diff --git a/R/yyy.R b/R/yyy.R index 744baa1..389072b 100644 --- a/R/yyy.R +++ b/R/yyy.R @@ -32,16 +32,16 @@ vertsumwrapper <- function(input = NULL, verbose = TRUE){ input$coordinateuncertaintyinmeters <- as.numeric(as.character(input$coordinateuncertaintyinmeters)) } mappable <- input[stats::complete.cases(input[,c('decimallatitude','decimallongitude')]),] - mappable <- subset(mappable, input$decimallatitude < 90 & input$decimallatitude > -90) - mappable <- subset(mappable, input$decimallongitude < 180 & input$decimallongitude > -180) + mappable <- subset(mappable, mappable$decimallatitude < 90 & mappable$decimallatitude > -90) + mappable <- subset(mappable, mappable$decimallongitude < 180 & mappable$decimallongitude > -180) if (nrow(mappable) < coords) { bad <- coords - nrow(mappable) mssg(verbose, paste(bad, " record(s) with bad coordinates")) coords <- coords - bad } if (is.null(errest)) { - mappable <- subset(mappable, input$coordinateuncertaintyinmeters > 0 & - input$coordinateuncertaintyinmeters < 20020000) + mappable <- subset(mappable, mappable$coordinateuncertaintyinmeters > 0 & + mappable$coordinateuncertaintyinmeters < 20020000) if ((errest <- nrow(mappable)) < coords) { bad <- coords - errest } diff --git a/tests/fixtures/vertsummary_prep_vertsearch.yml b/tests/fixtures/vertsummary_prep_vertsearch.yml index 21509c0..190aa67 100644 --- a/tests/fixtures/vertsummary_prep_vertsearch.yml +++ b/tests/fixtures/vertsummary_prep_vertsearch.yml @@ -6,7 +6,7 @@ http_interactions: encoding: '' string: '' headers: - User-Agent: libcurl/7.54.0 r-curl/4.3 crul/0.9.0 + User-Agent: libcurl/7.71.1 r-curl/4.3 crul/1.0.0 Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* response: @@ -19,16 +19,19 @@ http_interactions: cache-control: no-cache content-type: application/json charset: utf-8 - x-cloud-trace-context: a7d7e4968517ecf89d05bc663af1aa31 - date: Wed, 29 Jan 2020 16:57:16 GMT + set-cookie: _eauth=eyJ1c2VyX2lkIjpudWxsLCJzZXNzaW9uX2lkIjoiTHJUR1I5SFBLTXpWR1dJVG1MSVZqSSJ9|1597091065|8b8076a193020588ab8837b1bc0c88c35fdbb72b; 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+ Path=/ + x-cloud-trace-context: 56341307bdcf8102e7639f11612c9696 + date: Mon, 10 Aug 2020 20:24:26 GMT server: Google Frontend - content-length: '31836' + content-length: '169760' + expires: Mon, 10 Aug 2020 20:24:26 GMT body: encoding: UTF-8 file: no - string: '{"request_date": "2020-01-29T16:57:17.817124", "response_records": - 10, "submitted_query": "Oncorhynchus clarki henshawi", "request_origin": "45.505106,-122.675026", - "limit": 10, "cursor": "False:CqIGCpIDCuQC9wAAABP_____jIGJmo2LkZqL0o-QjYuek96WkZuah9LNz87M0s_H0s_H_wAA_3RtoKCZi4ygoP8AAP9dno-PmpGYlpGa_wAA_3N0bZaRm5qH_wAA_12biJz_AAD_c3Rtm5CcoJab_wAA_12cnozQjIrQio2R0pyei56TkJjSnJ6M0oyK0pacl9LMyM_Iz_8AAP9zf5yejNCMitCKjZHSnJ6LnpOQmNKcnozSjIrSlpyX0szIz8jP_wAA__8A_v_-jIGJmo2LkZqL0o-QjYuek96WkZuah9LNz87M0s_H0s_H_wB0baCgmYuMoKD_AF2ej4-akZiWkZr_AHN0bZaRm5qH_wBdm4ic_wBzdG2bkJyglpv_AF2cnozQjIrQio2R0pyei56TkJjSnJ6M0oyK0pacl9LMyM_Iz_8Ac3-cnozQjIrQio2R0pyei56TkJjSnJ6M0oyK0pacl9LMyM_Iz_8A__4QCiHbXi_RmyTUyTkAAAAA7P___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_SgUIAEDoBw", - "query_version": "search.py 2016-08-15T16:43+02:00", "recs": [{"haslifestage": - "1", "month": "10", "decimallongitude": "-121.0484020000", "verbatimlongitude": - "-121.048402\u00b0", "isarch": "0", "startdayofyear": "287", "networks": "FishNet,VertNet", - "vntype": "specimen", "title": "CAS Ichthyology (ICH)", "kingdom": "Animalia", - "dctype": "PhysicalObject", "iptrecordid": "urn:catalog:CAS:ICH:19007", "day": - "14", "occurrenceid": "urn:catalog:CAS:ICH:19007", "collectioncode": "ICH", - "verbatimeventdate": "1945-10-14", "coordinateuncertaintyinmeters": "418", - "higherclassification": "Actinopteri | Salmoniformes", "pubdate": "2019-07-15", + string: '{"request_date": "2020-08-10T20:24:26.462716", "response_records": + 60, "submitted_query": "Oncorhynchus clarki henshawi", "request_origin": "45.505106,-122.675026", + "limit": 1000, "cursor": null, "query_version": "search.py 2016-08-15T16:43+02:00", + "recs": [{"haslifestage": "1", "month": "10", "decimallongitude": "-121.0484020000", + "verbatimlongitude": "-121.048402\u00b0", "isarch": "0", "startdayofyear": + "287", "networks": "FishNet,VertNet", "vntype": "specimen", "title": "CAS + Ichthyology (ICH)", "kingdom": "Animalia", "dctype": "PhysicalObject", "iptrecordid": + "urn:catalog:CAS:ICH:19007", "day": "14", "occurrenceid": "urn:catalog:CAS:ICH:19007", + "collectioncode": "ICH", "verbatimeventdate": "1945-10-14", "coordinateuncertaintyinmeters": + "418", "higherclassification": "Actinopteri | Salmoniformes", "pubdate": "2019-07-15", "lifestage": "juvenile", "modified": "1999-11-30 00:00:00.0", "year": "1945", "wasinvasive": "0", "specificepithet": "clarki", "basisofrecord": "PreservedSpecimen", "geodeticdatum": "not recorded", "occurrenceremarks": "Small juvenile.", "highergeography": @@ -829,7 +834,1687 @@ http_interactions: (ICH). Record ID: urn:catalog:CAS:SU (ICH):37070. Source: http://ipt.calacademy.org:8080/ipt/resource.do?r=ich (source published on 2019-07-15)", "references": "http://portal.vertnet.org/o/cas/su?id=urn-catalog-cas-su-ich-37070", "genus": "Oncorhynchus", "gbifdatasetid": "5d6c10bd-ea31-4363-8b79-58c96d859f5b", - "order": "Salmoniformes", "catalognumber": "37070", "collectioncode": "SU"}], - "matching_records": 60, "api_version": "api.py 2017-11-24T12:16-03:00"}' - recorded_at: 2020-01-29 16:57:18 GMT - recorded_with: vcr/0.4.0, webmockr/0.5.0 + "order": "Salmoniformes", "catalognumber": "37070", "collectioncode": "SU"}, + {"haslifestage": "0", "individualcount": "1", "higherclassification": "Actinopteri + | Salmoniformes", "pubdate": "2019-07-15", "stateprovince": "Nevada", "hastypestatus": + "0", "basisofrecord": "PreservedSpecimen", "rank": 9, "georeferencesources": + "FishNet Collaborative Georeferencing Project", "decimallongitude": "-117.7396120000", + "phylum": "Chordata", "references": "http://portal.vertnet.org/o/cas/su?id=urn-catalog-cas-su-ich-4832", + "haslength": "0", "isarch": "0", "wasinvasive": "0", "wascaptive": "0", "specificepithet": + "clarki", "networks": "FishNet,VertNet", "recordedby": "Germain, F.", "bibliographiccitation": + "California Academy of Sciences. CAS Ichthyology (ICH). Record ID: urn:catalog:CAS:SU + (ICH):4832. Source: http://ipt.calacademy.org:8080/ipt/resource.do?r=ich (source + published on 2019-07-15)", "vntype": "specimen", "family": "Salmonidae", "locality": + "Winnemucca.", "orgname": "California Academy of Sciences", "hasmedia": "0", + "geodeticdatum": "not recorded", "coordinateuncertaintyinmeters": "2675", + "orgstateprovince": "California", "highergeography": "North America|United + States|Nevada|Humboldt County", "continent": "North America", "contact": "David + Catania", "lastindexed": "2019-08-04", "migrator": "no migrator", "hastissue": + "0", "hasmass": "0", "email": "dcatania@calacademy.org", "kingdom": "Animalia", + "infraspecificepithet": "henshawi", "citation": "California Academy of Sciences. + CAS Ichthyology (ICH). Source: http://ipt.calacademy.org:8080/ipt/resource.do?r=ich + (source published on 