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Change","sub_category":"Climate Data Access and Visualization","monthly_downloads":1375,"total_dependent_repos":12,"total_dependent_packages":1,"readme":"# ecmwfr \u003cimg src=\"man/figures/logo.png\" align=\"right\" height=\"138.5\"/\u003e\n\n[![R-CMD-check](https://github.com/bluegreen-labs/ecmwfr/workflows/R-CMD-check/badge.svg)](https://github.com/bluegreen-labs/ecmwfr/actions)\n[![codecov](https://codecov.io/gh/bluegreen-labs/ecmwfr/branch/master/graph/badge.svg)](https://app.codecov.io/gh/bluegreen-labs/ecmwfr)\n[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/ecmwfr)](https://cran.r-project.org/package=ecmwfr)\n[![Project Status: Active -- The project has reached a stable, usable\nstate and is being actively\ndeveloped.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![](https://cranlogs.r-pkg.org/badges/grand-total/ecmwfr)](https://cran.r-project.org/package=ecmwfr)\n[![DOI](https://zenodo.org/badge/156325084.svg)](https://zenodo.org/badge/latestdoi/156325084)\n\nProgrammatic interface to the two [European Centre for Medium-Range\nWeather Forecasts](https://www.ecmwf.int/) API services. The package\nprovides easy access to all available Data Stores from within R, matching and\nexpanding upon the ECMWF python tools. Support is provided for the \n[Climate Data Store](https://cds.climate.copernicus.eu), the \n[Atmosphere Data Store](https://ads.atmosphere.copernicus.eu) and the\n[Early Warning Data Store](https://ewds.climate.copernicus.eu) (from the \nCopernicus Emergency Management Services).\n\n## How to cite this package\n\nYou can cite this package like this \"we obtained data from the European\nCentre for Medium-Range Weather Forecasts API using the ecmwf R package\n(Hufkens, Stauffer, and Campitelli 2019)\". Here is the full\nbibliographic reference to include in your reference list (don't forget\nto update the 'last accessed' date):\n\n\u003e Hufkens, K., R. Stauffer, \u0026 E. Campitelli. (2019). ecmwfr:\n\u003e Programmatic interface to the two European Centre for Medium-Range\n\u003e Weather Forecasts API services. Zenodo.\n\u003e \u003chttps://doi.org/10.5281/zenodo.2647531\u003e.\n\n## Installation\n\n### stable release\n\nTo install the current stable release use a CRAN repository:\n\n``` r\ninstall.packages(\"ecmwfr\")\nlibrary(\"ecmwfr\")\n```\n\n### development release\n\nTo install the development releases of the package run the following\ncommands:\n\n``` r\nif(!require(remotes)){install.packages(\"remotes\")}\nremotes::install_github(\"bluegreen-labs/ecmwfr\")\nlibrary(\"ecmwfr\")\n```\n\nVignettes are not rendered by default, if you want to include additional\ndocumentation please use:\n\n``` r\nif(!require(remotes)){install.packages(\"remotes\")}\nremotes::install_github(\"bluegreen-labs/ecmwfr\", build_vignettes = TRUE)\nlibrary(\"ecmwfr\")\n```\n\n### breaking changes (\u003e= 2.0.0)\n\n#### querying data\n\nWith the introduction of version 2.0.0 and the migration to the new API some\nchanges to the package were implemented which will cause breaking changes. In particular\nthe `wf_request()` function(s) now use a default `ecmwfr` user field due to the\nconsolidation of the API, with a single sign-on across all services and the use\nof a Personal Access Token (PAT) rather than user and password credentials.\n\nIn order to migrate to version \u003e=2.0.0 you will have to provide a new PAT using `wf_set_key()` and remove the user argument from any `wf_request()` call, i.e.:\n\n```r\n# The original v1.x.x call\nwf_request(\n  request,\n  user = \"your_id\"\n)\n\n# The new v2.x.x call\nwf_request(\n  request\n)\n```\n\nThe requests themselves should translate mostly without intervention\nand remain nested lists of parameters.\n\n#### netCDF data format\n\nIn comparison with the original services the new API [regresses in terms\nof netCDF support](https://forum.ecmwf.int/t/changes-to-grib-to-netcdf-converter-on-cds-beta-ads-beta/4322). Those relying on common netCDF support such as ecosystem modellers will find this troubling. Note that both CDS and ADS have different policies and use different methods. Note that this regression in usability is not caused\nby this package. Please forward any issues you have with formatting of the data\nto the ECMWF using [the public forum](https://forum.ecmwf.int/t/changes-to-grib-to-netcdf-converter-on-cds-beta-ads-beta/4322). We suggest to fall back to grib files, and convert internally if netCDF driver files are needed. Sadly, consistency for now is not, and will not be, guaranteed it seems.