rOpenSci: The pangaear package

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pangaear is a data retrieval interface for the World Data Center PANGAEA (https://www.pangaea.de/). PANGAEA archieves published Earth & Environmental Science data under the following subjects: agriculture, atmosphere, biological classification, biosphere, chemistry, cryosphere, ecology, fisheries, geophysics, human dimensions, lakes & rives, land surface, lithosphere, oceans, and paleontology.

This package offers tools to interact with the PANGAEA Database, including functions for searching for data, fetching datasets by dataset ID, and working with the PANGAEA OAI-PMH service.

Info

Package API

  • pg_data
  • pg_list_metadata_formats
  • pg_identify
  • pg_list_records
  • pg_list_sets
  • pg_list_identifiers
  • pg_search
  • pg_get_record
  • pg_cache
  • pg_search_es
  • pg_cache_list
  • pg_cache_clear

Installation

Stable version

install.packages("pangaear")

Dev version

remotes::install_github('ropensci/pangaear')

Search for data

This is a thin wrapper around the GUI search interface on the page http://www.pangaea.de/. Everything you can do there, you can do here.

pg_search(query = 'water', bbox = c(-124.2, 41.8, -116.8, 46.1), count = 3)
#> # A tibble: 3 x 6
#>   score doi       size size_measure citation             supplement_to          
#>   <dbl> <chr>    <dbl> <chr>        <chr>                <chr>                  
#> 1 13.0  10.1594…     4 datasets     Krylova, EM; Sahlin… Krylova, EM; Sahling, …
#> 2 12.8  10.1594…     2 datasets     Simonyan, AV; Dultz… Simonyan, AV; Dultz, S…
#> 3  8.78 10.1594…  1148 data points  WOCE Surface Veloci… <NA>

Get data

res <- pg_data(doi = '10.1594/PANGAEA.807580')
res[[1]]
#> <Pangaea data> 10.1594/PANGAEA.807580
#>   parent doi: 10.1594/PANGAEA.807580
#>   url:        https://doi.org/10.1594/PANGAEA.807580
#>   citation:   Schiebel, Ralf; Waniek, Joanna J; Bork, Matthias; Hemleben, Christoph (2001): Physical oceanography during METEOR cruise M36/6. PANGAEA, https://doi.org/10.1594/PANGAEA.807580, In supplement to: Schiebel, R et al. (2001): Planktic foraminiferal production stimulated by chlorophyll redistribution and entrainment of nutrients. Deep Sea Research Part I: Oceanographic Research Papers, 48(3), 721-740, https://doi.org/10.1016/S0967-0637(00)00065-0
#>   path:       /Users/sckott/Library/Caches/R/pangaear/10_1594_PANGAEA_807580.txt
#>   data:
#> # A tibble: 32,179 x 13
#>    Event `Date/Time` Latitude Longitude `Elevation [m]` `Depth water [m…
#>    <chr> <chr>          <dbl>     <dbl>           <int>            <dbl>
#>  1 M36/… 1996-10-14…     49.0     -16.5           -4802             0   
#>  2 M36/… 1996-10-14…     49.0     -16.5           -4802             0.99
#>  3 M36/… 1996-10-14…     49.0     -16.5           -4802             1.98
#>  4 M36/… 1996-10-14…     49.0     -16.5           -4802             2.97
#>  5 M36/… 1996-10-14…     49.0     -16.5           -4802             3.96
#>  6 M36/… 1996-10-14…     49.0     -16.5           -4802             4.96
#>  7 M36/… 1996-10-14…     49.0     -16.5           -4802             5.95
#>  8 M36/… 1996-10-14…     49.0     -16.5           -4802             6.94
#>  9 M36/… 1996-10-14…     49.0     -16.5           -4802             7.93
#> 10 M36/… 1996-10-14…     49.0     -16.5           -4802             8.92
#> # … with 32,169 more rows, and 7 more variables: `Press [dbar]` <int>, `Temp
#> #   [°C]` <dbl>, Sal <dbl>, `Tpot [°C]` <dbl>, `Sigma-theta [kg/m**3]` <dbl>,
#> #   `Sigma in situ [kg/m**3]` <dbl>, `Cond [mS/cm]` <dbl>

Search for data then pass DOI to data function.

res <- pg_search(query = 'water', bbox = c(-124.2, 41.8, -116.8, 46.1), count = 3)
pg_data(res$doi[3])[1:3]
#> [[1]]
#> <Pangaea data> 10.1594/PANGAEA.405695
#>   parent doi: 10.1594/PANGAEA.405695
#>   url:        https://doi.org/10.1594/PANGAEA.405695
#>   citation:   WOCE Surface Velocity Program, SVP (2006): Water temperature and current velocity from surface drifter SVP_9524470. PANGAEA, https://doi.org/10.1594/PANGAEA.405695
#>   path:       /Users/sckott/Library/Caches/R/pangaear/10_1594_PANGAEA_405695.txt
#>   data:
#> # A tibble: 192 x 10
#>    `Date/Time` Latitude Longitude `Depth water [m… `Temp [°C]` `UC [cm/s]`
#>    <chr>          <dbl>     <dbl>            <int>       <dbl>       <dbl>
#>  1 1995-12-21…     42.9     -125.                0        12.4       NA   
#>  2 1995-12-22…     42.9     -125.                0        12.4        4.24
#>  3 1995-12-22…     42.8     -125.                0        12.4       -7.8 
#>  4 1995-12-22…     42.7     -125.                0        12.4      -12.7 
#>  5 1995-12-22…     42.7     -125.                0        12.4      -15.1 
#>  6 1995-12-23…     42.7     -125.                0        12.3      -24.1 
#>  7 1995-12-23…     42.7     -125.                0        12.3      -38.4 
#>  8 1995-12-23…     42.7     -125.                0        12.3      -37.2 
#>  9 1995-12-23…     42.7     -125.                0        12.3      -25.4 
#> 10 1995-12-24…     42.8     -125.                0        12.4      -18.5 
#> # … with 182 more rows, and 4 more variables: `VC [cm/s]` <dbl>, `Lat e` <dbl>,
#> #   `Lon e` <dbl>, Code <int>
#> 
#> [[2]]
#> NULL
#> 
#> [[3]]
#> NULL

OAI-PMH metadata

# Identify the service
pg_identify()

# List metadata formats
pg_list_metadata_formats()

# List identifiers
pg_list_identifiers(from = Sys.Date() - 2, until = Sys.Date())

# List sets
pg_list_sets()

# List records
pg_list_records(from = Sys.Date() - 1, until = Sys.Date())

# Get a record
pg_get_record(identifier = "oai:pangaea.de:doi:10.1594/PANGAEA.788382")

Contributors (reverse alphabetical)

  • Naupaka Zimmerman
  • Kara Woo
  • Gavin Simpson
  • Andrew MacDonald
  • Scott Chamberlain

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