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.
If you've not installed it yet, install from CRAN:
install.packages("pangaear")
Or the development version:
devtools::install_github("ropensci/pangaear")
library("pangaear")
pg_search is a thin wrapper around the GUI search interface on the page https://www.pangaea.de/. Everything you can do there, you can do here.
For example, query for the term 'water', with a bounding box, and return only three results.
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 12.8 10.1594… 2 datasets Simonyan, AV; Du… Simonyan, AV; Dultz,…
#> 2 8.70 10.1594… 598 data points WOCE Surface Vel… <NA>
#> 3 8.70 10.1594… 11390 data points WOCE Upper Ocean… <NA>
The resulting data.frame has details about different studies, and you can use the DOIs (Digital Object Identifiers) to get data and metadata for any studies you're interested in.
There's another search option with the pg_search_es function. It is an interface to the Pangaea Elasticsearch interface. This provides a very flexible interface for search Pangaea data - though it is different from what you're used to with the Pangaea website.
(res <- pg_search_es())
#> # A tibble: 10 x 41
#> `_index` `_type` `_id` `_score` `_source.intern… `_source.minEle…
#> * <chr> <chr> <chr> <dbl> <chr> <dbl>
#> 1 pangaea… panmd 8387… 1 2018-09-27T17:1… 0.35
#> 2 pangaea… panmd 7179… 1 2018-10-29T17:5… 2
#> 3 pangaea… panmd 7913… 1 2018-09-27T19:3… 198.
#> 4 pangaea… panmd 7791… 1 2018-09-27T20:0… 65.0
#> 5 pangaea… panmd 7198… 1 2018-10-29T17:4… 2
#> 6 pangaea… panmd 8363… 1 2018-09-27T17:2… 2.85
#> 7 pangaea… panmd 8255… 1 2018-09-27T17:5… 3.72
#> 8 pangaea… panmd 7950… 1 2018-09-27T19:2… 0
#> 9 pangaea… panmd 7993… 1 2018-09-27T19:1… 318.
#> 10 pangaea… panmd 8289… 1 2018-09-27T17:4… 0
#> # … with 35 more variables: `_source.sf-authortitle` <chr>,
#> # `_source.techKeyword` <list>, `_source.geocodes` <list>,
#> # `_source.sp-loginOption` <int>, `_source.agg-author` <list>,
#> # `_source.eastBoundLongitude` <dbl>, `_source.URI` <chr>,
#> # `_source.agg-pubYear` <int>, `_source.agg-geometry` <chr>,
#> # `_source.xml-thumb` <chr>, `_source.xml` <chr>,
#> # `_source.sf-idDataSet` <int>, `_source.elevationGeocode` <chr>,
#> # `_source.xml-sitemap` <chr>, `_source.westBoundLongitude` <dbl>,
#> # `_source.northBoundLatitude` <dbl>, `_source.sp-dataStatus` <int>,
#> # `_source.nDataPoints` <int>, `_source.sp-hidden` <lgl>,
#> # `_source.agg-location` <list>, `_source.internal-source` <chr>,
#> # `_source.southBoundLatitude` <dbl>, `_source.boost` <dbl>,
#> # `_source.oaiSet` <list>, `_source.maxElevation` <dbl>,
#> # `_source.agg-campaign` <chr>, `_source.minDateTime` <chr>,
#> # `_source.agg-mainTopic` <list>, `_source.maxDateTime` <chr>,
#> # `_source.agg-topic` <list>, `_source.agg-project` <list>,
#> # `_source.agg-device` <chr>, `_source.agg-basis` <chr>,
#> # `_source.meanPosition.lat` <dbl>, `_source.meanPosition.lon` <dbl>
The returned data.frame has a lot of columns. You can limit columns returned with the source parameter.
There are attributes on the data.frame that give you the total number of results found as well as the max score found.
