pangaear tutorial
for v0.3.0
Tools to interact with the [Pangaea Database](https:// www.pangaea.de), including functions for searching for data, fetching datasets by dataset ID, and working with the Pangaea OAI-PMH service.
Installation
Stable pangaear version from CRAN
install.packages("pangaear")
Or, the development version from Github
devtools::install_github("ropensci/pangaear")
library("pangaear")
Search for data
This 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.
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
#> <dbl> <chr> <dbl> <chr>
#> 1 21.19016 10.1594/PANGAEA.812094 2 datasets
#> 2 11.05477 10.1594/PANGAEA.862525 372 datasets
#> 3 10.84113 10.1594/PANGAEA.736010 9 datasets
#> # ... with 2 more variables: citation <chr>, supplement_to <chr>
Get data
res <- pg_data(doi = '10.1594/PANGAEA.761032')
res[[1]]
#> <Pangaea data> 10.1594/PANGAEA.761002
#> # A tibble: 250,201 x 9
#> Event `Date/Time` Latitude Longitude `Elevation [m]`
#> <chr> <chr> <dbl> <dbl> <int>
#> 1 NBP97-05/01 1997-08-04T12:09 -57.5007 -44.9915 -3090
#> 2 NBP97-05/01 1997-08-04T12:09 -57.5007 -44.9915 -3090
#> 3 NBP97-05/01 1997-08-04T12:09 -57.5007 -44.9915 -3090
#> 4 NBP97-05/01 1997-08-04T12:09 -57.5007 -44.9915 -3090
#> 5 NBP97-05/01 1997-08-04T12:09 -57.5007 -44.9915 -3090
#> 6 NBP97-05/01 1997-08-04T12:09 -57.5007 -44.9915 -3090
#> 7 NBP97-05/01 1997-08-04T12:09 -57.5007 -44.9915 -3090
#> 8 NBP97-05/01 1997-08-04T12:09 -57.5007 -44.9915 -3090
#> 9 NBP97-05/01 1997-08-04T12:09 -57.5007 -44.9915 -3090
#> 10 NBP97-05/01 1997-08-04T12:09 -57.5007 -44.9915 -3090
#> # ... with 250,191 more rows, and 4 more variables: `Depth water
#> # [m]` <int>, `Temp [°C]` <dbl>, Sal <dbl>, `Tpot [°C]` <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[1])
#> [[1]]
#> <Pangaea data> 10.1594/PANGAEA.812092
#> # A tibble: 12 x 18
#> Event Latitude Longitude `Elevation [m]` `Sample label`
#> <chr> <dbl> <dbl> <int> <chr>
#> 1 169-856H 48.434 -128.681 -2423 169-856H-55R-1
#> 2 169-856H 48.434 -128.681 -2423 169-856H-57R-1,52-54
#> 3 169-856H 48.434 -128.681 -2423 169-856H-64R-2,93-95
#> 4 169-856H 48.434 -128.681 -2423 169-856H-65R-1,35-38
#> 5 SO145/2_20 -14.153 -112.514 -2650 20DS4-surface
#> 6 SO145/2_20 -14.153 -112.514 -2650 20DS4-core
#> 7 SO145/2_29 -14.825 -111.907 -3355 29DS2-surface
#> 8 SO145/2_29 -14.825 -111.907 -3355 29DS2-core
#> 9 SO145/2_36 -14.892 -109.187 -3503 36DS1-surface
#> 10 SO145/2_36 -14.892 -109.187 -3503 36DS1-core
#> 11 SO145/2_36 -14.892 -109.187 -3503 43DS9-oxid. halo
#> 12 SO145/2_36 -14.892 -109.187 -3503 43DS9-core
#> # ... with 13 more variables: `Sample comment` <chr>, `Depth [m]` <dbl>,
#> # `Age [ka BP]` <int>, Rock <chr>, Alteration <chr>, `DBD
#> # [g/cm**3]` <dbl>, `Poros frac (MIP)` <dbl>, `Pore radius mean
#> # [mm]` <dbl>, `SSA [m**2/g]` <dbl>, `Poros frac (#1 NIR)` <dbl>, `Poros
