Provides automated downloading, parsing, cleaning, unit conversion and formatting of Global Surface Summary of the Day ('GSOD') weather data from the from the USA National Centers for Environmental Information ('NCEI'). Units are converted from from United States Customary System ('USCS') units to International System of Units ('SI'). Stations may be individually checked for number of missing days defined by the user, where stations with too many missing observations are omitted. Only stations with valid reported latitude and longitude values are permitted in the final data. Additional useful elements, saturation vapour pressure ('es'), actual vapour pressure ('ea') and relative humidity ('RH') are calculated from the original data using the improved August-Roche-Magnus approximation (Alduchov & Eskridge 1996) and included in the final data set. The resulting metadata include station identification information, country, state, latitude, longitude, elevation, weather observations and associated flags. For information on the 'GSOD' data from 'NCEI', please see the 'GSOD' 'readme.txt' file available from, < https://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
The GSOD or Global Surface Summary of the Day (GSOD) data provided by the US National Centers for Environmental Information (NCEI) are a valuable source of weather data with global coverage. However, the data files are cumbersome and difficult to work with. GSODR aims to make it easy to find, transfer and format the data you need for use in analysis and provides five main functions for facilitating this:
get_GSOD()
- this function queries and transfers files from the NCEI's
FTP server, reformats them and returns a tidy data frame in R. NOTE If you
have used file exporting capabilities in versions prior to 1.2.0, these have
been removed now in the latest version. This means less dependencies when
installing. Examples of how to export the data are found in the GSODR vignette.
reformat_GSOD()
- this function takes individual station files from the
local disk and re-formats them returning a tidy data frame in R
nearest_stations()
- this function returns a vector of station IDs that fall
within the given radius (kilometres) of a point given as latitude and longitude
update_station_list()
- this function downloads the latest station list from
the NCEI's FTP server updates the package's internal database of stations and
their metadata.
get_inventory()
- this function downloads the latest station inventory
information from the NCEI's FTP server and returns the header information about
the latest version as a message in the console and a tidy data frame of the
stations' inventory for each month that data are reported.
When reformatting data either with get_GSOD()
or reformat_GSOD()
, all units
are converted to International System of Units (SI), e.g., inches to
millimetres and Fahrenheit to Celsius. File output is returned as a tibble()
,
summarising each year by station, which also includes vapour pressure and
relative humidity elements calculated from existing data in GSOD. Additional
data are calculated by this R package using the original data and included in
the final data. These include vapour pressure (ea and es) and relative humidity.
For more information see the description of the data provided by NCEI, http://www7.ncdc.noaa.gov/CDO/GSOD_DESC.txt.
A stable version of GSODR is available from CRAN.
install.packages("GSODR")
A development version is available from from GitHub. If you wish to install the development version that may have new features or bug fixes before the CRAN version does (but also may not work properly), please install the remotes package, available from CRAN. We strive to keep the master branch on GitHub functional and working properly.
if (!require("remotes")) { install.packages("remotes", repos = "http://cran.rstudio.com/") library("remotes")} install_github("ropensci/GSODR")
There are several other sources of weather data and ways of retrieving them through R. Several are also rOpenSci projects.
The GSODTools by Florian Detsch is an R package that offers similar functionality as GSODR, but also has the ability to graph the data and working with data for time series analysis.
The gsod package from DataBrew aims to streamline the way that researchers and data scientists interact with and utilize weather data and relies on [GSODR], but provides data in the package rather than downloading so it is faster (though available data may be out of date).
rnoaa, from rOpenSci offers tools for interacting with and downloading weather data from the United States National Oceanic and Atmospheric Administration but lacks support for GSOD data.
bomrang, from rOpenSci provides functions to interface with Australia Government Bureau of Meteorology (BoM) data, fetching current and historical data including précis and marine forecasts, current weather data from stations, agriculture bulletin data, BoM 0900 or 1500 weather bulletins and satellite and radar imagery.
riem from rOpenSci allows to get weather data from Automated Surface Observing System (ASOS) stations (airports) in the whole world thanks to the Iowa Environment Mesonet website.
weathercan from rOpenSci makes it easier to search for and download multiple months/years of historical weather data from Environment and Climate Change Canada (ECCC) website.
