R client for working with ERDDAP servers
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README.md

rerddap

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rerddap is a general purpose R client for working with ERDDAP servers.

Installation

From CRAN

install.packages("rerddap")

Or development version from GitHub

devtools::install_github("ropensci/rerddap")
library('rerddap')

Some users may experience an installation error, stating to install 1 or more packages, e.g., you may need DBI, in which case do, for example, install.packages("DBI") before installing rerddap.

Background

ERDDAP is a server built on top of OPenDAP, which serves some NOAA data. You can get gridded data (griddap), which lets you query from gridded datasets, or table data (tabledap) which lets you query from tabular datasets. In terms of how we interface with them, there are similarties, but some differences too. We try to make a similar interface to both data types in rerddap.

NetCDF

rerddap supports NetCDF format, and is the default when using the griddap() function. NetCDF is a binary file format, and will have a much smaller footprint on your disk than csv. The binary file format means it's harder to inspect, but the ncdf4 package makes it easy to pull data out and write data back into a NetCDF file. Note the the file extension for NetCDF files is .nc. Whether you choose NetCDF or csv for small files won't make much of a difference, but will with large files.

Caching

Data files downloaded are cached in a single hidden directory ~/.rerddap on your machine. It's hidden so that you don't accidentally delete the data, but you can still easily delete the data if you like.

When you use griddap() or tabledap() functions, we construct a MD5 hash from the base URL, and any query parameters - this way each query is separately cached. Once we have the hash, we look in ~/.rerddap for a matching hash. If there's a match we use that file on disk - if no match, we make a http request for the data to the ERDDAP server you specify.

ERDDAP servers

You can get a data.frame of ERDDAP servers using the function servers(). Most I think serve some kind of NOAA data, but there are a few that aren't NOAA data. If you know of more ERDDAP servers, send a pull request, or let us know.

Search

First, you likely want to search for data, specify either griddadp or tabledap

ed_search(query = 'size', which = "table")
#> # A tibble: 10 x 2
#>                                                                          title
#>                                                                          <chr>
#>  1                                                        CalCOFI Larvae Sizes
#>  2 Channel Islands, Kelp Forest Monitoring, Size and Frequency, Natural Habita
#>  3             NWFSC Observer Fixed Gear Data, off West Coast of US, 2002-2006
#>  4                  NWFSC Observer Trawl Data, off West Coast of US, 2002-2006
#>  5                                         CalCOFI Larvae Counts Positive Tows
#>  6                                                                CalCOFI Tows
#>  7                          GLOBEC NEP MOCNESS Plankton (MOC1) Data, 2000-2002
#>  8                      GLOBEC NEP Vertical Plankton Tow (VPT) Data, 1997-2001
#>  9                                  OBIS - ARGOS Satellite Tracking of Animals
#> 10 AN EXPERIMENTAL DATASET: Underway Sea Surface Temperature and Salinity Aboa
#> # ... with 1 more variables: dataset_id <chr>
ed_search(query = 'size', which = "grid")
#> # A tibble: 290 x 2
#>                                                                          title
#>                                                                          <chr>
#>  1 COAWST Hindcast:MVCO/CBlast 2007:ripples with SWAN-40m res (00 dir roms) [t
#>  2 COAWST Hindcast:MVCO/CBlast 2007:ripples with SWAN-40m res (00 dir roms) [t
#>  3 COAWST Hindcast:MVCO/CBlast 2007:ripples with SWAN-40m res (00 dir roms) [t
#>  4 COAWST Hindcast:MVCO/CBlast 2007:ripples with SWAN-40m res (00 dir roms) [t
#>  5 COAWST Hindcast:MVCO/CBlast 2007:ripples with SWAN-40m res (00 dir roms) [t
#>  6 ROMS3.0 CBLAST2007 Ripples with SWAN-40m res (his case7 ar0fd 0001) [time][
#>  7 ROMS3.0 CBLAST2007 Ripples with SWAN-40m res (his case7 ar0fd 0001) [time][
#>  8 ROMS3.0 CBLAST2007 Ripples with SWAN-40m res (his case7 ar0fd 0001) [time][
#>  9 ROMS3.0 CBLAST2007 Ripples with SWAN-40m res (his case7 ar0fd 0001) [time][
#> 10 ROMS3.0 CBLAST2007 Ripples with SWAN-40m res (his case7 ar0fd 0001) [time][
#> # ... with 280 more rows, and 1 more variables: dataset_id <chr>