#> # frac (#2 NIR)` <dbl>, `Water dm [%]` <dbl>, Minerals <chr>
#>
#> [[2]]
#> <Pangaea data> 10.1594/PANGAEA.812093
#> # A tibble: 36 x 18
#> Event `Sample label` `Sample comment`
#> <chr> <chr> <chr>
#> 1 169-856H 169-856H-55R-1 complete altered, thickness of basalt =200 µm
#> 2 169-856H 169-856H-55R-1 complete altered, thickness of basalt =200 µm
#> 3 169-856H 169-856H-55R-1 complete altered, thickness of basalt =200 µm
#> 4 169-856H 169-856H-55R-1 complete altered, thickness of basalt =200 µm
#> 5 169-856H 169-856H-55R-1 complete altered, thickness of basalt =200 µm
#> 6 169-856H 169-856H-55R-1 complete altered, thickness of basalt =200 µm
#> 7 169-856H 169-856H-55R-1 complete altered, thickness of basalt =200 µm
#> 8 169-856H 169-856H-55R-1 complete altered, thickness of basalt =200 µm
#> 9 169-856H 169-856H-55R-1 complete altered, thickness of basalt =200 µm
#> 10 169-856H 169-856H-55R-1 complete altered, thickness of basalt =200 µm
#> # ... with 26 more rows, and 15 more variables: `Depth [m]` <dbl>,
#> # `Distance [µm]` <int>, `T tech [°C]` <dbl>, Run <chr>, `- (initial
#> # concentration of diff...)` <dbl>, `- (initial concentration of
#> # diff...)` <dbl>, `Poros frac (#1, from fit)` <dbl>, `Poros frac (#2,
#> # from fit)` <dbl>, `Diff coeff [10**-6 cm**2/s]` <dbl>, `Diff coeff std
#> # dev [±] (effective from fit)` <dbl>, `Diff coeff std dev [±]
#> # (effective total)` <dbl>, X <dbl>, `X (average)` <int>, F <int>, `-
#> # (m)` <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 = '2015-09-01', until = '2015-09-05')
#> Error in handle_errors(parsed): OAI-PMH errors: noRecordsMatch:
List sets
pg_list_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)
#> 10 BAH1966 PANGAEA tech-keyword 'BAH1966' (6 data sets)
#> # ... with 252 more rows
List records
pg_list_records(from = '2015-09-01', until = '2015-09-10')
#> Error in handle_errors(parsed): OAI-PMH errors: noRecordsMatch:
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 x 3
#> identifier datestamp
#> <chr> <chr>
#> 1 oai:pangaea.de:doi:10.1594/PANGAEA.788382 2017-08-08T17:50:18Z
#> # ... with 1 more variables: setSpec <chr>
#>
#> $`oai:pangaea.de:doi:10.1594/PANGAEA.788382`$metadata
#> # A tibble: 1 x 13
#> title
#> <chr>
#> 1 Trace metals in shells of mussels and clams from deep-sea hydrothermal vent
#> # ... with 12 more variables: creator <chr>, source <chr>,
#> # publisher <chr>, date <chr>, type <chr>, format <chr>,
#> # identifier <chr>, description <chr>, language <chr>, rights <chr>,
#> # coverage <chr>, subject <chr>
Citing
To cite pangaear in publications use:
Scott Chamberlain, Kara Woo, Andrew MacDonald, Naupaka Zimmerman and Gavin Simpson (2017). pangaear: Client for the ‘Pangaea’ Database. R package version 0.3.0. https://CRAN.R-project.org/package=pangaear
License and bugs
- License: MIT
- Report bugs at our Github repo for pangaear
