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Resources","sub_category":"Soil and Land","monthly_downloads":427,"total_dependent_repos":1,"total_dependent_packages":0,"readme":"---\ntitle: \"smapr\"\noutput: github_document\n---\n\n[![codecov](https://codecov.io/gh/ropensci/smapr/branch/master/graph/badge.svg)](https://codecov.io/gh/ropensci/smapr)\n[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/smapr)](https://cran.r-project.org/package=smapr)\n[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)\n[![](http://cranlogs.r-pkg.org/badges/grand-total/smapr)](http://cran.rstudio.com/web/packages/smapr/index.html) \n[![](https://badges.ropensci.org/231_status.svg)](https://github.com/ropensci/onboarding/issues/231)\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)\n\n\n```{r, echo = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/\"\n)\n```\n\n\nAn R package for acquisition and processing of [NASA (Soil Moisture Active-Passive) SMAP data](http://smap.jpl.nasa.gov/)\n\n## Installation\n\nTo install smapr from CRAN: \n\n```{r cran-installation, eval = FALSE}\ninstall.packages(\"smapr\")\n```\n\nTo install the development version from GitHub:\n\n```{r gh-installation, eval = FALSE}\n# install.packages(\"devtools\")\ndevtools::install_github(\"ropensci/smapr\")\n```\n\n#### Docker instructions (alternative to a local installation)\n\nIf a local installation is not possible for some reason, we have made a Docker \nimage available with smapr and all its dependencies.\n\n```\ndocker run -d -p 8787:8787 earthlab/smapr\n```\n\nIn a web browser, navigate to localhost:8787 and log in with \nusername: rstudio, password: rstudio.\n\n\n## Authentication\n\nAccess to the NASA SMAP data requires authentication through NASA's Earthdata \nportal. \nIf you do not already have a username and password through Earthdata, you can \nregister for an account here: https://urs.earthdata.nasa.gov/\nYou cannot use this package without an Earthdata account. \n\nOnce you have an account, you need to pass your Earthdata username (`ed_un`) \nand password (`ed_pw`) as environmental variables that can be read from within \nyour R session. \nThere are a couple of ways to do this: \n\n### Recommended approach\n\nUse `set_smap_credentials('yourusername', 'yourpasswd')`. \nThis will save your credentials by default, overwriting existing credentials if \n`overwrite = TRUE`. \n\n#### Alternative approaches\n\n- Use `Sys.setenv()` interactively in your R session to set your username and \npassword (not including the `\u003c` and `\u003e`):\n\n```{r, eval = FALSE}\nSys.setenv(ed_un = \"\u003cyour username\u003e\", ed_pw = \"\u003cyour password\u003e\")\n```\n\n- Create a text file `.Renviron` in your home directory, which contains your \nusername and password. \nIf you don't know what your home directory is, execute `normalizePath(\"~/\")` in \nthe R console and it will be printed.\nBe sure to include a new line at the end of the file or R will fail silently \nwhen loading it.\n\nExample `.Renviron file` (note the new line at the end!):\n\n```\ned_un=slkdjfsldkjfs\ned_pw=dlfkjDD124^\n\n```\n\nOnce this file is created, restart your R session and you should now be able to \naccess these environment variables (e.g., via `Sys.getenv(\"ed_un\")`).\n\n\n\n# SMAP data products\n\nMultiple SMAP data products are provided by the NSIDC, and these products vary \nin the amount of processing. \nCurrently, smapr primarily supports level 3 and level 4 data products, \nwhich represent global daily composite and global three hourly modeled data \nproducts, respectively. \nThere are a wide variety of data layers available in SMAP products, including surface soil moisture, root zone soil moisture, freeze/thaw status, surface temperature, vegetation water content, vegetation opacity, net ecosystem carbon exchange, soil temperature, and evapotranspiration. \nNSIDC provides documentation for all SMAP data products on their \n[website](https://nsidc.org/data/smap/smap-data.html), and we provide a summary \nof