README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->


```{r setup, include=FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  out.width = "100%"
)
library(tibble)
```

# rstac <img src="inst/extdata/img/logo.png" align="right" width="120"/>
R Client Library for SpatioTemporal Asset Catalog (rstac)


<!-- badges: start -->
[![Software License](https://img.shields.io/badge/license-MIT-green)](https://github.com/brazil-data-cube/rstac/blob/master/LICENSE)
<!-- [![Build Status](https://drone.dpi.inpe.br/api/badges/brazil-data-cube/rstac/status.svg)](https://drone.dpi.inpe.br/brazil-data-cube/rstac) -->
[![R-CMD-check](https://github.com/brazil-data-cube/rstac/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/brazil-data-cube/rstac/actions/workflows/R-CMD-check.yaml)
[![Build status](https://ci.appveyor.com/api/projects/status/73w7h6u46l1587jj?svg=true)](https://ci.appveyor.com/project/OldLipe/rstac)
[![codecov](https://codecov.io/gh/brazil-data-cube/rstac/branch/master/graph/badge.svg?token=ILQLPW19UT)](https://app.codecov.io/gh/brazil-data-cube/rstac)
[![Software Life Cycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html)
[![CRAN status](https://www.r-pkg.org/badges/version/rstac)](https://cran.r-project.org/package=rstac)
[![STAC API](https://img.shields.io/badge/STAC%20API-v1.0.0-informational)](https://github.com/radiantearth/stac-api-spec)
[![Join us at Discord](https://img.shields.io/discord/689541907621085198?logo=discord&logoColor=ffffff&color=7389D8)](https://discord.com/channels/689541907621085198#)
<!-- badges: end -->

STAC is a specification of files and web services used to describe geospatial 
information assets. The specification can be consulted in [https://stacspec.org/](https://stacspec.org/).

R client library for STAC (`rstac`) was designed to fully support STAC API v1.0.0.
It also supports earlier versions (>= v0.8.0).

## Installation

```{R install, eval=FALSE}
# install via CRAN 
install.packages("rstac")
```

### Development version

To install the development version of `rstac`, run the following commands

```{R install-dev, eval=FALSE}
remotes::install_github("brazil-data-cube/rstac")
```

Importing `rstac` package:

```{r load, echo=TRUE, message=FALSE, warning=FALSE}
library(rstac)
```


## Usage

`rstac` implements the following STAC endpoints:


```{R endpoints, echo=FALSE}

tibble::tribble(
  ~"**STAC** endpoints", ~"`rstac` functions", ~"API version",
  "`/`", "`stac()`", ">= 0.9.0",
  "`/stac`", "`stac()`", "< 0.9.0",
  "`/collections`", "`collections()`",  ">= 0.9.0",
  "`/collections/{collectionId}`", "`collections(collection_id)`", ">= 0.9.0",
  "`/collections/{collectionId}/items`", "`items()`", ">= 0.9.0",
  "`/collections/{collectionId}/items/{itemId}`", "`items(feature_id)`", ">= 0.9.0",
  "`/search`", "`stac_search()`", ">= 0.9.0",
  "`/stac/search`", "`stac_search()`", "< 0.9.0",
  "`/conformance`", "`conformance()`", ">= 0.9.0",
  "`/collections/{collectionId}/queryables`", "`queryables()`", ">= 1.0.0"
) %>% as.data.frame() %>% knitr::kable(format = "markdown")
```

These functions can be used to retrieve information from a STAC API service.
The code below creates a `stac` object and list the available collections of 
the STAC API of the [Brazil Data Cube](http://www.brazildatacube.org/en/home-page-2/) project of 
the Brazilian National Space Research Institute (INPE).

```{R stac-obj, echo=TRUE}
s_obj <- stac("https://brazildatacube.dpi.inpe.br/stac/")

get_request(s_obj)
```

The variable `s_obj` stores information to connect to the Brazil Data 
Cube STAC web service. The `get_request` method makes a HTTP GET connection
to it and retrieves a STAC Catalog document from the server. Each `links` 
entry is an available collection that can be accessed via STAC API.

In the code below, we get some STAC items of `CB4-16D-2` collection that
intersects the bounding box passed to the `bbox` parameter. To do this, we
call the `stac_search` function that implements the STAC `/search` 
endpoint. The returned document is a STAC Item Collection (a geojson 
containing a feature collection).

```{R bdc-items1, echo=TRUE}

it_obj <- s_obj %>%
  stac_search(collections = "CB4-16D-2",
              bbox = c(-47.02148, -17.35063, -42.53906, -12.98314),
              limit = 100) %>% 
  get_request()

it_obj
```

The `rstac` uses the [httr](https://github.com/r-lib/httr) package to manage 
HTTP requests, allowing the use of tokens from the authorization protocols OAuth
1.0 or 2.0 as well as other configuration options. In the code below, we present
an example of how to pass a parameter token on a HTTP request.

```{R bdc-items2, eval=FALSE}
it_obj <- s_obj %>%
  stac_search(collections = "CB4-16D-2",
              bbox = c(-47.02148, -17.35063, -42.53906, -12.98314)) %>%
  get_request(add_headers("x-api-key" = "MY-TOKEN"))
```

In addition to the functions mentioned above, the `rstac` package provides some 
extra functions for handling items and to bulk download the assets.

