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 = 2010))
#> Found 5 references.
#> $id
#> [1] 74 76 111 85 164
#>
#> $doi
#> [1] "10.1007/s10641-010-9606-0" "10.3989/scimar.2011.75n2309"
#> [3] "10.1071/mf09202" NA
#> [5] "10.1111/j.1461-0248.2009.01437.x"
#>
#> $first_author
#> [1] "ricciardi" "ronaldo angelini" "rayner" "angelini"
#> [5] "kaiser-bunbury"
#>
#> $year
#> [1] "2010" "2010" "2010" "2010" "2010"
#>
#> $jstor
#> [1] NA NA NA NA NA
#>
#> $pmid
#> [1] NA NA NA NA NA
#>
#> $bibtex
#> [1] "@article{Ricciardi_2010,doi = {10.1007/s10641-010-9606-0},url = {https://doi.org/10.1007%2Fs10641-010-9606-0},year = 2010,month = {feb},publisher = {Springer Nature},volume = {87},number = {4},pages = {333--347},author = {Francesco Ricciardi and Massimo Boyer and Jeff Ollerton},title = {Assemblage and interaction structure of the anemonefish-anemone mutualism across the Manado region of Sulawesi, Indonesia},journal = {Environmental Biology of Fishes}}"
#> [2] "@article{Angelini_2010, doi = {10.3989/scimar.2011.75n2309}, url = {https://doi.org/10.3989%2Fscimar.2011.75n2309}, year = 2010, month = {nov}, publisher = {Departmento de Publicaciones del {CSIC}}, volume = {75}, number = {2}, pages = {309--319}, author = {Ronaldo Angelini and Filomena Vaz-Velho}, title = {Ecosystem structure and trophic analysis of Angolan fishery landings}, journal = {Scientia Marina}}"
#> [3] "@article{Rayner_2010, doi = {10.1071/mf09202}, url = {https://doi.org/10.1071%2Fmf09202}, year = 2010, publisher = {{CSIRO} Publishing}, volume = {61}, number = {8}, pages = {909}, author = {Thomas S. Rayner and Bradley J. Pusey and Richard G. Pearson and Paul C. Godfrey}, title = {Food web dynamics in an Australian Wet Tropics river}, journal = {Marine and Freshwater Research}}"
#> [4] "@article{angelini2010mixed, title={Mixed food web control and stability in a Cerrado river (Brazil)}, author={Angelini, RONALDO and Aloisio, GUSTAVO RIBEIRO and Carvalho, ADRIANA ROSA}, journal={Pan-American Journal of Aquatic Sciences}, volume={5}, number={3}, pages={421--431}, year={2010}}"
#> [5] "@article{Kaiser_Bunbury_2010, doi = {10.1111/j.1461-0248.2009.01437.x}, url = {https://doi.org/10.1111%2Fj.1461-0248.2009.01437.x}, year = 2010, month = {apr}, publisher = {Wiley}, volume = {13}, number = {4}, pages = {442--452}, author = {Christopher N. Kaiser-Bunbury and Stefanie Muff and Jane Memmott and Christine B. Müller and Amedeo Caflisch}, title = {The robustness of pollination networks to the loss of species and interactions: a quantitative approach incorporating pollinator behaviour}, journal = {Ecology Letters}}"
#>
#> $paper_url
#> [1] "https://link.springer.com/article/10.1007%2Fs10641-010-9606-0"
#> [2] "https://doi.org/10.3989%2Fscimar.2011.75n2309"
#> [3] "http://www.publish.csiro.au/mf/MF09202"
#> [4] "https://panamjas.org/pdf_artigos/PANAMJAS_5(3)_421-431.pdf"
#> [5] "https://onlinelibrary.wiley.com/doi/full/10.1111/j.1461-0248.2009.01437.x"
#>
#> $data_url
#> [1] "https://www.nceas.ucsb.edu/interactionweb/data/anemone_fish/ricciardi-et-al-2010.xls"
#> [2] "https://globalwebdb.com/"
#> [3] "https://globalwebdb.com/"
#> [4] "https://globalwebdb.com/"
#> [5] "http://www.web-of-life.es/2.0/map.php"
#>
#> $created_at
#> [1] "2019-02-26T20:11:58.429Z" "2019-02-26T21:18:52.787Z"
#> [3] "2019-03-06T14:49:40.733Z" "2019-02-28T17:26:42.053Z"
#> [5] "2019-03-21T19:21:35.795Z"
#>