CliFlo from rOpenSci is a web portal to the New Zealand National Climate Database and provides public access (via subscription) to around 6,500 various climate stations (see https://cliflo.niwa.co.nz/ for more information). Collating and manipulating data from CliFlo (hence clifro) and importing into R for further analysis, exploration and visualisation is now straightforward and coherent. The user is required to have an Internet connection, and a current CliFlo subscription (free) if data from stations, other than the public Reefton electronic weather station, is sought.
weatherData provides a selection of functions to fetch weather data from Weather Underground and return it as a clean data frame.
90 m hole-filled SRTM digital elevation (Jarvis et al. 2008) was used to identify and correct/remove elevation errors in data for station locations between -60˚ and 60˚ latitude. This applies to cases here where elevation was missing in the reported values as well. In case the station reported an elevation and the DEM does not, the station reported is taken. For stations beyond -60˚ and 60˚ latitude, the values are station reported values in every instance. See https://github.com/ropensci/GSODR/blob/master/data-raw/fetch_isd-history.md for more detail on the correction methods.
Users of these data should take into account the following (from the NCEI website):
international commercial use. They can be used within the U.S. or for non-commercial international activities without restriction. The non-U.S. data cannot be redistributed for commercial purposes. Re-distribution of these data by others must provide this same notification." WMO Resolution 40. NOAA Policy
Please report any issues or bugs.
License: MIT
To cite GSODR, please use: Adam H Sparks, Tomislav Hengl and Andrew Nelson (2017). GSODR: Global Summary Daily Weather Data in R. The Journal of Open Source Software, 2(10). DOI: 10.21105/joss.00177.
Please note that the GSODR project is released with a Contributor Code of Conduct. By participating in the GSODR project you agree to abide by its terms.
Jarvis, A., Reuter, H. I., Nelson, A., Guevara, E. (2008) Hole-filled SRTM for the globe Version 4, available from the CGIAR-CSI SRTM 90m Database (http://srtm.csi.cgiar.org)
future_apply
in processing files after downloading. This allows for end
users to use a parallel process of their choice.Refactor internal functionality to be more clear and efficient in execution
country-list
is not loaded unless user has specified a country in
get_GSOD()
An instance where the FIPS code was determined twice was removed
Replace \dontrun{}
with \donttest{}
in documentation examples
Ensure that DESCRIPTION file follows CRAN guidelines
Format help files, fixing errors and formatting for attractiveness
Update internal database of station locations
Store internal database of station locations fields BEGIN
and END
as
integer, not double
Clarify code of conduct statement in README that it only applies to this, GSODR, project
Prompt user for input with warning about reproducibility if using the
update_station_list()
function
Adds metadata header to the tibble
returned by get_inventory()
Remove startup message to conform with rOpenSci guidelines
Remove extra code, clean up code-chunks and use hrbrthemes::theme_ipsum()
for
data-raw/fetch_isd-history.md
Fix bug in creating isd-history.rda
file where duplicate stations existed
in the file distributed with GSODR
but with different corrected elevation
values
Repatch bug reported and fixed previously in version 1.2.0 where Windows users could not successfully download files. This somehow snuck back in.
Introduce a message if a station ID is requested but files are not found on the server. This is in response to an inquiry from John Paul Bigouette where a station is reported as having data in the inventory but the files do not exist on the server.
Fix bug that removed a few hundred stations from the internal GSODR
database of stations in the data-raw
files.
Clean documentation, shortening long lines, fixing formatting, incomplete sentences and broken links
Clarify the reasons for errors that a user may encounter
Update internal databases of station metadata
Clean up this file
Remove ability to export files from get_GSOD()
to slim down the package
dependencies and this functions parameters. Examples of how to convert to a
spatial object (both sp and sf are shown) and export ESRI Shapefiles and
GeoPackage files are now included in the vignette.
