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

install.packages("devtools")
devtools::install_github('ropensci/pangaear')
library('pangaear')

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.

OAI-PMH metadata

List records

pg_list_records(from = Sys.Date() - 1, until = Sys.Date())
#> # A tibble: 670 x 121
#>    identifier datestamp setSpec setSpec.1 setSpec.2 setSpec.3 title creator
#>    <chr>      <chr>     <chr>   <chr>     <chr>     <chr>     <chr> <chr>  
#>  1 oai:panga… 2019-09-… citable suppleme… topicBio… topicPal… Calc… Hildeb…
#>  2 oai:panga… 2019-09-… citable suppleme… <NA>      <NA>      Mari… Schefu…
#>  3 oai:panga… 2019-09-… citable suppleme… topicOce… <NA>      Lipi… Schefu…
#>  4 oai:panga… 2019-09-… citable suppleme… topicChe… topicLit… Age … Verste…
#>  5 oai:panga… 2019-09-… citable suppleme… topicChe… topicLit… Comp… Liu, X…
#>  6 oai:panga… 2019-09-… citable suppleme… topicGeo… <NA>      Alke… Leider…
#>  7 oai:panga… 2019-09-… citable suppleme… topicLit… topicOce… Sedi… Verste…
#>  8 oai:panga… 2019-09-… citable suppleme… topicLan… topicLit… Radi… Chen, …
#>  9 oai:panga… 2019-09-… citable suppleme… topicBio… topicEco… Dino… Zonnev…
#> 10 oai:panga… 2019-09-… citable suppleme… <NA>      <NA>      Paly… Averdi…
#> # … with 660 more rows, and 113 more variables: creator.1 <chr>,
#> #   creator.2 <chr>, source <chr>, publisher <chr>, date <chr>,
#> #   type <chr>, format <chr>, identifier.2 <chr>, identifier.1 <chr>,
#> #   description <chr>, language <chr>, rights <chr>, rights.1 <chr>,
#> #   relation <chr>, coverage <chr>, subject <chr>, creator.3 <chr>,
#> #   creator.4 <chr>, creator.5 <chr>, setSpec.4 <chr>, creator.6 <chr>,
#> #   creator.7 <chr>, creator.8 <chr>, creator.9 <chr>, creator.10 <chr>,
#> #   relation.1 <chr>, creator.11 <chr>, creator.12 <chr>,
#> #   creator.13 <chr>, relation.2 <chr>, relation.3 <chr>,
#> #   relation.4 <chr>, setSpec.5 <chr>, setSpec.6 <chr>, setSpec.7 <chr>,
#> #   creator.14 <chr>, creator.15 <chr>, creator.16 <chr>,
#> #   creator.17 <chr>, creator.18 <chr>, creator.19 <chr>,
#> #   creator.20 <chr>, creator.21 <chr>, creator.22 <chr>,
#> #   creator.23 <chr>, creator.24 <chr>, creator.25 <chr>,
#> #   creator.26 <chr>, creator.27 <chr>, creator.28 <chr>,
#> #   creator.29 <chr>, creator.30 <chr>, creator.31 <chr>,
#> #   creator.32 <chr>, creator.33 <chr>, creator.34 <chr>,
#> #   creator.35 <chr>, creator.36 <chr>, creator.37 <chr>,
#> #   creator.38 <chr>, creator.39 <chr>, creator.40 <chr>,
#> #   creator.41 <chr>, relation.5 <chr>, relation.6 <chr>,
#> #   relation.7 <chr>, relation.8 <chr>, relation.9 <chr>,
#> #   relation.10 <chr>, relation.11 <chr>, relation.12 <chr>,
#> #   relation.13 <chr>, relation.14 <chr>, relation.15 <chr>,
#> #   relation.16 <chr>, relation.17 <chr>, relation.18 <chr>,
#> #   relation.19 <chr>, relation.20 <chr>, relation.21 <chr>,
#> #   relation.22 <chr>, relation.23 <chr>, relation.24 <chr>,
#> #   relation.25 <chr>, relation.26 <chr>, relation.27 <chr>,
#> #   relation.28 <chr>, relation.29 <chr>, relation.30 <chr>,
#> #   relation.31 <chr>, relation.32 <chr>, relation.33 <chr>,
#> #   relation.34 <chr>, relation.35 <chr>, relation.36 <chr>,
#> #   relation.37 <chr>, relation.38 <chr>, relation.39 <chr>,
#> #   relation.40 <chr>, relation.41 <chr>, …

Contributors (reverse alphabetical)

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

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