data products supported by smapr below. \n\n| Dataset id | Description                                         | Resolution |\n|------------|-----------------------------------------------------|------------|\n| SPL2SMAP_S | SMAP/Sentinel-1 Radiometer/Radar Soil Moisture      | 3 km       |\n| SPL3FTA    | Radar Northern Hemisphere Daily Freeze/Thaw State   | 3 km       |\n| SPL3SMA    | Radar Global Daily Soil Moisture                    | 3 km       |\n| SPL3SMP    | Radiometer Global Soil Moisture                     | 36 km      |\n| SPL3SMAP   | Radar/Radiometer Global Soil Moisture               | 9 km       |\n| SPL4SMAU   | Surface/Rootzone Soil Moisture Analysis Update      | 9 km       | \n| SPL4SMGP   | Surface/Rootzone Soil Moisture Geophysical Data     | 9 km       |\n| SPL4CMDL   | Carbon Net Ecosystem Exchange                       | 9 km       |\n\n## Typical workflow\n\nAt a high level, most workflows follow these steps:\n\n1. Find SMAP data with `find_smap()`\n2. Download data with `download_smap()`\n3. List data contents with `list_smap()`\n4. Extract data with `extract_smap()`\n\nEach of these steps are outlined below:\n\n### Finding SMAP data\n\nData are hosted on a server by the National Snow and Ice Data Center. \nThe `find_smap()` function searches for specific data products and returns a \ndata frame of available data.\nAs data mature and pass checks, versions advance. \nAt any specific time, not all versions of all datasets for all dates may exist. \nFor the most up to date overview of dataset versions, see the NSIDC SMAP data \nversion [webpage](https://nsidc.org/data/smap/smap-data.html).\n\n```{r find-data}\nlibrary(smapr)\nlibrary(terra)\navailable_data \u003c- find_smap(id = \"SPL3SMAP\", date = \"2015-05-25\", version = 3)\nstr(available_data)\n```\n\n### Downloading and inspecting SMAP data\n\nGiven a data frame produced by `find_smap`, `download_smap` downloads the data \nonto the local file system. \nUnless a directory is specified as an argument, the data are stored in the \nuser's cache. \n\n```{r download-data}\ndownloads \u003c- download_smap(available_data)\nstr(downloads)\n```\n\nThe SMAP data are provided in HDF5 format, and in any one file there are \nactually multiple data sets, including metadata. \nThe `list_smap` function allows users to inspect the contents of downloaded \ndata at a high level (`all = FALSE`) or in depth (`all = TRUE`). \n\n```{r list-data}\nlist_smap(downloads, all = FALSE)\n```\n\nTo see all of the data fields, set `all = TRUE`. \n\n### Extracting gridded data products\n\nThe `extract_smap` function extracts gridded data products \n(e.g., global soil moisture). \nIf more than one file has been downloaded and passed into the first argument, `extract_smap` extracts data for each file\n\n```{r extract-data, fig.align='center', fig.width=8, fig.height=7}\nsm_raster \u003c- extract_smap(downloads, \"Soil_Moisture_Retrieval_Data/soil_moisture\")\nplot(sm_raster, main = \"Level 3 soil moisture: May 25, 2015\")\n```\n\nThe path \"Soil_Moisture_Retrieval_Data/soil_moisture\" was determined from the \noutput of `list_smap(downloads, all = TRUE)`, which lists all of the data \ncontained in SMAP data files. \n\n### Saving GeoTIFF output\n\nThe data can be saved as a GeoTIFF using the `writeRaster` function \nfrom the terra pacakge. \n\n```{r}\nwriteRaster(sm_raster, \"sm_raster.tif\")\n```\n\n```{r, echo = FALSE, results='hide'}\n# cleanup\nfile.remove(\"sm_raster.tif\")\n```\n\n\n## Meta\n\n* Please [report any issues or bugs](https://github.com/ropensci/smapr/issues),\nafter reading our contribution [guidelines](CONTRIBUTING.md), and the \n[Contributor Code of Conduct](CONDUCT.md). \n* License: GPL-3\n* See `citation(\"smapr\")` in R to cite this package in publications. \n\n[![ropensci_footer](https://ropensci.org/public_images/ropensci_footer.png)](https://ropensci.org)\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://ost.ecosyste.ms/api/v1/projects/1025","html_url":"https://ost.ecosyste.ms/projects/1025"}