2019-07-15)", "hassex": "0", "orgcountry": "United States", + "source_url": "http://ipt.calacademy.org:8080/ipt/resource.do?r=ich", "institutioncode": + "CAS", "dctype": "PhysicalObject", "iptrecordid": "urn:catalog:CAS:SU (ICH):4832", + "icode": "CAS", "scientificname": "Oncorhynchus clarki henshawi", "preparations": + "alc-75% EtOH", "gbifpublisherid": "66522820-055c-11d8-b84e-b8a03c50a862", + "hashid": "6581", "georeferenceremarks": "Assuming locality is Humboldt River + at Winnemucca. Point is place at major river/road (US 80) crossing. Uncertainty + runs halfway to Weso.", "class": "Actinopteri", "keyname": "cas/su/urn-catalog-cas-su-ich-4832", + "isfossil": "0", "county": "Humboldt County", "decimallatitude": "40.9755220000", + "occurrenceid": "urn:catalog:CAS:SU (ICH):4832", "language": "en", "license": + "CC0", "country": "United States", "mappable": "1", "title": "CAS Ichthyology + (ICH)", "modified": "1999-11-30 00:00:00.0", "verbatimlatitude": "40.975522\u00b0", + "nomenclaturalcode": "ICZN", "haslicense": "1", "fieldnumber": "FG-WINNEMUCCA", + "verbatimlongitude": "-117.739612\u00b0", "genus": "Oncorhynchus", "gbifdatasetid": + "5d6c10bd-ea31-4363-8b79-58c96d859f5b", "order": "Salmoniformes", "catalognumber": + "4832", "collectioncode": "SU"}, {"haslifestage": "1", "decimallongitude": + "-120.033202", "isarch": "0", "networks": "FishNet,HerpNET,MaNIS,ORNIS,Paleo,VertNet", + "vntype": "specimen", "title": "Museum of Comparative Zoology, Harvard University, + Subset of data for VERTNET", "kingdom": "Animalia", "verbatimcoordinatesystem": + "decimal degrees", "dctype": "PhysicalObject", "iptrecordid": "MCZ:Ich:26805", + "identificationverificationstatus": "unverified", "occurrenceid": "MCZ:Ich:26805", + "collectioncode": "Ich", "verbatimeventdate": "[no verbatim date data]", "coordinateuncertaintyinmeters": + "18029", "higherclassification": "Animalia Chordata Craniata Gnathostomata + Osteichthyes Neopterygii Actinopterygii Salmoniformes Salmonidae Oncorhynchus + clarki henshawi", "pubdate": "2017-07-11", "lifestage": "adult", "modified": + "2018-01-24 14:23:03.0", "wasinvasive": "0", "specificepithet": "clarki", + "basisofrecord": "PreservedSpecimen", "geodeticdatum": "WGS84", "occurrenceremarks": + "age class: adult", "highergeography": "North America: United States: California", + "continent": "North America", "email": "bhaley@oeb.harvard.edu", "orgcountry": + "United States", "source_url": "http://digir.mcz.harvard.edu/ipt/resource.do?r=mcz_subset_for_vertnet", + "scientificname": "Oncorhynchus clarki henshawi", "disposition": "in collection", + "hashid": "7811", "hassex": "0", "language": "en", "institutionid": "b4640710-8e03-11d8-b956-b8a03c50a862", + "country": "United States", "hastissue": "0", "ownerinstitutioncode": "Museum + of Comparative Zoology, Harvard University", "genus": "Oncorhynchus", "georeferenceprotocol": + "MaNIS/HerpNET/ORNIS Georeferencing Guidelines", "family": "Salmonidae", "stateprovince": + "California", "rank": 9, "phylum": "Chordata", "references": "http://mczbase.mcz.harvard.edu/guid/MCZ:Ich:26805", + "georeferencedby": "Paul DeSalles", "hasmedia": "0", "verbatimlocality": "Lake + Tahoe", "countrycode": "US", "institutioncode": "MCZ", "orgstateprovince": + "Massachusetts", "hastypestatus": "0", "preparations": "whole animal (alcohol)", + "recordedby": "[no agent data]", "isfossil": "0", "license": "CC-BY-NC", "wascaptive": + "0", "dynamicproperties": "{\"age class\":\"adult\"}", "infraspecificepithet": + "henshawi", "haslicense": "1", "fieldnumber": "USNM:LAKETAHOE", "eventdate": + "[no verbatim