As a result of the previous point, the sp and rgdal packages are no longer Imports but are now in Suggests along with sf for examples in the GSOD vignette.
Fix a nasty bug where GSOD files downloaded using Windows would not untar
properly. This caused the get_GSOD()
function to fail. Thanks to Ross
Darnell, CSIRO, for reporting this.
Correct options in "GSODR use case: Specified years/stations vignette" on
line 201 where file
was incorrectly used in place of path
. Thanks to
Ross Darnell, CSIRO, for reporting this.
Correct documentation for reformat_GSOD()
Update internal databases of station metadata
Vignettes contain pre-built figures for faster package installation when building vignettes
Fix startup message formatting
Correct ORCID comment in author field of DESCRIPTION
Update internal databases for country list and isd_history
MAX_FLAG
and MIN_FLAG
columns now report NA
when there is no flagComment for Bob and Hugh in DESCRIPTION now only ORCID url
dplyr version set to >= 0.7.0 not 0.7 as before
Start-up message statement is more clear in relation to WMO resolution 40, that GSODR does not redistribute any weather data itself
Remove unnecessary function, .onLoad(), from zzz.R
Function titles in documentation now in title case
Correct grammar in documentation
The data.table and fields packages are no longer imported. All internal functions now use dplyr or base R functionality, reducing the dependencies of GSODR
Any data frames returned by GSODR functions are returned as a tibble()
object
The YEARMODA
column is now returned as Date
without time, rather than
Character
Add new function, get_inventory()
, which downloads the NCEI's station
inventory document and returns a tibble()
object of the data
Use larger images and provide a table of contents in vignettes
Updated and enhanced introductory vignette
Update internal stations list
Fix documentation in vignette where first example would not run due to changes in package data formats
Fix bug in GSODR vignette where examples would not run due to libraries not being loaded
Fix bug where prior server queries would be pre/appended to subsequent queries
Fix bug where invalid stations would return an empty dataframe, should
stop and return message about checking the station
value supplied to
get_GSOD()
and check if data are available for the years requested
Update Appendix 2 of GSODR vignette, map of station locations, to be more
clear and follow same format as that of bomrang
package
Update example output in GSODR vignette where applicable
Add welcome message on startup regarding data use and sharing
Update internal stations list
Fix bug where "Error in read_connection_(con):" when writing to CSV occurs
Fix typo in line 160 of get_GSOD()
where "Rda" should be "rda" to
properly load internal package files
Data distributed with GSODR are now internal to the package and not externally exposed to the user
Vignettes have been updated and improved with an improved order of information presented and some have been combined for easier use
Data for station locations and unique identifiers is now provided with the package on installation. Previously this was fetched each time from the ftp server.
The station metadata can now be updated if necessary by using
update_station_list()
, this change overwrites the internal data that were
originally distributed with the package. This operation will fetch the
latest list of stations and corresponding information from the NCEI ftp
server. Any changes will be overwritten when the R package is updated,
however, the package update should have the same or newer data included, so
this should not be an issue.
Replace plyr functions with purrr, plyr is no longer actively developed
plyr is no longer an import
get_station_list()
is no longer supported. Instead use the new
update_station_list()
to update the package's internal station database.
Improved documentation (i.e., spelling corrections and more descriptive)
More descriptive vignette for "GSODR use case: Specified years/stations vignette"
Round MAX/MIN temp to one decimal place, not two
Update SRTM elevation data
Update country list data
Fix missing images in README.html on CRAN
Update documentation for get_GSOD()
when using station
parameter
Edit paper.md for submission to JOSS
Remove extra packages listed as dependencies that are no longer necessary
Correct Working_with_spatial_and_climate_data.Rmd where it was missing the first portion of documentation and thus examples did not work
The get_GSOD()
function returns a data.frame
object in the current R
session with the option to save data to local disk
Multiple stations can be specified for download rather than just downloading a single station or all stations
A new function, nearest_stations()
is now included to find stations
within a user specified radius (in kilometres) of a point given as latitude
and longitude in decimal degrees
A general use vignette is now included
New vignette with a detailed use-case
Output files now include fields for State (US only) and Call (International Civil Aviation Organization (ICAO) Airport Code)
Use FIPS codes in place of ISO3c for file name and in output files because some stations do not have an ISO country code
Spatial file output is now in GeoPackage format (GPKG). This results in a single file output unlike shapefile and allows for long field names
Users can specify file name of output
R >= 3.2.0 now required
Field names in output files use "_" in place of "."