attributes(res)
#> $names
#> [1] "_index" "_type"
#> [3] "_id" "_score"
#> [5] "_source.internal-datestamp" "_source.minElevation"
#> [7] "_source.sf-authortitle" "_source.techKeyword"
#> [9] "_source.geocodes" "_source.sp-loginOption"
#> [11] "_source.agg-author" "_source.eastBoundLongitude"
#> [13] "_source.URI" "_source.agg-pubYear"
#> [15] "_source.agg-geometry" "_source.xml-thumb"
#> [17] "_source.xml" "_source.sf-idDataSet"
#> [19] "_source.elevationGeocode" "_source.xml-sitemap"
#> [21] "_source.westBoundLongitude" "_source.northBoundLatitude"
#> [23] "_source.sp-dataStatus" "_source.nDataPoints"
#> [25] "_source.sp-hidden" "_source.agg-location"
#> [27] "_source.internal-source" "_source.southBoundLatitude"
#> [29] "_source.boost" "_source.oaiSet"
#> [31] "_source.maxElevation" "_source.agg-campaign"
#> [33] "_source.minDateTime" "_source.agg-mainTopic"
#> [35] "_source.maxDateTime" "_source.agg-topic"
#> [37] "_source.agg-project" "_source.agg-device"
#> [39] "_source.agg-basis" "_source.meanPosition.lat"
#> [41] "_source.meanPosition.lon"
#>
#> $row.names
#> [1] 1 2 3 4 5 6 7 8 9 10
#>
#> $class
#> [1] "tbl_df" "tbl" "data.frame"
#>
#> $total
#> [1] 386124
#>
#> $max_score
#> [1] 1
attr(res, "total")
#> [1] 386124
attr(res, "max_score")
#> [1] 1
To get to the DOIs for each study, use
gsub("https://doi.org/", "", res$`_source.URI`)
#> [1] "10.1594/PANGAEA.838718" "10.1594/PANGAEA.717974"
#> [3] "10.1594/PANGAEA.791357" "10.1594/PANGAEA.779192"
#> [5] "10.1594/PANGAEA.719864" "10.1594/PANGAEA.836369"
#> [7] "10.1594/PANGAEA.825583" "10.1594/PANGAEA.795004"
#> [9] "10.1594/PANGAEA.799338" "10.1594/PANGAEA.828908"
The function pg_data fetches datasets for studies by their DOIs.
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 one or more DOIs to the pg_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.325191
#> parent doi: 10.1594/PANGAEA.325191
#> url: https://doi.org/10.1594/PANGAEA.325191
#> citation: WOCE Upper Ocean Thermal, UOT (2005): Water temperature XBT profiles from cruise 181991002 (DCQC). Marine Environmental Data Services Branch, Ontario, PANGAEA, https://doi.org/10.1594/PANGAEA.325191
#> path: /Users/sckott/Library/Caches/R/pangaear/10_1594_PANGAEA_325191.txt
#> data:
#> # A tibble: 5,695 x 6
#> `Date/Time` Latitude Longitude `Depth water [m… `Temp [°C]`
#> <chr> <dbl> <dbl> <int> <chr>
#> 1 1991-03-26… 38.6 -124. 1 10.57
#> 2 1991-03-26… 38.6 -124. 2 10.75
#> 3 1991-03-26… 38.6 -124. 3 10.89
#> 4 1991-03-26… 38.6 -124. 4 10.96
#> 5 1991-03-26… 38.6 -124. 5 11.04
#> 6 1991-03-26… 38.6 -124. 6 11.09
#> 7 1991-03-26… 38.6 -124. 7 11.12
#> 8 1991-03-26… 38.6 -124. 8 11.13
#> 9 1991-03-26… 38.6 -124. 9 11.15
#> 10 1991-03-26… 38.6 -124. 10 11.15
#> # … with 5,685 more rows, and 1 more variable: `Sample label` <chr>
#>
#> [[2]]
#> NULL
#>
#> [[3]]
#> NULL
OAI-PMH is a standard protocol for serving metadata around objects, in this case datasets. If you are already familiar with OAI-PMH you are in luck as you can can use what you know here. If not familiar, it's relatively straight-forward.
Note that you can't get data through these functions, rather only metadata about datasets.