date data]", "individualcount": "1", "bibliographiccitation": + "Museum of Comparative Zoology, Harvard University. Museum of Comparative + Zoology, Harvard University, Subset of data for VERTNET. Record ID: MCZ:Ich:26805. + Source: http://digir.mcz.harvard.edu/ipt/resource.do?r=mcz_subset_for_vertnet + (source published on 2017-07-11)", "citation": "Museum of Comparative Zoology, + Harvard University. Museum of Comparative Zoology, Harvard University, Subset + of data for VERTNET. Source: http://digir.mcz.harvard.edu/ipt/resource.do?r=mcz_subset_for_vertnet + (source published on 2017-07-11)", "georeferencesources": "unknown", "lastindexed": + "2018-09-22", "haslength": "0", "catalognumber": "26805", "emlrights": "Copyright + \u00a9 2013 The President and Fellows of Harvard College", "hasmass": "0", + "gbifdatasetid": "4bfac3ea-8763-4f4b-a71a-76a6f5f243d3", "locality": "Lake + Tahoe", "orgname": "Museum of Comparative Zoology, Harvard University", "keyname": + "mcz/ich/mcz-ich-26805", "migrator": "no migrator", "icode": "MCZ", "gbifpublisherid": + "b4640710-8e03-11d8-b956-b8a03c50a862", "class": "Osteichthyes", "identificationremarks": + "Donor: USNM;Donor Date: 00/00/1881", "decimallatitude": "39.096027", "mappable": + "1", "rightsholder": "President and Fellows of Harvard College", "othercatalognumbers": + "field number=USNM:LAKETAHOE; group number=129; previous number=USNM 24139", + "identifiedby": "Ledger", "nomenclaturalcode": "ICZN", "contact": "Brendan + Haley", "order": "Salmoniformes"}, {"haslifestage": "0", "individualcount": + "4", "higherclassification": "Actinopteri | Salmoniformes", "pubdate": "2019-07-15", + "stateprovince": "California", "hastypestatus": "0", "basisofrecord": "PreservedSpecimen", + "rank": 9, "georeferencesources": "FishNet Collaborative Georeferencing Project", + "decimallongitude": "-120.3096660000", "phylum": "Chordata", "references": + "http://portal.vertnet.org/o/cas/ich?id=urn-catalog-cas-ich-62375", "haslength": + "0", "isarch": "0", "wasinvasive": "0", "wascaptive": "0", "specificepithet": + "clarki", "networks": "FishNet,VertNet", "recordedby": "Behnke, Robert J.", + "hasmass": "0", "vntype": "specimen", "habitat": "freshwater", "locality": + "Independence Lake, Sierra & Nevada Cos., California", "orgname": "California + Academy of Sciences", "hasmedia": "0", "geodeticdatum": "not recorded", "occurrenceremarks": + "=Salmo clarki henshawi. 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Source: http://ipt.calacademy.org:8080/ipt/resource.do?r=ich (source + published on 2019-07-15)", "verbatimlongitude": "-120.309666\u00b0", "hassex": + "0", "orgcountry": "United States", "source_url": "http://ipt.calacademy.org:8080/ipt/resource.do?r=ich", + "institutioncode": "CAS", "dctype": "PhysicalObject", "iptrecordid": "urn:catalog:CAS:ICH:62375", + "icode": "CAS", "scientificname": "Oncorhynchus clarki henshawi", "preparations": + "skeletal", "gbifpublisherid": "66522820-055c-11d8-b84e-b8a03c50a862", "hashid": + "4168", "class": "Actinopteri", "infraspecificepithet": "henshawi", "keyname": + "cas/ich/urn-catalog-cas-ich-62375", "isfossil": "0", "decimallatitude": "39.4422980000", + "occurrenceid": "urn:catalog:CAS:ICH:62375", "language": "en", "license": + "CC0", "country": "United States", "mappable": "1", "title": "CAS Ichthyology + (ICH)", "modified": "2012-03-27 17:40:45.0", "verbatimlatitude": "39.442298\u00b0", + "nomenclaturalcode": "ICZN", "haslicense": "1", "fieldnumber": "Z62375", "bibliographiccitation": + "California Academy of Sciences. 