Long field names now used in file outputs
Country is specified using FIPS codes in file name and output file contents due to stations occurring in some locales that lack ISO 3166 3 letter country codes
The get_GSOD()
function will retrieve the latest station data from NCDC
and automatically merge it with the CGIAR-CSI SRTM elevation values provided
by this package. Previously, the package provided it's own list of station
information, which was difficult to keep up-to-date
A new reformat_GSOD()
function reformats station files in
"WMO-WBAN-YYYY.op.gz" format that have been downloaded from the United
States National Climatic Data Center's (NCDC) FTP server.
A new function, get_station_list()
allows for fetching latest station
list from the FTP server and querying by the user for a specified station or
location.
New data layers are provided through a separate package,
GSODRdata
, which provide
climate data formatted for use with GSODR.
CHELSA (climatic surfaces at 1 km resolution), http://chelsa-climate.org/,
MODCF - Remotely sensed high-resolution global cloud dynamics for predicting ecosystem and biodiversity distributions (http://www.earthenv.org/cloud),
ESACCI - ESA's CCI-LC snow cover probability (http://maps.elie.ucl.ac.be/CCI/viewer/index.php) and
CRU CL2.0 (climatic surfaces at 10 minute resolution) (https://crudata.uea.ac.uk/~timm/grid/CRU_CL_2_0.html)
Improved file handling for individual station downloads
Missing values are handled as NA
not -9999
Change from GPL >= 3 to MIT licence to bring into line with ropensci packages
Now included in ropensci, ropensci/GSODR
get_GSOD()
function optimised for speed as best possible after FTPing
files from NCDC server
All files are downloaded from server and then locally processed, previously these were sequentially downloaded by year and then processed
A progress bar is now shown when processing files locally after downloading
Reduced package dependencies
The get_GSOD()
function now checks stations to see if the years being
queried are provided and returns a message alerting user if the station and
years requested are not available
When stations are specified for retrieval using the station = ""
parameter, the get_GSOD()
function now checks to see if the file exists on
the server, if it does not, a message is returned and all other stations
that have files are processed and returned in output
Documentation has been improved throughout package
Better testing of internal functions
Fixed: Remove redundant code in get_GSOD()
function
Fixed: The stations data frame distributed with the package now include stations that are located above 60 latitude and below -60 latitude
Missing values are reported as NA for use in R, not -9999 as previously
The path
parameter is now instead called dsn
to be more inline with
other tools like readOGR()
and writeOGR()
Shapefile file out is no longer supported. Use GeoPackage (GPKG) instead
The option to remove stations with too many missing days is now optional, it now defaults to including all stations, the user must specify how many missing stations to check for an exclude
The max_missing
parameter is now user set, defaults to no check, return
all stations regardless of missing days
Users can now select to merge output for station queries across multiple
years. Previously one year = one file per station. Now are set by user,
merge_station_years = TRUE
parameter, only one output file is generated
Country list is now included in the package to reduce run time necessary when querying for a specific country. However, this means any time that the country-list.txt file is updated, this package needs to be updated as well
Updated stations
list with latest version from NCDC published 12-07-2016
Country list is now included in the package to reduce run time necessary when querying for a specific country. However, this means any time that the country-list.txt file is updated, this package needs to be updated as well
Country level, agroclimatology and global data query conversions and calculations are processed in parallel now to reduce runtime
Improved documentation with spelling fixes, clarification and updates
Enable ByteCompile
option upon installation for small increase in speed
Use write.csv.raw
from
[iotools]("https://cran.r-project.org/web/packages/iotools/index.html")