\n\n## Use:\n\nCreate a ECMWF account by [self\nregistering](https://www.ecmwf.int/user/login). Once your user account has been verified you can get your API token (or `key` in `ecmwfr`) by visiting one of the Data Stores user profiles, for example the CDS [user profile](https://cds.climate.copernicus.eu/profile). \n\nThe API Token is a [UUID](https://fr.wikipedia.org/wiki/Universally_unique_identifier) and should look something like:\n\n```\nAPI: abcd1234-foo-bar-98765431-XXXXXXXXXX\n```\n\nThis API Token gives you access to all Data Store services, including the climate atmosphere and emergency management services. This information is required to be able to retrieve data via the `ecmwfr` package. Use the\n`ecmwfr` [`wf_set_key`](references/wf_set_key.html) function to store\nyour login information in the system keyring (see below).\n\nIn order to download the data, you will also need to accept the licence agreement on the bottom of the [user profile page](https://cds.climate.copernicus.eu/profile).\n\n### Setup\n\nBefore using the package in `R` to download data you have to save your login\ninformation. The package does not allow you to use your key inline in scripts\nto limit security issues when sharing scripts on github or otherwise. \n\n**The following lines should NEVER be included in any script and run only once at setup.**\n\n``` r\n# set a key to the keychain\nwf_set_key(key = \"abcd1234-foo-bar-98765431-XXXXXXXXXX\")\n\n# you can retrieve the key using\nwf_get_key()\n\n# the output should be the key you provided\n# \"abcd1234-foo-bar-98765431-XXXXXXXXXX\"\n\n# Alternatively you can input your login info with an interactive request\n# if you do not put in the key directly\nwf_set_key()\n\n# you will get a command line request to provide the required details\n```\n\nBefore you can download any data you have to make sure to accept the\nterms and conditions here: Before downloading and processing data from\nCDS please make sure you accept the terms and conditions in the profile\npages of your Data Store of choice.\n\n### Data Requests\n\nTo download data use the [`wf_request`](references/wf_request.html)\nfunction, and a request string syntax. The simplest way to get the requests is \nto go to the Data Store website which offers an interactive interface to create\nthese requests e.g., for the CDS ERA-5 reanalysis data:\n\n-   [ERA-5 at pressure level data](https://cds.climate.copernicus.eu/datasets/reanalysis-era5-pressure-levels?tab=download)\n-   [ERA-5 land](https://cds.climate.copernicus.eu/datasets/reanalysis-era5-land?tab=download)\n-   ...\n\nAfter formatting the request online copy the API request python code to your script.\nThe request should include the _dataset_, _request_ and _target_ field (if available).\n\n![](https://github.com/user-attachments/assets/865fcf2a-e4da-4fd8-80a8-9ced448caabb)\n\nInstead of `json` formatting as shown in the online form the `ecmwfr` package \nuses a _R_ lists for all the arguments. This makes changing variables less prone\nto error, although overall we suggest not to manually create requests and use\nthe RStudio Addin to translate the python `json` request to _R_ as shown below.\n\nJust select the whole query, including the dataset and target fields, and click\non the Addins \u003e ECMWF Python to list. The original python query is listed below\nso you can try this routine yourself.\n\n![](https://github.com/user-attachments/assets/100cf392-3214-4bcd-b308-7ef7a50308a0)\n\n```python\n# The full python query, which you can translate to an R\n# list using the Addin\n\ndataset = \"reanalysis-era5-pressure-levels\"\nrequest = {\n  'product_type': ['reanalysis'],\n  'variable': ['temperature'],\n  'year': ['2000'],\n  'month': ['04'],\n  'day': ['04'],\n  'time': ['00:00'],\n  'pressure_level': ['850'],\n  'data_format': 'netcdf',\n  'download_format': 'unarchived',\n  'area': [70, -20, 60, 30]\n}\n```\n\nThis will give you a request as an annotated list. If no target file is\nspecified in the original request a _target_ field will be added to the list\nwith a default name `TMPFILE`. Replace this filename with something that matches\nyour preference and the specified data format. In this case the default name\nwas changed to `era5-demo.nc`, a netcdf file. This formatted request can now be\nused by the [`wf_request`](references/wf_request.html) function to query and download the\ndata. By default the process is verbose, and will give you plenty of feedback\non progress.\n\n``` r\n# This is an example of a request as converted from \nrequest \u003c- list(\n  dataset_short_name = \"reanalysis-era5-pressure-levels\",\n  product_type = \"reanalysis\",\n  variable = \"temperature\",\n  year = \"2000\",\n  month = \"04\",\n  day = \"04\",\n  time = \"00:00\",\n  pressure_level = \"850\",\n  data_format = \"netcdf\",\n  download_format = \"unarchived\",\n  area = c(70, -20, 60, 30),\n  target = \"era5-demo.nc\"\n)\n\n# If you have stored your user login information\n# in the keyring by calling cds_set_key you can\n# call:\nfile \u003c- wf_request(\n request  = request,  # the request\n transfer = TRUE,     # download the file\n path     = \".