First Steps with TileDB

This document introduces TileDB via several simple examples. A corresponding document with more complete API documentation is also available.

Getting started

Once the TileDB R package is installed, it can be loaded via library(tiledb). Installation is supported for Windows, Linux and macOS via the official CRAN package, on Linux and macOS via the conda package as well as from source.

Several “quickstart” examples that are discussed on the website are available in the examples directory. This vignette discusses similar examples.

In the following examples, the URIs describing arrays point to local file system object. When TileDB has been built with S3 support, and with proper AWS credentials in the usual environment variables, URIs such as s3://some/data/bucket can be used where a local file would be used. See the script ex_S3.R for an example.

Dense Arrays

Preliminaries

These illustrations use the array created by the file ex_1.R which one can run from within R, or on the command-line. To follow along with discussion that follows, it helps to run the example once to create the array after possibly adjusting the array location path from its default value (using the current directory or, if set as an option, an override).

Basic Reading of Dense Arrays

The file ex_1.R in the examples directory is a simple yet complete example extending quickstart_dense.R by adding a second and third attribute. In this as well as the following examples we will use tiledb_array() to access the array; the older variants tiledb_dense() and tiledb_sparse() remain supported but are deprecated and may be removed at some point in the future.

The first example extracts rows 1 to 2 and column 2 from an array. It also limits the selection to just one attribute (via attrs), asks for the return to be a data.frame (instead of a simpler list) and for the (row and column, if present as here) indices to not be printed (via extended=FALSE).

> A <- tiledb_array(uri = uri, attrs = "b",
+                   return_as = "data.frame", extended=FALSE))
> A[1:2,2]
[1] 101.5 104.0
>

Note that the examples create three two-dimensional attributes. The attributes can be selected via the attrs argument, or the attrs() method on the array object. The square-bracket indexing then selects with in the 2-d attribute object.

If multiple objects are returned (as list or data.frame), subsetting on the returned object works via [[var]] or $var. A numeric index also works (but needs to account for rows and cols).

> A <- tiledb_array(uri = uri, attrs = c("a","b"),
+                   return_as = "data.frame")
> A[1:2,2][["a"]]
[1] 2 7
> A[1:2,2]$a
[1] 2 7
>

This works analogously. Note that the results are generally returned as vectors, or as a columns of a data.frame object in case that option was set.

> A[6:9,3:4]
$a
[1] 28 29 33 34 38 39 43 44

$b
[1] 114.5 115.0 117.0 117.5 119.5 120.0 122.0 122.5

$c
[1] "fox" "A"   "E"   "F"   "J"   "K"   "O"   "P"
>

Read 2-D with attribute selection

> A <- tiledb_dense(uri = uri, attrs = c("b","c"),
+                   return_as = "data.frame", extended=FALSE)
> A[6:9,2:4]
       b     c
1  114.0 brown
2  114.5   fox
3  115.0     A
4  116.5     D
5  117.0     E
6  117.5     F
7  119.0     I
8  119.5     J
9  120.0     K
10 121.5     N
11 122.0     O
12 122.5     P
>

This also illustrated the effect of setting return_as = "data.frame" when opening the array.

This scheme can be generalized to variable cells, or cells where N>1, as we can expand each (atomistic) value over corresponding row and column indices.

The column types correspond to the attribute typed in the array schema, subject to the constraint mentioned above on R types. (The char comes in as a factor variable as is still the R 3.6.* default which is about to change. We can also override, users can too.)

> A <- tiledb_array("/tmp/tiledb/ex_1/", attrs=c("b","c"),
+                   return_as = "data.frame", extended=TRUE)
> sapply(A[6:9, 3:4], "class")
       rows        cols           b           c
  "integer"   "integer"   "numeric" "character"
>

Consistent with the data.frame semantics, now requesting a named column reduces to a vector as this happens at the R side:

Sparse Arrays

Basic Reading and Writing of Sparse Arrays

Basic reading returns the coordinates and any attributes. The following examples use the array created by the quickstart_sparse example.

> A <- tiledb_array(uri = uri, is.sparse = TRUE)
> A[]
$rows
[1] 1 2 2

$cols
[1] 1 3 4

$a
[1] 1 3 2

>

We can also request a data.frame object, either when opening or by changing this object characteristic on the fly:

> return.data.frame(A) <- TRUE
> A[]
  a rows cols
1 1    1    1
2 3    2    3
3 2    2    4

For sparse arrays, the return type is by default ‘extended’ showing rows and column but this can be overridden.

> A[4,2] <- 42L
> A[]
> A[]
  rows cols  a
1    1    1  1
2    2    3  3
3    2    4  2
4    4    2 42
>

> A[2,]
  rows cols a
1    2    3 3
2    2    4 2
> A[,2]
  rows cols  a
1    4    2 42
>

Date(time) Attributes

Similar to the dense array case described earlier, the file ex_2.R illustrates some basic operations on sparse arrays. It also shows date and datetime types instead of just integer and double precision floats.

> A <- tiledb_array(uri = uri, return_as = "data.frame")
> A[1577858403:1577858408]
        rows cols a   b          d                       e
1 1577858403    1 3 103 2020-01-11 2020-01-02 18:24:33.844
2 1577858404    1 4 104 2020-01-15 2020-01-05 02:28:36.214
3 1577858405    1 5 105 2020-01-19 2020-01-05 00:44:04.805
4 1577858406    1 6 106 2020-01-21 2020-01-06 12:58:51.770
5 1577858407    1 7 107 2020-01-25 2020-01-09 04:29:56.309
6 1577858408    1 8 108 2020-01-26 2020-01-07 13:55:10.240
>

The row coordinate is currently a floating point representation of the underlying time type. We can both select attributes (here we excluded the “a” column) and select rows by time (as the time stamps get converted to the required floating point value).

> attrs(A) <- c("b", "d", "e")
> A[as.POSIXct("2020-01-01"):as.POSIXct("2020-01-01 00:00:03")]
        rows cols   b          d                       e
1 1577858401    1 101 2020-01-05 2020-01-01 03:03:07.548
2 1577858402    1 102 2020-01-10 2020-01-02 21:02:19.747
3 1577858403    1 103 2020-01-11 2020-01-02 18:24:33.844
>

More extended examples are available showing indexing by date(time) as well as character dimension.

Additional Information

The TileDB R package is documented via R help functions (e.g. help("tiledb_array") shows information for the tiledb_array() function) as well as via a website regrouping all documentation. Extended API documentation is available, as is a examples/ directory.