to
greatly improve runtime by decreasing time used to write CSV files to disk
Use writeOGR()
from rgdal
, in place of raster's
shapefile
to
improve runtime by decreasing time used to write shapefiles to disk
Country level, agroclimatology and global data query conversions and calculations are processed in parallel now to reduce runtime
Improved documentation with spelling fixes, clarification and updates
Enable ByteCompile
option upon installation for small increase in speed
Use write.csv.raw
from
[iotools]("https://cran.r-project.org/web/packages/iotools/index.html")
to greatly improve runtime by decreasing time used to write CSV files to
disk
Fix bug with connection timing out for single station queries commit: a126641e00dc7acc21844ff0436e5702f8b6e04a
Somehow the previously working function that checked country names broke
with the toupper()
function. A new
function from juba fixes this issue and
users can now select country again
User entered values for a single station are now checked against actual station values for validity
stations.rda is compressed
stations.rda now includes a field for "corrected" elevation using hole-filled SRTM data from Jarvis et al. 2008, see https://github.com/ropensci/GSODR/blob/master/data-raw/fetch_isd-history.md for a description
Set NA or missing values in CSV or shapefile to -9999 from -9999.99 to align with other data sources such as Worldclim
Fix issues with MIN/MAX where MIN referred to MAX (Issue 5)
Fix bug where the tf
item was incorrectly set as
tf < - "~/tmp/GSOD-2010.tar
, not tf < - tempfile
, in get_GSOD()
(Issue 6)
CITATION file is updated and corrected
User now has the ability to generate a shapefile as well as CSV file output (Issue 3)
Documentation is more complete and easier to use
Fix issue when reading .op files into R where temperature was incorrectly read causing negative values where T >= 100F, this issue caused RH values of
100% and incorrect TEMP values (Issue 1)
Spelling corrections
Include MIN/MAX flag column
Station data is now included in package rather than downloading from NCDC every time get_GSOD() is run, this data has some corrections where stations with missing LAT/LON values or elevation are omitted, this is not the original complete station list provided by NCDC
Fixed bug where YDAY not correctly calculated and reported in CSV file
CSV files for station only queries now are names with the Station Identifier. Previously named same as global data
Likewise, CSV files for agroclimatology now are names with the Station Identifier. Previously named same as global data
Set values where MIN > MAX to NA
Set more MIN/MAX/DEWP values to NA. GSOD README indicates that 999 indicates missing values in these columns, this does not appear to always be true. There are instances where 99 is the value recorded for missing data. While 99F is possible, the vast majority of these recorded values are missing data, thus the function now converts them to NA
Bug fix in MIN/MAX with flags. Some columns have differing widths, which caused a flag to be left attached to some values
Correct URL in README.md for CRAN to point to CRAN not GitHub
Bug fix in importing isd-history.csv file. Previous issues caused all lat/lon/elev values to be >0.
Bug fix where WDSP was mistyped as WDPS causing the creation of a new column, rather than the conversion of the existing
Bug fix if Agroclimatology selected. Previously this resulted in no records.
Set the default encoding to UTF8.
Bug fix for country selection. Some countries did not return proper ISO code.
Bug fix where WDSP was mistyped as WDPS causing the creation of a new column, rather than the conversion of the existing
Use write.csv, not readr::write_csv due to issue converting double to string: https://github.com/hadley/readr/issues/387
Now available on CRAN
Add single quotes around possibly misspelled words and spell out comma-separated values and geographic information system rather than just using "CSV" or "GIS" in DESCRIPTION.
Add full name of GSOD (Global Surface Summary of the Day) and URL for GSOD, https://data.noaa.gov/dataset/dataset/global-surface-summary-of-the-day-gsod/ to DESCRIPTION as requested by CRAN.
Require user to specify directory for resulting .csv file output so that any files written to disk are interactive and with user's permission