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
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
#> 7 datacite4 http://schema.datacite.org/meta/kernel-4.1/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
#> 7 http://datacite.org/schema/kernel-4
pg_list_identifiers(from = Sys.Date() - 2, until = Sys.Date())
#> # A tibble: 514 x 11
#> identifier datestamp setSpec setSpec.1 setSpec.2 setSpec.3 setSpec.4
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 oai:panga… 2019-08-… citable hmmv suppleme… topicOce… <NA>
#> 2 oai:panga… 2019-08-… citable suppleme… <NA> <NA> <NA>
#> 3 oai:panga… 2019-08-… citable suppleme… <NA> <NA> <NA>
#> 4 oai:panga… 2019-08-… citable suppleme… topicBio… topicEco… topicOce…
#> 5 oai:panga… 2019-08-… citable suppleme… <NA> <NA> <NA>
#> 6 oai:panga… 2019-08-… citable suppleme… <NA> <NA> <NA>
#> 7 oai:panga… 2019-08-… citable suppleme… topicLit… topicOce… topicPal…
#> 8 oai:panga… 2019-08-… citable suppleme… topicLan… topicLit… topicPal…
#> 9 oai:panga… 2019-08-… citable suppleme… topicChe… topicGeo… topicLit…
#> 10 oai:panga… 2019-08-… citable suppleme… topicLan… topicLit… <NA>
#> # … with 504 more rows, and 4 more variables: setSpec.5 <chr>,
#> # setSpec.6 <chr>, setSpec.7 <chr>, setSpec.8 <chr>
pg_list_sets()
#> # A tibble: 282 x 2
#> setSpec setName
#> <chr> <chr>
#> 1 ACD PANGAEA set / keyword 'ACD' (2 data sets)
#> 2 ASPS PANGAEA set / keyword 'ASPS' (59 data sets)
#> 3 AWIXRFraw PANGAEA set / keyword 'AWIXRFraw' (1 data sets)
#> 4 BAH1960 PANGAEA set / keyword 'BAH1960' (2 data sets)
#> 5 BAH1961 PANGAEA set / keyword 'BAH1961' (2 data sets)
#> 6 BAH1962 PANGAEA set / keyword 'BAH1962' (7 data sets)
#> 7 BAH1963 PANGAEA set / keyword 'BAH1963' (7 data sets)
#> 8 BAH1964 PANGAEA set / keyword 'BAH1964' (7 data sets)
#> 9 BAH1965 PANGAEA set / keyword 'BAH1965' (7 data sets)
#> 10 BAH1966 PANGAEA set / keyword 'BAH1966' (6 data sets)
#> # … with 272 more rows
pg_list_records(from = Sys.Date() - 1, until = Sys.Date())
#> # A tibble: 331 x 586
#> identifier datestamp setSpec setSpec.1 setSpec.2 setSpec.3 setSpec.4
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 oai:panga… 2019-08-… citable suppleme… topicBio… topicEco… topicOce…
#> 2 oai:panga… 2019-08-… citable suppleme… <NA> <NA> <NA>
#> 3 oai:panga… 2019-08-… citable suppleme… topicLit… topicOce… topicPal…
#> 4 oai:panga… 2019-08-… citable suppleme… topicLan… topicLit… topicPal…
#> 5 oai:panga… 2019-08-… citable <NA> <NA> <NA> <NA>
#> 6 oai:panga… 2019-08-… citable suppleme… topicLit… <NA> <NA>
#> 7 oai:panga… 2019-08-… BCCR suppleme… topicLan… topicLit… <NA>
#> 8 oai:panga… 2019-08-… citable suppleme… <NA> <NA> <NA>
#> 9 oai:panga… 2019-08-… citable <NA> <NA> <NA> <NA>
#> 10 oai:panga… 2019-08-… citable suppleme… topicLit… <NA> <NA>
#> # … with 321 more rows, and 579 more variables: title <chr>,
#> # creator <chr>, creator.1 <chr>, creator.2 <chr>, creator.3 <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>, creator.4 <chr>, relation <chr>, creator.5 <chr>,
#> # creator.6 <chr>, creator.7 <chr>, creator.8 <chr>, creator.9 <chr>,
#> # creator.10 <chr>, creator.11 <chr>, relation.1 <chr>,
#> # relation.2 <chr>, relation.3 <chr>, relation.4 <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>, relation.42 <chr>, relation.43 <chr>,
#> # relation.44 <chr>, relation.45 <chr>, relation.46 <chr>,
#> # relation.47 <chr>, relation.48 <chr>, relation.49 <chr>,
#> # relation.50 <chr>, relation.51 <chr>, relation.52 <chr>,
#> # relation.53 <chr>, relation.54 <chr>, relation.55 <chr>,
#> # relation.56 <chr>, relation.57 <chr>, relation.58 <chr>,
#> # relation.59 <chr>, relation.60 <chr>, relation.61 <chr>,
#> # relation.62 <chr>, relation.63 <chr>, relation.64 <chr>,
#> # relation.65 <chr>, relation.66 <chr>, relation.67 <chr>,
#> # relation.68 <chr>, relation.69 <chr>, relation.70 <chr>,
#> # relation.71 <chr>, relation.72 <chr>, relation.73 <chr>, …
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 x 3
#> identifier datestamp setSpec
#> <chr> <chr> <chr>
#> 1 oai:pangaea.de:doi:10.1594… 2019-02-13T10:… citable;supplement;topicChem…
#>
#> $`oai:pangaea.de:doi:10.1594/PANGAEA.788382`$metadata
#> # A tibble: 1 x 13
#> title creator source publisher date type format identifier description
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Trac… Demina… P.P. … PANGAEA 2012… Data… appli… https://d… Bioaccumul…
#> # … with 4 more variables: language <chr>, rights <chr>, coverage <chr>,
#> # subject <chr>