# amadeus <a href="https://niehs.github.io/amadeus/"><img src="man/figures/logo.svg" align="right" width="185" alt="amadeus website" /></a>

[![R-CMD-check](https://github.com/NIEHS/amadeus/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/NIEHS/amadeus/actions/workflows/check-standard.yaml)
[![cov](https://NIEHS.github.io/amadeus/badges/coverage.svg)](https://github.com/NIEHS/amadeus/actions)
[![lint](https://github.com/NIEHS/amadeus/actions/workflows/lint.yaml/badge.svg)](https://github.com/NIEHS/amadeus/actions/workflows/lint.yaml)
[![pkgdown](https://github.com/NIEHS/amadeus/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/NIEHS/amadeus/actions/workflows/pkgdown.yaml)
[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![CRAN](https://www.r-pkg.org/badges/version/amadeus?color=blue)](https://cran.r-project.org/package=amadeus)
[![downloads](https://cranlogs.r-pkg.org/badges/grand-total/amadeus)](https://cran.r-project.org/package=amadeus)

`amadeus` is **a** **m**ech**a**nism for **d**ata, **e**nvironments, and **u**ser **s**etup for common environmental and climate health datasets in R. `amadeus` has been developed to improve access to and utility with large scale, publicly available environmental data in R.

See the peer-reviewed publication, [Amadeus: Accessing and analyzing large scale environmental data in R](https://www.sciencedirect.com/science/article/pii/S1364815225000362), for full description and details.

Cite `amadeus` as:
> Manware, M., Song, I., Marques, E. S., Kassien, M. A., Clark, L. P., & Messier, K. P. (2025). Amadeus: Accessing and analyzing large scale environmental data in R. Environmental Modelling & Software, 186, 106352.

## Installation

`amadeus` can be installed from CRAN with `install.packages` or from GitHub with `pak`.

```r
install.packages("amadeus")
```
```r
pak::pak("NIEHS/amadeus")
```

## Download

`download_data` accesses and downloads raw geospatial data from a variety of open source data repositories. The function is a wrapper that calls source-specific download functions, each of which account for the source's unique combination of URL, file naming conventions, and data types. Download functions cover the following sources:

| Data Source | File Type | Data Genre | Spatial Extent | Function Suffix |
| :---- | :-- | :--- | :--- | :--- |
| [Climatology Lab TerraClimate](https://www.climatologylab.org/terraclimate.html) | netCDF | Meteorology | Global | `_terraclimate` |
| [Climatology Lab GridMet](https://www.climatologylab.org/gridmet.html) | netCDF | Climate<br>Water | Contiguous United States | `_gridmet` |
| [Köppen-Geiger Climate Classification](https://www.nature.com/articles/sdata2018214) | GeoTIFF | Climate Classification | Global | `_koppen_geiger` |
| [MRLC[^1] Consortium National Land Cover Database (NLCD)](https://www.mrlc.gov/data) | GeoTIFF | Land Use | United States | `_nlcd` |
| [NASA[^2] Moderate Resolution Imaging Spectroradiometer (MODIS)](https://modis.gsfc.nasa.gov/data/) | HDF | Atmosphere<br>Meteorology<br>Land Use<br>Satellite | Global | `_modis` |
| [NASA Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA-2)](https://www.nature.com/articles/sdata2018214) | netCDF | Atmosphere<br>Meteorology | Global | `_merra2` |
| [NASA SEDAC[^3] UN WPP-Adjusted Population Density](https://earthdata.nasa.gov/data/catalog/sedac-ciesin-sedac-gpwv4-apdens-wpp-2015-r11-4.11) | GeoTIFF<br>netCDF | Population | Global | `_population` |
| [NASA SEDAC Global Roads Open Access Data Set](https://data.nasa.gov/dataset/global-roads-open-access-data-set-version-1-groadsv1) | Shapefile<br>Geodatabase | Roadways | Global | `_groads` |
| [NASA Goddard Earth Observing System Composition Forcasting (GEOS-CF)](https://gmao.gsfc.nasa.gov/GEOS_systems/) | netCDF | Atmosphere<br>Meteorology | Global | `_geos` |
| [NOAA Hazard Mapping System Fire and Smoke Product](https://www.ospo.noaa.gov/products/land/hms.html#about) | Shapefile<br>KML | Wildfire Smoke | North America | `_hms` |
| [NOAA NCEP[^4] North American Regional Reanalysis (NARR)](https://psl.noaa.gov/data/gridded/data.narr.html) | netCDF | Atmosphere<br>Meteorology | North America | `_narr` |
| [US EPA[^5] Air Data Pre-Generated Data Files](https://aqs.epa.gov/aqsweb/airdata/download_files.html) | CSV | Air Pollution | United States | `_aqs` |
| [US EPA Ecoregions](https://www.epa.gov/eco-research/ecoregions) | Shapefile | Climate Regions | North America | `_ecoregions` |
| [US EPA National Emissions Inventory (NEI)](https://www.epa.gov/air-emissions-inventories) | CSV | Emissions | United States | `_nei` |
| [US EPA Toxic Release Inventory (TRI) Program](https://www.epa.gov/toxics-release-inventory-tri-program/tri-basic-data-files-calendar-years-1987-present) | CSV | Chemicals<br>Pollution | United States | `_tri` |
| [USGS[^6] Global Multi-resolution Terrain Elevation Data (GMTED2010)](https://www.usgs.gov/coastal-changes-and-impacts/gmted2010) | ESRI ASCII Grid | Elevation | Global | `_gmted` |

