Search for a specific reference using a keyword or a Digital Object
Identifier (DOI).
If the query is a character string, then all character columns in the table
are searched and the entries for which at least one
partial match was found are returned.
Alternatively, a named list can be used to look for an exact match in a
specific column (see Details section).
Arguments
- query
either a character string including a single keyword or a named list containing a custom query (see details section below). Note that if an empty character string is passed, then all available entries are returned.
- doi
charactera Digital Object Identifier (DOI) of the article. Note thatqueryis ignored ifdoiis specified.- ...
Additional arguments passed to
rmangal_request(), including the argumentcachethat allows requests caching.
Value
An object of class mgSearchReferences, which is a list that includes a
wide range of details associated to the reference, including all datasets
and networks related to the publication that are included in Mangal database.
Details
Names of the list should match one of the column names within the table.
For the reference table, those are:
id: unique identifier of the referencefirst_author: first authordoi: usedoiinsteadjstor: JSTOR identifieryear: year of publication.
Note that for lists with more than one element, only the first element is used, the others are ignored. An example is provided below.
Examples
# \donttest{
search_references(doi = "10.2307/3225248")
#> Found 1 reference.
#> $id
#> [1] 132
#>
#> $doi
#> [1] "10.2307/3225248"
#>
#> $first_author
#> [1] "koslucher"
#>
#> $year
#> [1] "1973"
#>
#> $jstor
#> [1] "https://www.jstor.org/stable/3225248"
#>
#> $pmid
#> [1] NA
#>
#> $bibtex
#> [1] "@article{Koslucher_1973, doi = {10.2307/3225248}, url = {https://doi.org/10.2307%2F3225248}, year = 1973, month = {jul}, publisher = {{JSTOR}}, volume = {92}, number = {3}, pages = {441}, author = {Dale G. Koslucher and G. Wayne Minshall}, title = {Food Habits of Some Benthic Invertebrates in a Northern Cool-Desert Stream (Deep Creek, Curlew Valley, Idaho-Utah)}, journal = {Transactions of the American Microscopical Society}}"
#>
#> $paper_url
#> [1] "https://www.jstor.org/stable/pdf/3225248.pdf?refreqid=excelsior%3Ae2741b937f74579b7875d7ade8f58f47"
#>
#> $data_url
#> [1] "https://globalwebdb.com/"
#>
#> $created_at
#> [1] "2019-03-08T19:27:48.551Z"
#>
#> $updated_at
#> [1] "2019-03-08T19:27:48.551Z"
#>
#> $datasets
#> id name
#> 1 133 koslucher_minshall_1973
#> description
#> 1 Food web strucutre of a noterhen cool-desert stream (Deep Creek), Curlew Valley, Idaho-Utah
#> public created_at updated_at ref_id user_id
#> 1 TRUE 2019-03-08T19:27:50.152Z 2019-03-08T19:27:50.152Z 132 4
#>
#> $networks
#> $networks[[1]]
#> id name date
#> 1 1517 koslucher_minshall_1973 1969-11-01T00:00:00.000Z
#> description
#> 1 Food web strucutre of a noterhen cool-desert stream (Deep Creek), Curlew Valley, Idaho-Utah
#> public all_interactions created_at updated_at
#> 1 TRUE FALSE 2019-03-08T19:27:51.061Z 2019-03-08T19:27:51.061Z
#> dataset_id user_id geom_type geom_lon geom_lat
#> 1 133 4 <NA> NA NA
#>
#>
#> attr(,"row.names")
#> [1] 1
#> attr(,"class")
#> [1] "mgSearchReferences"
search_references(list(jstor = 3683041))
#> Found 1 reference.
#> $id
#> [1] 9
#>
#> $doi
#> [1] "10.2307/3683041"
#>
#> $first_author
#> [1] "elberling"
#>
#> $year
#> [1] "1999"
#>
#> $jstor
#> [1] "3683041"
#>
#> $pmid
#> [1] NA
#>
#> $bibtex
#> [1] "@article{10.2307/3683041, ISSN = {09067590, 16000587}, URL = {http://www.jstor.org/stable/3683041}, author = {Heidi Elberling and Jens M. Olesen}, journal = {Ecography}, number = {3}, pages = {314-323}, publisher = {[Nordic Society Oikos, Wiley]}, title = {The Structure of a High Latitude Plant-Flower Visitor System: The Dominance of Flies}, volume = {22}, year = {1999}}"
#>
#> $paper_url
#> [1] "https://www.jstor.org/stable/3683041?seq=1#page_scan_tab_contents"
#>
#> $data_url
#> [1] "https://www.nceas.ucsb.edu/interactionweb/data/plant_pollinator/excel/elberling&olesen_1999.xls"
#>
#> $created_at
#> [1] "2019-02-22T20:09:13.872Z"
#>
#> $updated_at
#> [1] "2019-02-22T20:09:13.872Z"
#>
#> $datasets
#> id name
#> 1 9 elberling_olesen_1999
#> description public
#> 1 Flower-visiting insect at Mt. Latnjatjarro, northern Sweden TRUE
#> created_at updated_at ref_id user_id
#> 1 2019-02-22T20:09:17.994Z 2019-02-22T20:09:17.994Z 9 2
#>
#> $networks
#> $networks[[1]]
#> id name date
#> 1 909 elberling_olesen_1999_19940823_909 1994-08-23T00:00:00.000Z
#> description public
#> 1 Flower-visiting insect at Mt. Latnjatjarro, northern Sweden TRUE
#> all_interactions created_at updated_at dataset_id
#> 1 FALSE 2019-02-24T22:21:32.444Z 2019-02-24T22:21:32.444Z 9
#> user_id geom_type geom_lon geom_lat
#> 1 2 Point 18.5 68.35
#>
#>
#> attr(,"row.names")
#> [1] 1
#> attr(,"class")
#> [1] "mgSearchReferences"
search_references(list(year = 2001))
#> Found 3 references.
