Giters

astrotuna201 / pangaear

R client for the Pangaea database

Home Page:https://ropensci.github.io/pangaear/

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

pangaear

Build Status Build status codecov rstudio mirror downloads cran version

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_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')

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 × 6
#>      score                    doi  size size_measure
#> *    <dbl>                  <chr> <dbl>        <chr>
#> 1 21.82342 10.1594/PANGAEA.812094     2     datasets
#> 2 11.09736 10.1594/PANGAEA.862525   372     datasets
#> 3 10.92194 10.1594/PANGAEA.736010     9     datasets
#> # ... with 2 more variables: citation <chr>, supplement_to <chr>

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. doi: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, doi:10.1016/S0967-0637(00)00065-0
#>   path:       /Users/sacmac/Library/Caches/pangaear/10_1594_PANGAEA_807580.txt
#>   data:
#> # A tibble: 32,179 × 13
#>                Event      `Date/Time` Latitude Longitude `Elevation [m]`
#>                <chr>            <chr>    <dbl>     <dbl>           <int>
#> 1  M36/6-CTD-365_003 1996-10-14T12:24  48.9667  -16.4633           -4802
#> 2  M36/6-CTD-365_003 1996-10-14T12:24  48.9667  -16.4633           -4802
#> 3  M36/6-CTD-365_003 1996-10-14T12:24  48.9667  -16.4633           -4802
#> 4  M36/6-CTD-365_003 1996-10-14T12:24  48.9667  -16.4633           -4802
#> 5  M36/6-CTD-365_003 1996-10-14T12:24  48.9667  -16.4633           -4802
#> 6  M36/6-CTD-365_003 1996-10-14T12:24  48.9667  -16.4633           -4802
#> 7  M36/6-CTD-365_003 1996-10-14T12:24  48.9667  -16.4633           -4802
#> 8  M36/6-CTD-365_003 1996-10-14T12:24  48.9667  -16.4633           -4802
#> 9  M36/6-CTD-365_003 1996-10-14T12:24  48.9667  -16.4633           -4802
#> 10 M36/6-CTD-365_003 1996-10-14T12:24  48.9667  -16.4633           -4802
#> # ... with 32,169 more rows, and 8 more variables: `Depth water
#> #   [m]` <dbl>, `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.77406
#>   parent doi: 10.1594/PANGAEA.736010
#>   url:        https://doi.org/10.1594/PANGAEA.77406
#>   citation:   Archer, David E; Devol, Alan H (1992): Benthic oxygen flixes on the Washington shelf and slope. doi:10.1594/PANGAEA.736010,Supplement to: Archer, DE; Devol, AH (1992): Benthic oxygen fluxes on the Washington shelf and slope: A comparison of in situ microelectrode and chamber flux measurements. Limnology and Oceanography, 37(3), 614-629, doi:10.4319/lo.1992.37.3.0614
#>   path:       /Users/sacmac/Library/Caches/pangaear/10_1594_PANGAEA_77406.txt
#>   data:
#> # A tibble: 1 × 4
#>   `Depth [m]` `SOD [mmol/m**2/day]` `SOD [mmol/m**2/day]` `O2 [µmol/l]`
#>         <int>                 <dbl>                 <dbl>         <dbl>
#> 1           0                  1.51                  0.74            25
#>
#> [[2]]
#> <Pangaea data> 10.1594/PANGAEA.77397
#>   parent doi: 10.1594/PANGAEA.736010
#>   url:        https://doi.org/10.1594/PANGAEA.77397