#> $updated_at
#> [1] "2019-02-26T20:11:58.429Z" "2019-02-26T21:18:52.787Z"
#> [3] "2019-03-06T14:49:40.733Z" "2019-02-28T17:26:42.053Z"
#> [5] "2019-03-21T19:21:35.795Z"
#>
#> $datasets
#> id name
#> 1 75 ricciardi_2010
#> 2 77 angelini_2010
#> 3 112 rayner_et_al_2010
#> 4 86 angelini_et_al_2010
#> 5 167 kaiser-bunbury_et_al_2010
#> description
#> 1 structure of local anemonefish-anemone networks across the Manado region of Sulawesi, Indonesia
#> 2 Food web of the Angolan fishery landings
#> 3 Food web structure of a wet Tropic river (Mulgrave River), Australia
#> 4 Interaction of a mixed food web in the Corrente River in the Paraná River Basin, Brazil
#> 5 Plant-pollinator system at two sites in Black River Gorges National Park, Mauritius
#> public created_at updated_at ref_id user_id
#> 1 TRUE 2019-02-26T20:12:00.676Z 2019-02-26T20:12:00.676Z 74 2
#> 2 TRUE 2019-02-26T21:18:55.909Z 2019-02-26T21:18:55.909Z 76 3
#> 3 TRUE 2019-03-06T14:49:42.906Z 2019-03-06T14:49:42.906Z 111 4
#> 4 TRUE 2019-02-28T17:26:45.617Z 2019-02-28T17:26:45.617Z 85 4
#> 5 TRUE 2019-03-21T19:21:38.571Z 2019-03-21T19:21:38.571Z 164 4
#>
#> $networks
#> $networks[[1]]
#> id name date
#> 1 1071 ricciardi_2010_20060701_1071 2006-07-01T00:00:00.000Z
#> description
#> 1 structure of local anemonefish-anemone networks across the Manado region of Sulawesi, Indonesia, Bajo
#> public all_interactions created_at updated_at
#> 1 TRUE FALSE 2019-02-26T20:12:57.710Z 2019-02-26T20:12:57.710Z
#> dataset_id user_id geom_type geom_lon geom_lat
#> 1 75 2 Point 124.778 1.787
#>
#> $networks[[2]]
#> id name date
#> 1 1101 angelini_2010_20100601_1101 2010-06-01T00:00:00.000Z
#> description public all_interactions
#> 1 Food web of the Angolan fishery landings TRUE FALSE
#> created_at updated_at dataset_id user_id
#> 1 2019-02-26T21:19:01.124Z 2019-02-26T21:19:01.124Z 77 3
#> geom_type
#> 1 Polygon
#> geom_lon
#> 1 10.95337, 11.62354, 11.64551, 12.12891, 13.60107, 11.95312, 10.70068, 10.95337, 10.95337
#> geom_lat
#> 1 -17.25000, -17.25000, -15.53838, -13.96605, -11.13529, -5.00000, -5.00000, -17.25000, -17.25000
#>
#> $networks[[3]]
#> id name date
#> 1 1488 rayner_et_al_2010_20040401_1488 2004-04-01T00:00:00.000Z
#> description public
#> 1 Food web structure of a wet Tropic river (Mulgrave River), Australia TRUE
#> all_interactions created_at updated_at dataset_id
#> 1 FALSE 2019-03-06T14:49:45.109Z 2019-03-06T14:49:45.109Z 112
#> user_id geom_type geom_lon geom_lat
#> 1 4 Point 145.8646 -17.12026
#>
#> $networks[[4]]
#> id name date
#> 1 1448 angelini_et_al_2010_20030501_1448 2003-05-01T00:00:00.000Z
#> description
#> 1 Interaction of a mixed food web in the Corrente River in the Paraná River Basin
#> public all_interactions created_at updated_at
#> 1 TRUE FALSE 2019-02-28T17:26:47.593Z 2019-02-28T17:26:47.593Z
#> dataset_id user_id geom_type geom_lon geom_lat
#> 1 86 4 Point -52.0155 -18.56476
#>
#> $networks[[5]]
#> id name date
#> 1 1599 kaiser-bunbury_et_al_2010_1 2003-09-01T00:00:00.000Z
#> description
#> 1 Plant-pollinator system at two sites in Black River Gorges National Park, Mauritius
#> public all_interactions created_at updated_at
#> 1 TRUE FALSE 2019-03-21T19:23:49.316Z 2019-03-21T19:23:49.316Z
#> dataset_id user_id geom_type geom_lon geom_lat
#> 1 167 4 Point 57.45094 -20.42637
#>
#>
#> attr(,"row.names")
#> [1] 1 2 3 4 5
#> attr(,"class")
#> [1] "mgSearchReferences"
# }