#> $id
#> [1] 57 109 81
#>
#> $doi
#> [1] "10.1071/mf99152" NA
#> [3] "10.1007/978-94-017-2934-5_28"
#>
#> $first_author
#> [1] "c. bulman" "nybakken" "alcorlo"
#>
#> $year
#> [1] "2001" "2001" "2001"
#>
#> $jstor
#> [1] NA NA NA
#>
#> $pmid
#> [1] NA NA NA
#>
#> $bibtex
#> [1] "@article{Bulman_2001, doi = {10.1071/mf99152}, url = {https://doi.org/10.1071%2Fmf99152}, year = 2001, publisher = {{CSIRO} Publishing}, volume = {52}, number = {4}, pages = {537}, author = {C. Bulman and F. Althaus and X. He and N. J. Bax and A. Williams}, title = {Diets and trophic guilds of demersal fishes of the south-eastern Australian shelf}, journal = {Marine and Freshwater Research}}"
#> [2] "@book{nybakken2001marine, title={Marine biology: an ecological approach}, author={Nybakken, James Willard and Bertness, Mark D}, volume={5}, year={2001}, publisher={Benjamin Cummings San Francisco}"
#> [3] "@incollection{Alcorlo_2001,\tdoi = {10.1007/978-94-017-2934-5_28}, url = {https://doi.org/10.1007%2F978-94-017-2934-5_28}, year = 2001, publisher = {Springer Netherlands}, pages = {307--316}, author = {Paloma Alcorlo and Angel Baltan{'{a}}s and Carlos Montes}, title = {Food-web structure in two shallow salt lakes in Los Monegros ({NE} Spain): energetic vs dynamic constraints}, booktitle = {Saline Lakes}}"
#>
#> $paper_url
#> [1] ""
#> [2] NA
#> [3] "https://link.springer.com/article/10.1023/A:1014594408119"
#>
#> $data_url
#> [1] "https://globalwebdb.com/" "https://globalwebdb.com/"
#> [3] "https://globalwebdb.com/"
#>
#> $created_at
#> [1] "2019-02-25T03:00:59.456Z" "2019-03-05T19:45:40.738Z"
#> [3] "2019-02-27T16:34:04.537Z"
#>
#> $updated_at
#> [1] "2019-02-25T03:00:59.456Z" "2019-03-05T19:45:40.738Z"
#> [3] "2019-02-27T16:34:04.537Z"
#>
#> $datasets
#> id name
#> 1 58 bulman_2001
#> 2 110 nybakken_2001
#> 3 82 alcorlo_et_al_2001
#> description
#> 1 Dietary matrix of demersal fishes of the south-eastern Australian shelf
#> 2 Food web structure of an exposed intertidal sand beach community, California
#> 3 The biotic interactions within two shallow salt lake, Los Monegros, Spain
#> public created_at updated_at ref_id user_id
#> 1 TRUE 2019-02-25T03:01:02.681Z 2019-02-25T03:01:02.681Z 57 3
#> 2 TRUE 2019-03-05T19:45:43.583Z 2019-03-05T19:45:43.583Z 109 4
#> 3 TRUE 2019-02-27T16:34:14.178Z 2019-02-27T16:34:14.178Z 81 4
#>
#> $networks
#> $networks[[1]]
#> id name date
#> 1 1102 bulman_2001_19930701_1102 1993-07-01T00:00:00.000Z
#> description
#> 1 Dietary matrix of demersal fishes of the south-eastern Australian shelf
#> public all_interactions created_at updated_at
#> 1 TRUE FALSE 2019-02-26T23:22:13.839Z 2019-02-26T23:22:13.839Z
#> dataset_id user_id geom_type geom_lon geom_lat
#> 1 58 3 Point 120.4333 22.45
#>
#> $networks[[2]]
#> id name date
#> 1 1485 nybakken_2001__1485 NA
#> description
#> 1 Food web structure of an exposed intertidal sand beach community, California
#> public all_interactions created_at updated_at
#> 1 TRUE FALSE 2019-03-05T19:45:45.269Z 2019-03-05T19:45:45.269Z
#> dataset_id user_id geom_type geom_lon geom_lat
#> 1 110 4 <NA> NA NA
#>
#> $networks[[3]]
#> id name date
#> 1 1440 alcorlo_et_al_2001_19941101_1440 1994-11-01T00:00:00.000Z
#> description public
#> 1 The biotic interactions within the Lake_La_Muerte, Los Monegros, Spain TRUE
#> all_interactions created_at updated_at dataset_id
#> 1 FALSE 2019-02-27T23:51:07.287Z 2019-02-27T23:51:07.287Z 82
#> user_id geom_type geom_lon geom_lat
#> 1 4 Point -0.2617805 41.40156
#>
#>
#> attr(,"row.names")
#> [1] 1 2 3
#> attr(,"class")
#> [1] "mgSearchReferences"
# }