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Fix a few typos and links in the vignette #131

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Jun 15, 2020
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Fix a few typos and links in the vignette #131

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28 changes: 16 additions & 12 deletions vignettes/introduction.Rmd
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Expand Up @@ -30,15 +30,14 @@ 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
[examples/ex_S3.R](https://github.com/TileDB-Inc/TileDB-R/blob/master/inst/examples/ex_S3.R) for an
example.
[examples/ex_S3.R][ex_s3] for an example.
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@eddelbuettel eddelbuettel Jun 15, 2020 •
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I actually put that in as absolute URL for a reason ... so that it would resolve to the file nomatter how the vignette is viewed.

What we have now seems incorrect in the sense that [...][...] (i.e. two sets of square brackets) is not valid markdown AFAIK. Never mind. Reading to the end helps. Not my preferred style to split'em but whatever works.

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Those are reference links: https://spec.commonmark.org/0.29/#link-reference-definition.

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Since they're referenced multiple times in the text I thought it was beneficial to have all the URLs in once place.

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That is a valid argument.


# Dense Arrays

## Basic Reading of Dense Arrays

We can consider the file [`ex_1.R`](../inst/ex_1.R) in the examples directory. It is a simple yet
complete example extending `quickstart_dense.R` by adding a second attribute.
We can consider the file [`ex_1.R`][ex_1] in the examples directory. It is a simple yet
complete example extending [`quickstart_dense.R`][qs_dense] by adding a second attribute.

*Read 1-D*

Expand Down Expand Up @@ -183,9 +182,7 @@ The attribute selection works with `as.data.frame=TRUE` as well:
*Simple Examples*

Basic reading returns the coordinates and any attributes. The following examples use the array
created by the
[quickstart_sparse](https://github.com/TileDB-Inc/TileDB/blob/dev/examples/cpp_api/quickstart_sparse.cc)
example.
created by the [quickstart_sparse][qs_sparse] example.

R> A <- tiledb_sparse(uri = uri)
R> A[]
Expand All @@ -196,7 +193,7 @@ example.
[1] 1 3 2


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

R> return.data.frame(A) <- TRUE
R> A[]
Expand All @@ -205,7 +202,7 @@ We can also request a data.frame object, either when opening or by changing this
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 overridden.
For sparse arrays, the return type is by default ‘extended’ showing rows and column but this can be overridden.

Assignment works similarly:

Expand All @@ -217,7 +214,7 @@ Assignment works similarly:
3 3 2 3
4 2 2 4

Reads can select rows and or colums:
Reads can select rows and or columns:

R> A[2,]
a rows cols
Expand All @@ -231,7 +228,7 @@ Attributes can be selected similarly.

## Date(time) Attributes

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

Expand All @@ -243,7 +240,7 @@ just integer and double precision floats.
3 5 105 2020-01-19 2020-01-05 00:44:04.805775 1577858700

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 stampt
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).

R> attrs(A) <- c("b", "d", "e")
Expand All @@ -267,3 +264,10 @@ numb
TileDB itself has extensive [installation](https://docs.tiledb.com/developer/installation),
[quickstart](https://docs.tiledb.com/developer/quickstart), and [overall
documentation](https://docs.tiledb.com/developer/) as well as a [support forum](https://forum.tiledb.com/).

[ex_1]: https://github.com/TileDB-Inc/TileDB-R/blob/master/inst/examples/ex_1.R
[ex_2]: https://github.com/TileDB-Inc/TileDB-R/blob/master/inst/examples/ex_2.R
[ex_s3]: https://github.com/TileDB-Inc/TileDB-R/blob/master/inst/examples/ex_S3.R

[qs_dense]: https://github.com/TileDB-Inc/TileDB-R/blob/master/inst/examples/quickstart_dense.R
[qs_sparse]: https://github.com/TileDB-Inc/TileDB/blob/dev/examples/cpp_api/quickstart_sparse.cc