See the "[download_data](https://niehs.github.io/amadeus/articles/download_functions.html)" vignette for a detailed description of source-specific download functions.

Example use of `download_data` using NOAA NCEP North American Regional Reanalysis's (NARR) "weasd" (Daily Accumulated Snow at Surface) variable.

```r
directory <- "/  EXAMPLE  /  FILE  /  PATH  /"
download_data(
  dataset_name = "narr",
  year = 2022,
  variable = "weasd",
  directory_to_save = directory,
  acknowledgement = TRUE,
  download = TRUE,
  hash = TRUE
)
```
```
Downloading requested files...
Requested files have been downloaded.
[1] "5655d4281b76f4d4d5bee234c2938f720cfec879"
```
```r
list.files(file.path(directory, "weasd"))
```
```
[1] "weasd.2022.nc"
```

## Process

`process_covariates` imports and cleans raw geospatial data (downloaded with `download_data`), and returns a single `SpatRaster` or `SpatVector` into the user's R environment. `process_covariates` "cleans" the data by defining interpretable layer names, ensuring a coordinate reference system is present, and managing `timedata (if applicable).

To avoid errors when using `process_covariates`, **do not edit the raw downloaded data files**. Passing user-generated or edited data into `process_covariates` may result in errors as the underlying functions are adapted to each sources' raw data file type.

Example use of `process_covariates` using the downloaded "weasd" data.

```r
weasd_process <- process_covariates(
  covariate = "narr",
  date = c("2022-01-01", "2022-01-05"),
  variable = "weasd",
  path = file.path(directory, "weasd"),
  extent = NULL
)
```
```
Detected monolevel data...
Cleaning weasd data for 2022...
Returning daily weasd data from 2022-01-01 to 2022-01-05.
```
```r
weasd_process
```
```
class       : SpatRaster
dimensions  : 277, 349, 5  (nrow, ncol, nlyr)
resolution  : 32462.99, 32463  (x, y)
extent      : -16231.49, 11313351, -16231.5, 8976020  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=lcc +lat_0=50 +lon_0=-107 +lat_1=50 +lat_2=50 +x_0=5632642.22547 +y_0=4612545.65137 +datum=WGS84 +units=m +no_defs
source      : weasd.2022.nc:weasd
varname     : weasd (Daily Accumulated Snow at Surface)
names       : weasd_20220101, weasd_20220102, weasd_20220103, weasd_20220104, weasd_20220105
unit        :         kg/m^2,         kg/m^2,         kg/m^2,         kg/m^2,         kg/m^2
time        : 2022-01-01 to 2022-01-05 UTC
```

## Calculate Covariates

`calculate_covariates` stems from the [`beethoven`](https://github.com/NIEHS/beethoven) project's need for various types of data extracted at precise locations. `calculate_covariates`, therefore, extracts data from the "cleaned" `SpatRaster` or `SpatVector` object at user defined locations. Users can choose to buffer the locations. The function returns a `data.frame`, `sf`, or `SpatVector` with data extracted at all locations for each layer or row in the `SpatRaster` or `SpatVector` object, respectively.

