Name: pangaear
Owner: rOpenSci
Description: R client for the Pangaea database
Created: 2014-09-02 16:08:16.0
Updated: 2017-11-18 22:38:20.0
Pushed: 2018-01-05 19:39:27.0
Homepage: https://ropensci.github.io/pangaear/
Size: 297
Language: R
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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.
Stable version
all.packages("pangaear")
Dev version
all.packages("devtools")
ools::install_github('ropensci/pangaear')
ary('pangaear')
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.
earch(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_?
<dbl> <chr> <dbl> <chr> <chr> <chr>
20.0 10.1594/PANGAEA.812094 2.00 datasets Simonyan? Simonyan, A?
11.0 10.1594/PANGAEA.736010 9.00 datasets Archer, ? Archer, DE;?
10.9 10.1594/PANGAEA.874893 4152 data points Uhlig, C? Uhlig, C; L?
<- pg_data(doi = '10.1594/PANGAEA.807580')
[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/pangaear/10_1594_PANGAEA_807580.txt
data:
A tibble: 32,179 x 13
Event `Dat? Lati? Long? `Ele? `Dep? `Pre? `Tem? Sal `Tpo? `Sig? `Sig?
<chr> <chr> <dbl> <dbl> <int> <dbl> <int> <dbl> <dbl> <dbl> <dbl> <dbl>
1 M36/? 1996? 49.0 -16.5 -4802 0 0 15.7 35.7 15.7 26.4 26.4
2 M36/? 1996? 49.0 -16.5 -4802 0.990 1 15.7 35.7 15.7 26.4 26.4
3 M36/? 1996? 49.0 -16.5 -4802 1.98 2 15.7 35.7 15.7 26.4 26.4
4 M36/? 1996? 49.0 -16.5 -4802 2.97 3 15.7 35.7 15.7 26.4 26.4
5 M36/? 1996? 49.0 -16.5 -4802 3.96 4 15.7 35.7 15.7 26.4 26.4
6 M36/? 1996? 49.0 -16.5 -4802 4.96 5 15.7 35.7 15.7 26.4 26.4
7 M36/? 1996? 49.0 -16.5 -4802 5.95 6 15.7 35.7 15.7 26.4 26.4
8 M36/? 1996? 49.0 -16.5 -4802 6.94 7 15.7 35.7 15.7 26.4 26.4
9 M36/? 1996? 49.0 -16.5 -4802 7.93 8 15.7 35.7 15.7 26.4 26.4
0 M36/? 1996? 49.0 -16.5 -4802 8.92 9 15.7 35.7 15.7 26.4 26.4
... with 32,169 more rows, and 1 more variable: `Cond [mS/cm]` <dbl>
Search for data then pass DOI to data function.
<- pg_search(query = 'water', bbox = c(-124.2, 41.8, -116.8, 46.1), count = 3)
ata(res$doi[3])[1:3]
[1]]
Pangaea data> 10.1594/PANGAEA.874893
parent doi: 10.1594/PANGAEA.874893
url: https://doi.org/10.1594/PANGAEA.874893
citation: Uhlig, Christiane; Loose, Brice (2017): Methane oxidation in Arctic seawater, Utqiagvik, Alaska. PANGAEA, https://doi.org/10.1594/PANGAEA.874893,Supplement to: Uhlig, C; Loose, B (2017): Using stable isotopes and gas concentrations for independent constraints on microbial methane oxidation at Arctic Ocean temperatures. Limnology and Oceanography-Methods, 15 pp, https://doi.org/10.1002/lom3.10199
path: /Users/sckott/Library/Caches/pangaear/10_1594_PANGAEA_874893.txt
data:
A tibble: 270 x 22
Event `Date? Latit? Longi? `Dep? `Dep? `Dep? `Sam? Treat `N [? `Durat?