#>   citation:   Archer, David E; Devol, Alan H (1992): Benthic oxygen flixes on the Washington shelf and slope. doi:10.1594/PANGAEA.736010,Supplement to: Archer, DE; Devol, AH (1992): Benthic oxygen fluxes on the Washington shelf and slope: A comparison of in situ microelectrode and chamber flux measurements. Limnology and Oceanography, 37(3), 614-629, doi:10.4319/lo.1992.37.3.0614
#>   path:       /Users/sacmac/Library/Caches/pangaear/10_1594_PANGAEA_77397.txt
#>   data:
#> # A tibble: 27 × 6
#>    `Depth [m]` `O2 [µmol/l]` `Poros frac` `Mn [µmol/l]` `Fe [µmol/l]`
#>          <dbl>         <dbl>        <dbl>         <dbl>         <dbl>
#> 1       -0.010          97.7          1.0            NA            NA
#> 2       -0.005          96.2          1.0            NA            NA
#> 3       -0.001          93.2          1.0            NA            NA
#> 4        0.000          61.3          0.9            NA            NA
#> 5        0.001          35.8          0.9            NA            NA
#> 6        0.002          19.0          0.9           1.9            NA
#> 7        0.003           5.4          0.9           4.0           2.2
#> 8        0.004           0.1          0.8            NA            NA
#> 9        0.005           0.0          0.8            NA            NA
#> 10       0.006           0.4          0.7            NA            NA
#> # ... with 17 more rows, and 1 more variables: `TOC [%]` <dbl>
#>
#> [[3]]
#> <Pangaea data> 10.1594/PANGAEA.77398
#>   parent doi: 10.1594/PANGAEA.736010
#>   url:        https://doi.org/10.1594/PANGAEA.77398
#>   citation:   Archer, David E; Devol, Alan H (1992): Benthic oxygen flixes on the Washington shelf and slope. doi:10.1594/PANGAEA.736010,Supplement to: Archer, DE; Devol, AH (1992): Benthic oxygen fluxes on the Washington shelf and slope: A comparison of in situ microelectrode and chamber flux measurements. Limnology and Oceanography, 37(3), 614-629, doi:10.4319/lo.1992.37.3.0614
#>   path:       /Users/sacmac/Library/Caches/pangaear/10_1594_PANGAEA_77398.txt
#>   data:
#> # A tibble: 27 × 6
#>    `Depth [m]` `O2 [µmol/l]` `Poros frac` `Mn [µmol/l]` `Fe [µmol/l]`
#>          <dbl>         <dbl>        <dbl>         <dbl>         <dbl>
#> 1      -0.0100          91.8          1.0            NA            NA
#> 2      -0.0050          85.6          1.0            NA            NA
#> 3      -0.0010          80.5          1.0            NA            NA
#> 4       0.0000          45.2          1.0            NA            NA
#> 5       0.0005          33.7           NA            NA            NA
#> 6       0.0010          20.7          0.9            NA            NA
#> 7       0.0015           6.6           NA            NA            NA
#> 8       0.0020           2.4          0.8           0.5            NA
#> 9       0.0030           1.8          0.7           3.8            NA
#> 10      0.0040           1.7          0.7            NA           5.9
#> # ... with 17 more rows, and 1 more variables: `TOC [%]` <dbl>

