ranges<-

Set selected_ranges return values for the array
show,tiledb_dense-method

Prints a tiledb_dense array object
tiledb_array_create

Creates a new TileDB array given an input schema.
tiledb_array_close

Close a TileDB Array
show,tiledb_config-method

Prints the config object to STDOUT
show,tiledb_domain-method

Prints an domain object
show,tiledb_sparse-method

Prints a tiledb_sparse array object
[<-,tiledb_config,ANY,ANY,ANY-method

Sets a config parameter value
tiledb_array_schema-class

An S4 class for the TileDB array schema
[<-,tiledb_dense,ANY,ANY,ANY-method

Sets a dense array value
tiledb_array-class

An S4 class for a TileDB Array
check

Check the schema for correctness
dim.tiledb_dim

Retrieves the dimension of the tiledb_dim domain
filter_list<-,tiledb_attr-method

Sets the TileDB Filter List for the TileDB Attribute object
dim.tiledb_domain

Retrieve the dimension (domain extent) of the domain
allows_dups

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

An S4 class for a TileDB configuration
tiledb_dim-class

An S4 class for a TileDB dimension object
filter_list<-,tiledb_dim-method

Sets the TileDB Filter List for the TileDB Dimension object
tiledb_dim

Contructs a tiledb_dim object
tiledb_config

Creates a tiledb_config object
tiledb_array_schema

Constructs a tiledb_array_schema object
query_layout

Retrieve query_layout values for the array
name,tiledb_attr-method

Return the tiledb_attr name
tiledb_filter

Constructs a tiledb_filter object
capacity<-

Sets the schema capacity (for sparse fragments)
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
tile,tiledb_dim-method

Return the tiledb_dim tile extent
schema,tiledb_dense-method

Returns the tiledb_dense array tiledb_schema object
[,tiledb_sparse,ANY-method

Gets a sparse array value
schema,tiledb_array-method

Return a schema from a tiledb_array object
name,tiledb_dim-method

Return the tiledb_dim name
tiledb_array

Constructs a tiledb_array object backed by a persisted tiledb array uri
tiledb_array_is_heterogeneous

Check for Heterogeneous Domain
[<-,tiledb_array,ANY,ANY,ANY-method

Sets a tiledb array value or value range
capacity

Retrieve schema capacity (for sparse fragments)
selected_ranges

Retrieve selected_ranges values for the array
show,tiledb_array-method

Prints a tiledb_array object
tiledb_array_open

Open a TileDB Array
tiledb_attribute_set_fill_value

Set the fill value for a TileDB Attribute
tiledb_array_schema_set_coords_filter_list

Set a Filter List for Coordinate of a TileDB Schema
tiledb_attribute_set_nullable

Set the TileDB Attribute Nullable flags
allows_dups<-

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

Get the fill value for a TileDB Attribute
tiledb_array_open_at

Open a TileDB Array at Timestamp
tiledb_attribute_get_cell_size

Get the TileDB Attribute cell size
tiledb_attribute_get_nullable

Get the TileDB Attribute Nullable flag value
tiledb_config_unset

Unset a TileDB Config parameter to its default value
tiledb_ctx-class

An S4 class for a TileDB context
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_get_metadata

Return a TileDB Array Metadata object given by key
tiledb_filter_get_option

Returns the filter's option
tiledb_config_load

Load a saved tiledb_config file from disk
cell_val_num

Return the number of scalar values per attribute cell
tiledb-package

tiledb - Interface to the TileDB Storage Manager API
tiledb_array_schema_set_offsets_filter_list

Set a Filter List for Variable-Sized Offsets of a TileDB Schema
tile_order,tiledb_array_schema-method

Returns the tile layout string associated with the tiledb_array_schema
tiledb_domain_has_dimension

Check a domain for a given dimension name
tiledb_filter-class

An S4 class for a TileDB filter
tiledb_domain-class

An S4 class for a TileDB domain
tiledb_attribute_is_variable_sized

Check whether TileDB Attribute is variable-sized
tiledb_arrow_array_ptr

Allocate (or Release) Arrow Array and Schema Pointers
tiledb_get_all_metadata

Return a TileDB Array Metadata object given by key
tiledb_get_context

Retrieve a TileDB context object from the package cache
tiledb_domain

Constructs a tiledb_domain object
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
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_get_vfs

Retrieve a TileDB VFS object from the package environment and cache
tiledb_config_save

Save a tiledb_config object ot a local text file
tiledb_query_create_buffer_ptr

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

An S4 class for a TileDB attribute
tiledb_attr

Contructs a tiledb_attr object
tiledb_array_is_homogeneous

Check for Homogeneous Domain
tiledb_stats_raw_get

Gets internal TileDB statistics as JSON string
tiledb_query_get_buffer_char

Retrieve content from a Query character buffer
tiledb_set_vfs

Store a TileDB VFS object in the package environment
tiledb_stats_raw_print

Print internal TileDB statistics as JSON
tiledb_sparse-class

An S4 class for a TileDB sparse array
tiledb_query_create_buffer_ptr_char

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

Retrieve content from a Query buffer
cell_val_num<-

Set the number of scalar values per attribute cell
tiledb_domain_get_dimension_from_index

Returns a Dimension indicated by index for the given TileDB Domain
tiledb_ctx

Creates a tiledb_ctx object
tiledb_ctx_set_default_tags

Sets default context tags
tiledb_query-class

An S4 class for a TileDB Query object
tiledb_query_get_est_result_size_var

Retrieve the estimated result size for a query and variable-sized attribute
tiledb_ndim,tiledb_domain-method

