Package: amadeus 1.2.0

Kyle Messier

amadeus: Accessing and Analyzing Large-Scale Environmental Data

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>.

Authors:Mitchell Manware [aut, ctb], Insang Song [aut, ctb], Eva Marques [aut, ctb], Mariana Alifa Kassien [aut, ctb], Elizabeth Scholl [ctb], Kyle Messier [aut, cre], Spatiotemporal Exposures and Toxicology Group [cph]

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amadeus.pdf |amadeus.html
amadeus/json (API)
NEWS

# Install 'amadeus' in R:
install.packages('amadeus', repos = c('https://niehs.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/niehs/amadeus/issues

On CRAN:

6.36 score 7 stars 7 scripts 373 downloads 120 exports 105 dependencies

Last updated 4 days agofrom:3d7da8d352. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winOKNov 19 2024
R-4.5-linuxOKNov 19 2024
R-4.4-winOKNov 19 2024
R-4.4-macOKNov 19 2024
R-4.3-winOKNov 19 2024
R-4.3-macOKNov 19 2024

Exports:apply_extentas_mysftimecalc_check_timecalc_messagecalc_prepare_locscalc_return_locscalc_setcolumnscalc_timecalc_workercalculate_covariatescalculate_ecoregioncalculate_geoscalculate_gmtedcalculate_gridmetcalculate_hmscalculate_koppen_geigercalculate_laggedcalculate_merra2calculate_modiscalculate_modis_dailycalculate_narrcalculate_neicalculate_nlcdcalculate_sedac_groadscalculate_sedac_populationcalculate_temporal_dummiescalculate_terraclimatecalculate_tricheck_destfilecheck_for_null_parameterscheck_geomcheck_mysfcheck_mysftimecheck_url_statuscheck_urlsdownload_aqsdownload_cropscapedownload_datadownload_ecoregiondownload_epa_certificatedownload_geosdownload_gmteddownload_gridmetdownload_hashdownload_hmsdownload_hucdownload_koppen_geigerdownload_merra2download_modisdownload_narrdownload_neidownload_nlcddownload_permitdownload_prismdownload_remove_commanddownload_remove_zipsdownload_rundownload_sanitize_pathdownload_sedac_groadsdownload_sedac_populationdownload_setup_dirdownload_sinkdownload_terraclimatedownload_tridownload_unzipdt_as_mysftimeextract_urlsgenerate_date_sequencegenerate_time_sequenceis_date_propernarr_variableprocess_aqsprocess_blackmarbleprocess_blackmarble_cornersprocess_collectionprocess_conformityprocess_covariatesprocess_cropscapeprocess_ecoregionprocess_flatten_sdsprocess_geosprocess_gmtedprocess_gmted_codesprocess_gridmetprocess_gridmet_codesprocess_hmsprocess_hucprocess_koppen_geigerprocess_locs_radiusprocess_locs_vectorprocess_merra2process_merra2_timeprocess_modis_mergeprocess_modis_sdsprocess_modis_swathprocess_modis_warpprocess_narrprocess_neiprocess_nlcdprocess_prismprocess_sedac_codesprocess_sedac_groadsprocess_sedac_populationprocess_terraclimateprocess_terraclimate_codesprocess_triprocess_variable_codesread_commandsrename_timesf_as_mysftimesftime_as_mysftimesftime_as_sfsftime_as_spatrastersftime_as_spatrdssftime_as_spatvectorspatraster_as_sftimespatrds_as_sftimespatvector_as_sftimesum_edctest_download_functions

Dependencies:abindarchivearrowaskpassassertthatbitbit64briocachemcallrclassclassIntclicliprcollapsecpp11crayoncurldata.tabledataRetrievalDBIdescdiffobjdigestdplyre1071evaluateexactextractrfansifastmapfsfstfstcoregenericsgluehmshttrhydroloomjsonliteKernSmoothlatticelifecyclelubridatemagrittrmaplegendmapsfmaptilesMASSmemoisemimenhdplusToolsopensslparallellypbapplypillarpkgbuildpkgconfigpkgloadpngpraiseprettyunitsprocessxprogressproxypspurrrR.methodsS3R.ooR.utilsR6RANNrasterrbibutilsRcppRdpackreadrrlangrprojrootrvests2selectrsfsftimeslippymathspstarsstringistringrsysterratestthattibbletidyrtidyselecttimechangetzdbunitsutf8vctrsvroomwaldowithrwkxml2zip

amadeus workflow

Rendered fromworkflow.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2024-11-13
Started: 2024-07-30