OAI-PMH metadata

Identify the service

pg_identify()
#> <Pangaea>
#>   repositoryName: PANGAEA - Data Publisher for Earth & Environmental Science
#>   baseURL: https://ws.pangaea.de/oai/provider
#>   protocolVersion: 2.0
#>   adminEmail: tech@pangaea.de
#>   adminEmail: tech@pangaea.de
#>   earliestDatestamp: 2015-01-01T00:00:00Z
#>   deletedRecord: transient
#>   granularity: YYYY-MM-DDThh:mm:ssZ
#>   compression: gzip
#>   description: oaipangaea.de:oai:pangaea.de:doi:10.1594/PANGAEA.999999

List metadata formats

pg_list_metadata_formats()
#>   metadataPrefix                                                 schema
#> 1         oai_dc         http://www.openarchives.org/OAI/2.0/oai_dc.xsd
#> 2         pan_md      http://ws.pangaea.de/schemas/pangaea/MetaData.xsd
#> 3            dif http://gcmd.gsfc.nasa.gov/Aboutus/xml/dif/dif_v9.4.xsd
#> 4       iso19139               http://www.isotc211.org/2005/gmd/gmd.xsd
#> 5  iso19139.iodp               http://www.isotc211.org/2005/gmd/gmd.xsd
#> 6      datacite3  http://schema.datacite.org/meta/kernel-3/metadata.xsd
#>                             metadataNamespace
#> 1 http://www.openarchives.org/OAI/2.0/oai_dc/
#> 2              http://www.pangaea.de/MetaData
#> 3  http://gcmd.gsfc.nasa.gov/Aboutus/xml/dif/
#> 4            http://www.isotc211.org/2005/gmd
#> 5            http://www.isotc211.org/2005/gmd
#> 6         http://datacite.org/schema/kernel-3

List identifiers

pg_list_identifiers(from = Sys.Date() - 2, until = Sys.Date())
#> # A tibble: 7,596 × 9
#>                                   identifier            datestamp setSpec
#>                                        <chr>                <chr>   <chr>
#> 1   oai:pangaea.de:doi:10.1594/PANGAEA.55417 2017-03-08T13:19:32Z citable
#> 2   oai:pangaea.de:doi:10.1594/PANGAEA.57910 2017-03-08T13:17:50Z  ORFOIS
#> 3   oai:pangaea.de:doi:10.1594/PANGAEA.77250 2017-03-08T13:19:59Z citable
#> 4  oai:pangaea.de:doi:10.1594/PANGAEA.149999 2017-03-07T09:22:22Z citable
#> 5  oai:pangaea.de:doi:10.1594/PANGAEA.208129 2017-03-08T13:19:16Z citable
#> 6  oai:pangaea.de:doi:10.1594/PANGAEA.314690 2017-03-07T11:47:26Z citable
#> 7  oai:pangaea.de:doi:10.1594/PANGAEA.351146 2017-03-08T13:18:19Z citable
#> 8  oai:pangaea.de:doi:10.1594/PANGAEA.611095 2017-03-07T11:01:44Z citable
#> 9  oai:pangaea.de:doi:10.1594/PANGAEA.693923 2017-03-08T13:17:24Z citable
#> 10 oai:pangaea.de:doi:10.1594/PANGAEA.716835 2017-03-07T10:52:54Z citable
#> # ... with 7,586 more rows, and 6 more variables: setSpec.1 <chr>,
#> #   setSpec.2 <chr>, setSpec.3 <chr>, setSpec.4 <chr>, setSpec.5 <chr>,
#> #   setSpec.6 <chr>

List sets

pg_list_sets()
#> # A tibble: 257 × 2
#>      setSpec                                        setName
#>        <chr>                                          <chr>
#> 1        ACD       PANGAEA tech-keyword 'ACD' (2 data sets)
#> 2       ASPS     PANGAEA tech-keyword 'ASPS' (59 data sets)
#> 3  AWIXRFraw PANGAEA tech-keyword 'AWIXRFraw' (1 data sets)
#> 4    BAH1960   PANGAEA tech-keyword 'BAH1960' (2 data sets)
#> 5    BAH1961   PANGAEA tech-keyword 'BAH1961' (2 data sets)
#> 6    BAH1962   PANGAEA tech-keyword 'BAH1962' (7 data sets)
#> 7    BAH1963   PANGAEA tech-keyword 'BAH1963' (7 data sets)
#> 8    BAH1964   PANGAEA tech-keyword 'BAH1964' (7 data sets)
#> 9    BAH1965   PANGAEA tech-keyword 'BAH1965' (7 data sets)
#> 10   BAH1966   PANGAEA tech-keyword 'BAH1966' (6 data sets)
#> # ... with 247 more rows