Information

Then you can get information on a single dataset

info('noaa_esrl_027d_0fb5_5d38')
#> <ERDDAP info> noaa_esrl_027d_0fb5_5d38
#>  Dimensions (range):
#>      time: (1850-01-01T00:00:00Z, 2014-05-01T00:00:00Z)
#>      latitude: (87.5, -87.5)
#>      longitude: (-177.5, 177.5)
#>  Variables:
#>      air:
#>          Range: -20.9, 19.5
#>          Units: degC

griddap (gridded) data

(out <- info('noaa_esrl_027d_0fb5_5d38'))
#> <ERDDAP info> noaa_esrl_027d_0fb5_5d38
#>  Dimensions (range):
#>      time: (1850-01-01T00:00:00Z, 2014-05-01T00:00:00Z)
#>      latitude: (87.5, -87.5)
#>      longitude: (-177.5, 177.5)
#>  Variables:
#>      air:
#>          Range: -20.9, 19.5
#>          Units: degC
(res <- griddap(out,
  time = c('2012-01-01', '2012-01-31'),
  latitude = c(25, 20),
  longitude = c(-80, -79)
))
#> <ERDDAP griddap> noaa_esrl_027d_0fb5_5d38
#>    Path: [/Users/sacmac/Library/Caches/R/rerddap/255eef5d77931489e5282a3db6e807d9.nc]
#>    Last updated: [2017-07-11 13:30:33]
#>    File size:    [0 mb]
#>    Dimensions (dims/vars):   [3 X 1]
#>    Dim names: time, latitude, longitude
#>    Variable names: CRUTEM3: Surface Air Temperature Monthly Anomaly
#>    data.frame (rows/columns):   [4 X 4]
#> # A tibble: 4 x 4
#>                   time   lat   lon   air
#>                  <chr> <dbl> <dbl> <dbl>
#> 1 2012-01-01T00:00:00Z  27.5 -77.5    NA
#> 2 2012-01-01T00:00:00Z  22.5 -77.5    NA
#> 3 2012-02-01T00:00:00Z  27.5 -77.5     2
#> 4 2012-02-01T00:00:00Z  22.5 -77.5    NA

tabledap (tabular) data

(out <- info('erdCinpKfmBT'))
#> <ERDDAP info> erdCinpKfmBT
#>  Variables:
#>      Aplysia_californica_Mean_Density:
#>          Range: 0.0, 0.95
#>          Units: m-2
#>      Aplysia_californica_StdDev:
#>          Range: 0.0, 0.35
#>      Aplysia_californica_StdErr:
#>          Range: 0.0, 0.1
#>      Crassedoma_giganteum_Mean_Density:
#>          Range: 0.0, 0.92
#>          Units: m-2
#>      Crassedoma_giganteum_StdDev:
#>          Range: 0.0, 0.71
#>      Crassedoma_giganteum_StdErr:
...
tabledap('erdCinpKfmBT', 'time>=2007-06-24', 'time<=2007-07-01')
#> <ERDDAP tabledap> erdCinpKfmBT
#>    Path: [/Users/sacmac/Library/Caches/R/rerddap/268b2474e9e613336b900d3289304bb0.csv]
#>    Last updated: [2017-07-11 13:30:37]
#>    File size:    [0.01 mb]
#> # A tibble: 37 x 53
#>                       station         longitude         latitude depth
#>  *                      <chr>             <chr>            <chr> <chr>
#>  1       Anacapa_AdmiralsReef -119.416666666667             34.0  16.0
#>  2   Anacapa_BlackSeaBassReef -119.383333333333             34.0  17.0
#>  3      Anacapa_CathedralCove -119.366666666667             34.0   6.0
#>  4       Anacapa_EastFishCamp -119.383333333333             34.0  11.0
#>  5            Anacapa_Keyhole -119.416666666667             34.0  11.0
#>  6        Anacapa_LandingCove           -119.35 34.0166666666667   5.0
#>  7         Anacapa_Lighthouse           -119.35             34.0   8.0
#>  8   SanClemente_BoyScoutCamp -118.533333333333             33.0  11.0
#>  9       SanClemente_EelPoint -118.533333333333            32.95  10.0
#> 10 SanClemente_HorseBeachCove            -118.4             32.8  13.0
#> # ... with 27 more rows, and 49 more variables: time <chr>,
#> #   Aplysia_californica_Mean_Density <chr>,
#> #   Aplysia_californica_StdDev <dbl>, Aplysia_californica_StdErr <dbl>,
#> #   Crassedoma_giganteum_Mean_Density <chr>,
#> #   Crassedoma_giganteum_StdDev <dbl>, Crassedoma_giganteum_StdErr <dbl>,
#> #   Haliotis_corrugata_Mean_Density <chr>,
#> #   Haliotis_corrugata_StdDev <dbl>, Haliotis_corrugata_StdErr <dbl>,
#> #   Haliotis_fulgens_Mean_Density <chr>, Haliotis_fulgens_StdDev <dbl>,
...

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for rerddap in R doing citation(package = 'rerddap')
  • Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

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