\"       # store data in current working directory\n )\n```\n\nThe Data Store services are quite fast, however, if you request a lot of\nvariables, multiple levels, and data over several years these requests\nmight take quite a while! You can check the scope of your query and if\nit is out of bounds in the right hand `Request Validation` panel when\nformatting your original data request in the web interface.\n\n**Note**: If you need to download larger\namounts of data it is suggested to split the downloads, e.g., download\nthe data in chunks (e.g., month-by-month, or year-by-year). A progress\nindicator will keep you informed on the status of your request. Keep in\nmind that all data downloaded will be buffered in memory limiting the\ndownloads to \\~6GB on low end systems.\n\n#### ERA5 demo \n\nThe above request uses ERA-5 reanalysis data on pressure levels.\n\n* `dataset`: downloading ERA-5 reanalysis on pressure level(s)\n* `product_type`: (deterministic) reanalysis data\n* `variable`/`pressure_level`: requesting temperature on 850 hectopascal\n* `year`/`month`/`day`: April 4, 2000 (one day in this example)\n* `time`: valid at 00:00 UTC (date/time always in UTC),\n* `area`: custom subset covering northern Europe\n* `format`: output format NetCDF\n* `target`: local output file `era5-demo.nc`\n\nThe data set as specified above can be downloaded calling the\n`wf_request` function, and upon request returns the location of the \nNetCDF file on your system. The `file` variable can then be used directly\nfor further processing (note: should the download be interupted the job ID in your\ndownload queue is returned and the job can be resumed using `wf_transfer()`).\n\nOnce the retrieval has finished you should now be the owner of a NetCDF containing\nthe requested information located in the current working directory, called `era5-demo.nc`.\n\nWe can quickly visualize this data using the `terra` geospatial library using:\n\n```r\n# Open NetCDF file and plot the data\n# (trap read error on mac - if gdal netcdf support is missing)\nr \u003c- terra::rast(file)\nterra::plot(r, main = \"ERA-5 Reanalysis Demo (2m Temperature 850 hPa)\")\nmaps::map(\"world\", add = TRUE)\n```\n\n![spatial-plot](https://github.com/user-attachments/assets/27a89664-7aaf-483f-94dd-8d9992e862be)\n\n## File and system based keychains\n\nOn linux you can opt to use a file based keyring, instead of a GUI based\nkeyring manager. This is helpful for headless setups such as servers.\nFor this option to work linux users must set an environmental option.\n\n``` r\noptions(keyring_backend=\"file\")\n```\n\nYou will be asked to provide a password to encrypt the keyring with.\nUpon the start of each session you will be asked to provide this\npassword, unlocking all `ecmwfr` credentials for this session. Should\nyou ever forget the password just delete the file at:\n`~/.config/r-keyring/ecmwfr.keyring` and re-enter all your credentials.\n\n## Date specification\n\nFor those familiar with the old ECMWF *mars* syntax: CDS/ADS/CEMS does not accept\n`date = \"2000-01-01/to/2000-12-31\"` specifications. It is possible to\nspecify one specific date via `date = \"2000-01-01\"` or multiple days via\n`date = [\"2000-01-01\",\"2000-01-02\",\"2000-10-20\"]` or\n`date = \"YYYY-MM-DD/YYYY-MM-DD\"`.\n\n## Citation\n\nHufkens, K., R. Stauffer, \u0026 E. Campitelli. (2019). ecmwfr: Programmatic\ninterface to the two European Centre for Medium-Range Weather Forecasts\nAPI services. Zenodo. \u003chttps://doi.org/10.5281/zenodo.2647531\u003e.\n\n## Acknowledgements\n\nThis project is maintained by BlueGreen Labs (BV). This project was in the past\npartially supported by the Belgian Science Policy office\nCOBECORE project (BELSPO; grant BR/175/A3/COBECORE), a \"Fonds voor\nWetenschappelijk Onderzoek\" travel grant (FWO; V438318N) and the Marie\nSkłodowska-Curie Action (H2020 grant 797668). Logo design elements are\ntaken from the FontAwesome library according to [these\nterms](https://fontawesome.com/license), where the globe element was\ninverted and intersected.\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.2647531"],"works":{"http://doi.org/10.5281/zenodo.2647531":null},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["geolocation","soil","oceanography","climate","ecology","bird"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/834","html_url":"https://ost.ecosyste.ms/projects/834"}