List records

pg_list_records(from = Sys.Date() - 1, until = Sys.Date())
#> # A tibble: 6,363 × 48
#>                                   identifier            datestamp setSpec         setSpec.1         setSpec.2
#>                                        <chr>                <chr>   <chr>             <chr>             <chr>
#> 1   oai:pangaea.de:doi:10.1594/PANGAEA.55417 2017-03-08T13:19:32Z citable citableWithChilds        supplement
#> 2   oai:pangaea.de:doi:10.1594/PANGAEA.57910 2017-03-08T13:17:50Z  ORFOIS           citable citableWithChilds
#> 3   oai:pangaea.de:doi:10.1594/PANGAEA.77250 2017-03-08T13:19:59Z citable citableWithChilds        supplement
#> 4  oai:pangaea.de:doi:10.1594/PANGAEA.208129 2017-03-08T13:19:16Z citable citableWithChilds        supplement
#> 5  oai:pangaea.de:doi:10.1594/PANGAEA.351146 2017-03-08T13:18:19Z citable citableWithChilds        supplement
#> 6  oai:pangaea.de:doi:10.1594/PANGAEA.693923 2017-03-08T13:17:24Z citable citableWithChilds        supplement
#> 7  oai:pangaea.de:doi:10.1594/PANGAEA.726410 2017-03-08T13:17:54Z citable citableWithChilds        supplement
#> 8  oai:pangaea.de:doi:10.1594/PANGAEA.757616 2017-03-08T13:18:05Z citable citableWithChilds        supplement
#> 9  oai:pangaea.de:doi:10.1594/PANGAEA.758696 2017-03-08T13:19:02Z citable citableWithChilds        supplement
#> 10 oai:pangaea.de:doi:10.1594/PANGAEA.760166 2017-03-09T14:54:46Z    BCCR            IMAGES       Past4Future
#> # ... with 6,353 more rows, and 43 more variables: title <chr>, creator <chr>, creator.1 <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>, coverage <chr>, subject <chr>, setSpec.3 <chr>, creator.2 <chr>, creator.3 <chr>, relation <chr>,
#> #   relation.1 <chr>, relation.2 <chr>, relation.3 <chr>, relation.4 <chr>, creator.4 <chr>, creator.5 <chr>, creator.6 <chr>, creator.7 <chr>, setSpec.4 <chr>, setSpec.5 <chr>, setSpec.6 <chr>,
#> #   source.1 <chr>, creator.8 <chr>, creator.9 <chr>, creator.10 <chr>, creator.11 <chr>, creator.12 <chr>, creator.13 <chr>, relation.5 <chr>, relation.6 <chr>, relation.7 <chr>, relation.8 <chr>,
#> #   creator.14 <chr>

Get a record

pg_get_record(identifier = "oai:pangaea.de:doi:10.1594/PANGAEA.788382")
#> $`oai:pangaea.de:doi:10.1594/PANGAEA.788382`
#> $`oai:pangaea.de:doi:10.1594/PANGAEA.788382`$header
#> # A tibble: 1 × 3
#>                                  identifier            datestamp                              setSpec
#>                                       <chr>                <chr>                                <chr>
#> 1 oai:pangaea.de:doi:10.1594/PANGAEA.788382 2016-06-25T14:58:45Z citable;citableWithChilds;supplement
#>
#> $`oai:pangaea.de:doi:10.1594/PANGAEA.788382`$metadata
#> # A tibble: 1 × 13
#>                                                                                                                                title                                      creator
#>                                                                                                                                <chr>                                        <chr>
#> 1 Trace metals in shells of mussels and clams from deep-sea hydrothermal vent fields of the Mid-Atlantic Ridge and East Pacific Rise Demina, Lyudmila L;Galkin, Sergey V;Dara, OM
#> # ... with 11 more variables: source <chr>, publisher <chr>, date <chr>, type <chr>, format <chr>, identifier <chr>, description <chr>, language <chr>, rights <chr>, coverage <chr>, subject <chr>

Contributors (reverse alphabetical)

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

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for pangaear in R doing citation(package = 'pangaear')
  • 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.

ro_footer

About

R client for the Pangaea database

https://ropensci.github.io/pangaear/

License:Other

Languages

Language:R 100.0%