Example of `calculate_covariates` using processed "weasd" data.

```r
locs <- data.frame(id = "001", lon = -78.8277, lat = 35.95013)
weasd_covar <- calculate_covariates(
  covariate = "narr",
  from = weasd_process,
  locs = locs,
  locs_id = "id",
  radius = 0,
  geom = "sf"
)
```
```
Detected `data.frame` extraction locations...
Calculating weasd covariates for 2022-01-01...
Calculating weasd covariates for 2022-01-02...
Calculating weasd covariates for 2022-01-03...
Calculating weasd covariates for 2022-01-04...
Calculating weasd covariates for 2022-01-05...
Returning extracted covariates.
```
```r
weasd_covar
```
```
Simple feature collection with 5 features and 3 fields
Geometry type: POINT
Dimension:     XY
Bounding box:  xmin: 8184606 ymin: 3523283 xmax: 8184606 ymax: 3523283
Projected CRS: unnamed
   id       time     weasd_0                geometry
1 001 2022-01-01 0.000000000 POINT (8184606 3523283)
2 001 2022-01-02 0.000000000 POINT (8184606 3523283)
3 001 2022-01-03 0.000000000 POINT (8184606 3523283)
4 001 2022-01-04 0.000000000 POINT (8184606 3523283)
5 001 2022-01-05 0.001953125 POINT (8184606 3523283)
```

## Connecting Health Outcomes Research Data Systems 

The `amadeus` package has been developed as part of the National Institute of Environmental Health Science's (NIEHS) Connecting Health Outcomes Research Data Systems (CHORDS) program. CHORDS aims to "build and strengthen data infrastructure for patient-centered outcomes research on environment and health" by providing curated data, analysis tools, and educational resources.

## Additional Resources

The following R packages can also be used to access climate and weather data in R, but each differs from `amadeus` in the data sources covered or type of functionality provided.

| Package | Source |
| :--- | :----- |
| [`dataRetrieval`](https://cran.r-project.org/package=dataRetrieval) | [USGS Hydrological Data](https://www.usgs.gov/mission-areas/water-resources/data) and [EPA Water Quality Data](https://www.epa.gov/waterdata/water-quality-data) |
| [`daymetr`](https://cran.r-project.org/package=daymetr) | [Daymet](https://daac.ornl.gov/cgi-bin/dataset_lister.pl?p=32) |
| [`ecmwfr`](https://cran.r-project.org/package=ecmwfr) | [ECMWF Reanalysis v5 (ERA5)](https://www.ecmwf.int/en/forecasts/dataset/ecmwf-reanalysis-v5) |
| [`RClimChange`[^7]](https://github.com/hllauca/RClimChange/) | [NASA Earth Exchange Global Daily Downscaled Projections (NEX-GDDP-CMIP6)](https://www.nccs.nasa.gov/services/data-collections/land-based-products/nex-gddp-cmip6) |
| [`rNOMADS`](https://cran.r-project.org/package=rNOMADS) | [NOAA Operational Model Archive and Distribution System](https://nomads.ncep.noaa.gov/) |
| [`sen2r`[^8]](https://github.com/ranghetti/sen2r) | [Sentinel-2](https://sentiwiki.copernicus.eu/web/s2-mission) |

## Contribution

To add or edit functionality for new data sources or datasets, open a [Pull request](https://github.com/NIEHS/amadeus/pulls) into the main branch with a detailed description of the proposed changes. Pull requests must pass all status checks, and then will be approved or rejected by `amadeus`'s authors.

Utilize [Issues](https://github.com/NIEHS/amadeus/issues) to notify the authors of bugs, questions, or recommendations. Identify each issue with the appropriate label to help ensure a timely response.

[^1]: Multi-Resolution Land Characteristics
[^2]: National Aeronautics and Space Administration
[^3]: Socioeconomic Data and Applications Center
[^4]: National Centers for Environmental Prediction
[^5]: United States Environmental Protection Agency
[^6]: United States Geological Survey
[^7]: Last updated more than two years ago.
[^8]: Archived; no longer maintained.