Readme and manuals

Help Manual

Help pageTopics
Create an 'sftime' objectas_mysftime
Calculate covariates wrapper functioncalculate_covariates
Calculate ecoregions covariatescalculate_ecoregion
Calculate atmospheric composition covariatescalculate_geos
Calculate elevation covariatescalculate_gmted
Calculate gridMET covariatescalculate_gridmet
Calculate wildfire smoke covariatescalculate_hms
Calculate climate classification covariatescalculate_koppen_geiger
Calculate temporally lagged covariatescalculate_lagged
Calculate meteorological and atmospheric covariatescalculate_merra2
Calculate MODIS product covariates in multiple CPU threadscalculate_modis
A single-date MODIS workercalculate_modis_daily
Calculate meteorological covariatescalculate_narr
Calculate road emissions covariatescalculate_nei
Calculate land cover covariatescalculate_nlcd
Calculate roads covariatescalculate_sedac_groads
Calculate population density covariatescalculate_sedac_population
Calculate temporal dummy covariatescalculate_temporal_dummies
Calculate TerraClimate covariatescalculate_terraclimate
Calculate toxic release covariatescalculate_tri
Download air quality datadownload_aqs
Download CropScape datadownload_cropscape
Download raw data wrapper functiondownload_data
Download ecoregion datadownload_ecoregion
Download atmospheric composition datadownload_geos
Download elevation datadownload_gmted
Download gridMET datadownload_gridmet
Download wildfire smoke datadownload_hms
Download National Hydrography Dataset (NHD) datadownload_huc
Download climate classification datadownload_koppen_geiger
Download meteorological and atmospheric datadownload_merra2
Download MODIS product filesdownload_modis
Download meteorological datadownload_narr
Download road emissions datadownload_nei
Download land cover datadownload_nlcd
Download PRISM datadownload_prism
Download roads datadownload_sedac_groads
Download population density datadownload_sedac_population
Download TerraClimate datadownload_terraclimate
Download toxic release datadownload_tri
Convert a 'data.table' to an 'sftime'dt_as_mysftime
Process U.S. EPA AQS daily CSV dataprocess_aqs
Assign VIIRS Black Marble products corner coordinates to retrieve a merged rasterprocess_blackmarble
Process Black Marble cornersprocess_blackmarble_corners
Process raw data wrapper functionprocess_covariates
Process CropScape dataprocess_cropscape
Process ecoregion dataprocess_ecoregion
Process MODIS layersprocess_flatten_sds
Process atmospheric composition dataprocess_geos
Process elevation dataprocess_gmted
Process gridMET dataprocess_gridmet
Process wildfire smoke dataprocess_hms
Retrieve Hydrologic Unit Code (HUC) dataprocess_huc
Process climate classification dataprocess_koppen_geiger
Process meteorological and atmospheric dataprocess_merra2
Process MODIS .hdf filesprocess_modis_merge
Process MODIS sub-datasetsprocess_modis_sds
Mosaic MODIS swathsprocess_modis_swath
Warp MODIS swath data into rectilinear grid rasterprocess_modis_warp
Process meteorological dataprocess_narr
Process road emissions dataprocess_nei
Process land cover dataprocess_nlcd
Process PRISM dataprocess_prism
Process roads dataprocess_sedac_groads
Process population density dataprocess_sedac_population
Process TerraClimate dataprocess_terraclimate
Process toxic release dataprocess_tri
Convert an 'sf' to an 'sftime'sf_as_mysftime
Convert an 'sftime' to a 'mysftime'sftime_as_mysftime
Convert an 'sftime' to an 'sf'sftime_as_sf
Convert an 'sftime' to a 'SpatRaster'sftime_as_spatraster
Convert an 'sftime' to a 'SpatRasterDataset'sftime_as_spatrds
Convert an 'sftime' to a 'SpatVector'sftime_as_spatvector
Convert a 'SpatRaster' to an 'sftime'spatraster_as_sftime
Convert a 'SpatRasterDataset' to an 'sftime'spatrds_as_sftime
Convert a 'SpatVector' to an 'sftime'spatvector_as_sftime
Calculate Sum of Exponentially Decaying Contributions (SEDC) covariatessum_edc