### Items functions

`rstac` provides some functions that facilitates the interaction with STAC data.
In the example below, we get how many items matched the search criteria:

```{R bdc-items3, echo=TRUE}
# it_obj variable from the last code example
it_obj %>% 
  items_matched()
```

However, if we count how many items there are in `it_obj` variable, we get `10`,
meaning that more items could be fetched from the STAC service:

```{R bdc-items4, echo=TRUE}
it_obj %>% 
  items_length()
```


```{R bdc-items5, echo=TRUE}
# fetch all items from server 
# (but don't stored them back in it_obj)
it_obj <- it_obj %>% 
  items_fetch(progress = FALSE) 

it_obj %>%
  items_length()
```

### Download assets

All we've got in previous example was metadata to STAC Items, including
links to geospatial data called `assets`. To download all `assets` in a
STAC Item Collection we can use `assets_download()` function, that returns
an update STAC Item Collection referring to the downloaded assets. The code
below downloads the `thumbnail` assets (.png files) of `10` items stored in
`it_obj` variable.

```{R download, eval=FALSE}
download_items <- it_obj %>%
  assets_download(assets_name = "thumbnail", items_max = 10)
```

### CQL2 query filter

`rstac` also supports advanced query filter using common query language (CQL2).
Users can write complex filter expressions using R code in an easy and 
natural way. For a complete 

```{R cql2, echo=TRUE}
s_obj <- stac("https://planetarycomputer.microsoft.com/api/stac/v1")

it_obj <- s_obj %>% 
  ext_filter(
    collection == "sentinel-2-l2a" && `s2:vegetation_percentage` >= 50 &&
      `eo:cloud_cover` <= 10 && `s2:mgrs_tile` == "20LKP" && 
      anyinteracts(datetime, interval("2020-06-01", "2020-09-30"))
  ) %>%
  post_request()
```

## Getting help

You can get a full explanation about each STAC (v1.0.0) endpoint at [STAC API spec](https://github.com/radiantearth/stac-api-spec/tree/master/ogcapi-features). A detailed
documentation with examples on how to use each endpoint and other functions
available in the `rstac` package can be obtained by typing `?rstac` in R 
console.

## Citation

To cite rstac in publications use:

R. Simoes, F. C. de Souza, M. Zaglia, G. R. de Queiroz, R. D. C. dos Santos
and K. R. Ferreira, "Rstac: An R Package to Access Spatiotemporal Asset
Catalog Satellite Imagery," 2021 IEEE International Geoscience and Remote
Sensing Symposium IGARSS, 2021, pp. 7674-7677, doi:
10.1109/IGARSS47720.2021.9553518.

## Acknowledgements for financial support

We acknowledge and thank the project funders that provided financial and material support:

- Amazon Fund, established by the Brazilian government with financial contribution from Norway, through the project contract between the Brazilian Development Bank (BNDES) and the Foundation for Science, Technology and Space Applications (FUNCATE), for the establishment of the Brazil Data Cube, process 17.2.0536.1.

- Radiant Earth Foundation and STAC Project Steering Committee for the advance of STAC ecosystem programme.

- OpenGeoHub Foundation and the European Commission (EC) through the project Open-Earth-Monitor Cyberinfrastructure: Environmental information to support EU’s Green Deal (1 Jun. 2022 – 31 May 2026 - 101059548)

## How to contribute?

The `rstac` package was implemented based on an extensible architecture, so 
feel free to contribute by implementing new STAC API 
[extensions/fragments](https://github.com/radiantearth/stac-api-spec/tree/master/fragments) 
based on the STAC API specifications.

1. Make a project
[fork](https://docs.github.com/en/github/getting-started-with-github/fork-a-repo).
2. Create a file inside the `R/` directory called `ext_{extension_name}.R`.
3. In the code, you need to specify a subclass name (e.g.`my_subclass`) for 
your extension and use it when calling [`rstac_query()`](https://github.com/brazil-data-cube/rstac/blob/master/R/query-funs.R) function. You also need to implement for your subclass the following S3 generic functions: [`before_request()`](https://github.com/brazil-data-cube/rstac/blob/master/R/extensions.R), [`after_response()`](https://github.com/brazil-data-cube/rstac/blob/master/R/extensions.R), and [`parse_params()`](https://github.com/brazil-data-cube/rstac/blob/master/R/extensions.R). With these S3 generics methods you 
can define how parameters should be submitted to the HTTP request and the types 
of the returned documents. See the implemented [ext_filter](https://github.com/brazil-data-cube/rstac/blob/master/R/ext_filter.R) 
API extension as an example.
4. Make a [Pull Request](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request) on the most recent [development branch](https://github.com/brazil-data-cube/rstac/).