<chr> <chr> <dbl> <dbl> <dbl> <int> <int> <int> <chr> <int> <dbl>
1 Elson? 2016-? 71.3 -156 1.50 NA NA 7 0.2x? 2 0.0100
2 Elson? 2016-? 71.3 -156 1.50 NA NA 7 0.2x? 3 6.03
3 Elson? 2016-? 71.3 -156 1.50 NA NA 7 0.2x? 2 8.88
4 Elson? 2016-? 71.3 -156 1.50 NA NA 7 0.2x? 4 10.8
5 Utqia? 2016-? 71.4 -157 6.50 NA NA 10 0.2x 2 0.0100
6 Utqia? 2016-? 71.4 -157 6.50 NA NA 10 0.2x 2 6.15
7 Utqia? 2016-? 71.4 -157 6.50 NA NA 10 0.2x 2 8.99
8 Utqia? 2016-? 71.4 -157 6.50 NA NA 10 0.2x 2 10.8
9 Utqia? 2016-? 71.4 -157 5.00 NA NA 13 0.2x 2 0.0100
0 Utqia? 2016-? 71.4 -157 5.00 NA NA 13 0.2x 2 6.15
... with 260 more rows, and 11 more variables: `Duration std dev [±]`
<dbl>, `CH4 [nmol/l]` <dbl>, `CH4 std dev [±]` <dbl>, `ln(CH4) [nmol]`
<dbl>, `ln(CH4) std dev [±]` <dbl>, `d13C CH4 [per mil PDB]` <dbl>,
`d13C CH4 std dev [±]` <dbl>, `Y-axis high mean` <dbl>, `Y-axis high
std dev [±]` <dbl>, `Y-axis low mean` <dbl>, `Y-axis low std dev [±]`
<dbl>
[2]]
ULL
[3]]
ULL
dentify()
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
ist_metadata_formats()
metadataPrefix schema
oai_dc http://www.openarchives.org/OAI/2.0/oai_dc.xsd
pan_md http://ws.pangaea.de/schemas/pangaea/MetaData.xsd
dif http://gcmd.gsfc.nasa.gov/Aboutus/xml/dif/dif_v9.4.xsd
iso19139 http://www.isotc211.org/2005/gmd/gmd.xsd
iso19139.iodp http://www.isotc211.org/2005/gmd/gmd.xsd
datacite3 http://schema.datacite.org/meta/kernel-3/metadata.xsd
metadataNamespace
http://www.openarchives.org/OAI/2.0/oai_dc/
http://www.pangaea.de/MetaData
http://gcmd.gsfc.nasa.gov/Aboutus/xml/dif/
http://www.isotc211.org/2005/gmd
http://www.isotc211.org/2005/gmd
http://datacite.org/schema/kernel-3
ist_identifiers(from = Sys.Date() - 2, until = Sys.Date())
A tibble: 224 x 7
identifier datestamp setSpec setSpec.1 setSpec? setSpe? setSp?
<chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 oai:pangaea.de:d? 2018-01-0? citable citableW? deNBIch? supple? <NA>
2 oai:pangaea.de:d? 2018-01-0? Yangeta? citable citable? deNBIc? suppl?
3 oai:pangaea.de:d? 2018-01-0? citable citableW? supplem? <NA> <NA>
4 oai:pangaea.de:d? 2018-01-0? citable citableW? supplem? <NA> <NA>
5 oai:pangaea.de:d? 2018-01-0? citable citableW? supplem? <NA> <NA>
6 oai:pangaea.de:d? 2018-01-0? citable citableW? deNBIch? supple? <NA>
7 oai:pangaea.de:d? 2018-01-0? citable citableW? deNBIch? supple? <NA>
8 oai:pangaea.de:d? 2018-01-0? citable citableW? deNBIch? supple? <NA>
9 oai:pangaea.de:d? 2018-01-0? Yangeta? citable citable? deNBIc? <NA>
0 oai:pangaea.de:d? 2018-01-0? citable citableW? <NA> <NA> <NA>
... with 214 more rows
ist_sets()
A tibble: 262 x 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)
0 BAH1966 PANGAEA tech-keyword 'BAH1966' (6 data sets)
... with 252 more rows
ist_records(from = Sys.Date() - 1, until = Sys.Date())
A tibble: 173 x 45
iden? date? setS? setS? setS? setS? setS? title crea? crea? crea? crea?
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 oai:? 2018? Yang? cita? cita? deNB? supp? Seaw? de P? McCo? Cohe? Dill?
2 oai:? 2018? cita? cita? supp? <NA> <NA> Chem? Cart? <NA> <NA> <NA>
3 oai:? 2018? cita? cita? supp? <NA> <NA> Dist? Step? Obro? Hytt? Krup?
4 oai:? 2018? cita? cita? supp? <NA> <NA> Desc? Cron? <NA> <NA> <NA>
5 oai:? 2018? cita? cita? deNB? supp? <NA> Seaw? Dueń? Rait? de N? Reic?
6 oai:? 2018? cita? cita? deNB? supp? <NA> Seaw? Ries? <NA> <NA> <NA>
7 oai:? 2018? cita? cita? deNB? supp? <NA> Seaw? Brad? Warn? Dave? Smit?
8 oai:? 2018? Yang? cita? cita? deNB? <NA> Seaw? Chau? Deni? Cuet? <NA>
9 oai:? 2018? cita? cita? <NA> <NA> <NA> The ? Llor? Rovi? Meri? Rubi?
0 oai:? 2018? cita? cita? supp? <NA> <NA> Seis? Diez? Eise? Hofs? Bohl?
... with 163 more rows, and 33 more variables: 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>, subject <chr>, relation <chr>, relation.1 <chr>,
coverage <chr>, creator.4 <chr>, creator.5 <chr>, creator.6 <chr>,
creator.7 <chr>, relation.2 <chr>, creator.8 <chr>, creator.9 <chr>,
source.1 <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>
et_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>
oai:pangaea.de:doi:10.1594/PANGAEA.788382 2017-08-08T17:50:18Z citable;?
`oai:pangaea.de:doi:10.1594/PANGAEA.788382`$metadata
A tibble: 1 x 13
title crea? sour? publ? date type form? iden? desc? lang? righ? cove?
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
Trace? Demi? P.P.? PANG? 2012? Data? appl? http? Bioa? en CC-B? MEDI?
... with 1 more variable: subject <chr>
pangaear in R doing citation(package = 'pangaear')