Returns the number of dimensions of the tiledb_domain
tiledb_put_metadata

Store an object in TileDB Array Metadata under given key
tiledb_query_get_est_result_size

Retrieve the estimated result size for a query and attribute
tiledb_ndim,tiledb_dim-method

Returns the number of dimensions for a tiledb domain object
set_max_chunk_size

Set the filter_list's max_chunk_size
max_chunk_size

Returns the filter_list's max_chunk_size
tiledb_num_metadata

Return count of TileDB Array Metadata objects
tiledb_ctx_set_tag

Sets a string:string "tag" on the Ctx
tiledb_object_ls

List TileDB resources at a given root URI path
tiledb_filter_list-class

An S4 class for a TileDB filter list
tiledb_group_create

Creates a TileDB group object at given uri path
tiledb_delete_metadata

Delete a TileDB Array Metadata object given by key
tiledb_filter_list

Constructs a tiledb_filter_list object
tiledb_has_metadata

Test if TileDB Array has Metadata
tiledb_query_add_range

Set a range for a given query
tiledb_query_finalize

Finalize TileDB Query
tiledb_query

Creates a 'tiledb_query' object
tiledb_query_export_buffer

Export Query Buffer to Pair of Arrow IO Pointers
tiledb_vfs_create_bucket

Create a VFS Bucket
tiledb_query_set_subarray

Set subarray for TileDB Query object
tiledb_schema_get_types

Get all Dimension and Attribute Types
tiledb_query_status

Get TileDB Query status
tiledb_set_context

Store a TileDB context object in the package cache
tiledb_vfs_open

Open a TileDB VFS Filehandle for reading or writing
tiledb_vfs_create_dir

Create a VFS Directory
tiledb_vfs_read

Read from a TileDB VFS Filehandle
tiledb_vfs_remove_file

Remove a VFS File
tiledb_vfs_sync

Sync a TileDB VFS Filehandle
tiledb_vfs_file_size

Return VFS File Size
tiledb_vfs_empty_bucket

Empty a VFS Bucket
tiledb_is_supported_fs

Query if a TileDB backend is supported
tiledb_query_get_fragment_timestamp_range

Retrieve the timestamp range for a given Query Fragment
tiledb_query_get_fragment_num

Retrieve the Number of Fragments for Query
tiledb_query_set_buffer

Set TileDB Query buffer
tiledb_query_submit_async

Submit TileDB Query asynchronously without a callback returning immediately
tiledb_stats_print

Print internal TileDB statistics
tiledb_stats_raw_dump

Dumps internal TileDB statistics as JSON to file
tiledb_query_set_buffer_ptr

Assigns to a Query buffer for a given attribute
tiledb_query_submit

Submit TileDB Query
tiledb_vfs_is_dir

Test for VFS Directory
tiledb_vfs_is_bucket

Check for VFS Bucket
tiledb_query_import_buffer

Import to Query Buffer from Pair of Arrow IO Pointers
tiledb_ndim,tiledb_array_schema-method

Return the number of dimensions associated with the tiledb_array_schema
tiledb_query_alloc_buffer_ptr_char_subarray

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

Set the filter's option
tiledb_filter_type

Returns the type of the filter used
tiledb_domain_get_dimension_from_name

Returns a Dimension indicated by name for the given TileDB Domain
tiledb_object_rm

Removes a TileDB resource
tiledb_object_mv

Move a TileDB resource to new uri path
tiledb_query_result_buffer_elements

Get TileDB Query result buffer elements
tiledb_query_get_fragment_uri

Retrieve the URI for a given Query Fragment
tiledb_query_get_range_num

Retrieve the number of ranges for a query dimension
tiledb_query_get_layout

Get TileDB Query layout
tiledb_query_get_range

Retrieve the query range for a query dimension and range index
tiledb_query_buffer_alloc_ptr

Allocate a Query buffer for a given type
tiledb_stats_reset

Reset internal TileDB statistics counters
tiledb_query_set_buffer_ptr_char

Assign a buffer to a Query attribute
tiledb_query_set_layout

Set TileDB Query layout
tiledb_schema_get_names

Get all Dimension and Attribute Names
tiledb_query_type

Return TileDB Query type
tiledb_sparse

Constructs a tiledb_sparse object backed by a persisted tiledb array uri
tiledb_stats_enable

Enable internal TileDB statistics counters
tiledb_stats_dump

Dumps internal TileDB statistics to file
tiledb_vfs_touch

Touch a VFS URI Resource
tiledb_stats_disable

Disable internal TileDB statistics counters
tiledb_vfs_is_empty_bucket

Check for empty VFS Bucket
tiledb_vfs-class

An S4 class for a TileDB VFS object
tiledb_version

The version of the libtiledb library
tiledb_vfs_move_dir

Move (or rename) a VFS Directory
tiledb_vfs_move_file

Move (or rename) a VFS File
tiledb_vfs_is_file

Test for VFS File
tiledb_vfs_write

Write to a TileDB VFS Filehandle
tiledb_subarray

Query a array using a subarray vector
tiledb_vfs

Creates a tiledb_vfs object
tiledb_vfs_close

Close a TileDB VFS Filehandle
tiledb_vfs_remove_bucket

Remove a VFS Bucket
tiledb_vfs_remove_dir

Remove a VFS Directory