amadeus1.3.2.1 package

Accessing and Analyzing Large-Scale Environmental Data

process_merra2

Process meteorological and atmospheric data

calculate_lagged

Calculate temporally lagged covariates

calculate_merra2

Calculate meteorological and atmospheric covariates

calculate_modis_daily

A single-date MODIS worker

calculate_modis

Calculate MODIS product covariates in multiple CPU threads

download_terraclimate

Download TerraClimate data

download_tri

Download toxic release data

download_unzip

Unzip zip files

dt_as_mysftime

Convert a data.table to an sftime

extract_urls

Extract download URLs

generate_date_sequence

Generate date sequence

generate_time_sequence

Generate time sequence

interactive

Open interactive session with container.sif container.

is_date_proper

Check date format

narr_variable

Sort NOAA NARR variables

process_aqs

Process U.S. EPA AQS daily CSV data

process_blackmarble_corners

Process Black Marble corners

download_run

Run download commands

download_sanitize_path

Sanitize directory

download_setup_dir

Setup directory

download_sink

Sink download commands

process_locs_vector

Process locations as SpatVector

process_merra2_time

Process MERRA2 time steps

sftime_as_spatvector

Convert an sftime to a SpatVector

spatraster_as_sftime

Convert a SpatRaster to an sftime

spatrds_as_sftime

Convert a SpatRasterDataset to an sftime

spatvector_as_sftime

Convert a SpatVector to an sftime

check_geom

Check that geom value is one of FALSE, "sf", or "terra"

check_mysf

Check sf object

apply_extent

Apply extent to the processed data

as_mysftime

Create an sftime object

calc_check_time

Check time values

calc_message

Send progress messages

calc_prepare_locs

Prepare extraction locations

calc_return_locs

Prepare covariates for return

calc_setcolumns

Set column names

calc_time

Prepare time values

calc_worker

Perform covariate extraction

calculate_covariates

Calculate covariates wrapper function

calculate_cropscape

Calculate Cropscape covariates

calculate_ecoregion

Calculate ecoregions covariates

calculate_geos

Calculate atmospheric composition covariates

calculate_gmted

Calculate elevation covariates

calculate_gridmet

Calculate gridMET covariates

check_mysftime

Check sftime object

check_url_status

Check HTTP status

calculate_groads

Calculate roads covariates

calculate_hms

Calculate wildfire smoke covariates

calculate_huc

Calculate HUC covariates

calculate_koppen_geiger

Calculate climate classification covariates

check_urls

Implement check_url_status

collapse_nlcd

Collapse listed NLCD values while filling in NA for sites outside data...

calculate_narr

Calculate meteorological covariates

calculate_nei

Calculate road emissions covariates

calculate_nlcd

Calculate land cover covariates

calculate_population

Calculate population density covariates

cov

Calculate code coverage of the beethoven package with the `container...

calculate_prism

Calculate PRISM covariates

calculate_temporal_dummies

Calculate temporal dummy covariates

calculate_terraclimate

Calculate TerraClimate covariates

calculate_tri

Calculate toxic release covariates

check_destfile

Check if destination file exists or is 0 bytes.

check_for_null_parameters

Check parameters

download_aqs

Download air quality data

download_cropscape

Download CropScape data

download_data

Download raw data wrapper function

download_ecoregion

Download ecoregion data

download_edgar

Download EDGAR Emissions Data

download_nei

Download road emissions data

download_geos

Download atmospheric composition data

download_gmted

Download elevation data

download_gridmet

Download gridMET data

download_groads

Download roads data

download_hash

Create hash of downloaded files.

download_hms

Download wildfire smoke data

download_huc

Download National Hydrography Dataset (NHD) data

download_koppen_geiger

Download climate classification data

download_merra2

Download meteorological and atmospheric data

download_modis

Download MODIS product files

download_narr

Download meteorological data

download_nlcd

Download land cover data

download_permit

Check data download acknowledgement

download_population

Download population density data

download_prism

Download PRISM data

download_remove_command

Remove download commands

download_remove_zips

Remove zip files

process_blackmarble

Assign VIIRS Black Marble products corner coordinates to retrieve a me...

process_collection

Process GEOS-CF and MERRA2 collection codes

process_conformity

Check input assumptions

process_covariates

Process raw data wrapper function

process_cropscape

Process CropScape data

process_ecoregion

Process ecoregion data

process_flatten_sds

Process MODIS layers

process_geos

Process atmospheric composition data

process_gmted_codes

Process elevation statistic and resolution codes

process_gmted

Process elevation data

process_gridmet_codes

Process gridMET variable codes

process_gridmet

Process gridMET data

process_groads

Process roads data

process_hms

Process wildfire smoke data

process_huc

Retrieve Hydrologic Unit Code (HUC) data

process_koppen_geiger

Process climate classification data

process_locs_radius

Process locations buffer

process_modis_merge

Process MODIS .hdf files

process_modis_sds

Process MODIS sub-datasets

process_modis_swath

Mosaic MODIS swaths

process_modis_warp

Warp MODIS swath data into rectilinear grid raster

process_narr

Process meteorological data

process_nei

Process road emissions data

process_nlcd

Process land cover data

process_population

Process population density data

process_prism

Process PRISM data

process_sedac_codes

Process population resolution code

process_terraclimate_codes

Process terraClimate variable codes

process_terraclimate

Process TerraClimate data

process_tri

Process toxic release data

process_variable_codes

Filter gridMET and terraClimate variable names and variable codes

read_commands

Import download commands

rename_time

Rename $time

sf_as_mysftime

Convert an sf to an sftime

sftime_as_mysftime

Convert an sftime to a mysftime

sftime_as_sf

Convert an sftime to an sf

sftime_as_spatraster

Convert an sftime to a SpatRaster

sftime_as_spatrds

Convert an sftime to a SpatRasterDataset

sum_edc

Calculate isotropic Sum of Exponentially Decaying Contributions (SEDC)...

test_download_functions

Download unit tests

test

Run all tests within a single file from tests/testthat/ directory wi...

Functions are designed to facilitate access to and utility with large scale, publicly available environmental data in R. The package contains functions for downloading raw data files from web URLs (download_data()), processing the raw data files into clean spatial objects (process_covariates()), and extracting values from the spatial data objects at point and polygon locations (calculate_covariates()). These functions call a series of source-specific functions which are tailored to each data sources/datasets particular URL structure, data format, and spatial/temporal resolution. The functions are tested, versioned, and open source and open access. For sum_edc() method details, see Messier, Akita, and Serre (2012) <doi:10.1021/es203152a>.

  • Maintainer: Kyle Messier
  • License: MIT + file LICENSE
  • Last published: 2026-01-26