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Source: http://ipt.calacademy.org:8080/ipt/resource.do?r=ich + (source published on 2019-07-15)", "waterbody": "Walker Lake", "genus": "Oncorhynchus", + "gbifdatasetid": "5d6c10bd-ea31-4363-8b79-58c96d859f5b", "order": "Salmoniformes", + "catalognumber": "66313", "collectioncode": "ICH"}, {"haslifestage": "0", + "month": "12", "decimallongitude": "-119.3377778", "isarch": "0", "startdayofyear": + "337", "networks": "FishNet,HerpNET,MaNIS,ORNIS,VertNet", "vntype": "specimen", + "title": "LACM Vertebrate Collection", "accessrights": "http://vertnet.org/resources/norms.html", + "kingdom": "Animalia", "dctype": "PhysicalObject", "iptrecordid": "EFF067C4-6BE8-4A2E-AB2A-0D5280D5941C", + "day": "3", "occurrenceid": "EFF067C4-6BE8-4A2E-AB2A-0D5280D5941C", "collectioncode": + "Fish", "verbatimeventdate": "12/3/1975", "gbifdatasetid": "7a25f7aa-03fb-4322-aaeb-66719e1a9527", + "pubdate": "2019-10-03", "infraspecificepithet": "henshawi", "year": "1975", + "wasinvasive": "0", "specificepithet": "clarki", "basisofrecord": "PreservedSpecimen", + "geodeticdatum": "not recorded (forced WGS84)", "highergeography": "North + America | USA | California | Mono | | | |", "continent": "North America", + "email": "rfeeney@nhm.org", "orgcountry": "United States", "source_url": "http://ipt.vertnet.org:8080/ipt/resource.do?r=lacm_verts", + "scientificname": "Oncorhynchus clarki henshawi", "hashid": "887", "hassex": + "0", "language": "en", "institutionid": "http://biocol.org/urn:lsid:biocol:org:34802", + "country": "United States", "hastissue": "0", "genus": "Oncorhynchus", "family": + "Salmonidae", "stateprovince": "California", "rank": 8, "county": "Mono", + "phylum": "Chordata", "references": "http://portal.vertnet.org/o/lacm/fish?id=eff067c4-6be8-4a2e-ab2a-0d5280d5941c", + "taxonrank": "subspecies", "hasmedia": "0", "verbatimlocality": "North America + | USA | California | Mono | By-day Creek, T5N R24E NW 1/4 S28", "countrycode": + "US", "institutioncode": "LACM", "orgstateprovince": "California", "occurrencestatus": + "present", "hastypestatus": "0", "preparations": "alcohol", "recordedby": + "Wayburn, Patridge", "georeferenceremarks": "Estimated latitude/longitude + using Encarta World Atlas 2001. 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UAIC Ichthyological Collection. + Source: http://ipt.vertnet.org:8080/ipt/resource.do?r=uaic_fish (source published + on 2015-02-16)", "collectioncode": "UAIC", "occurrencestatus": "present", + "hassex": "0", "orgcountry": "United States", "source_url": "http://ipt.vertnet.org:8080/ipt/resource.do?r=uaic_fish", + "institutioncode": "UA", "dctype": "PhysicalObject", "iptrecordid": "bf34d77e-f301-11e3-8701-005056a90e32", + "icode": "UA", "scientificname": "Oncorhynchus clarki henshawi", "preparations": + "70% EtOH - 5", "gbifpublisherid": "79324e30-d4c7-11d8-bf69-b8a03c50a862", + "hashid": "3246", "class": "Actinopterygii", "keyname": "ua/uaic/bf34d77e-f301-11e3-8701-005056a90e32", + "isfossil": "0", "county": "Elko", "decimallatitude": "41.6397222", "occurrenceid": + "bf34d77e-f301-11e3-8701-005056a90e32", "language": "en", "license": "CC0", + "institutionid": "http://grbio.org/cool/8eci-0a0e", "country": "United States", + "mappable": "1", "georeferenceverificationstatus": "requires verification", + "infraspecificepithet": "henshawi", "modified": "2014-07-15", "eventdate": + "2001-08-16", "identifiedby": "D.A. Neely/2001", "nomenclaturalcode": "ICZN", + "haslicense": "1", "hastissue": "1", "verbatimeventdate": "2001-8-16", "title": + "UAIC Ichthyological Collection", "lastindexed": "2016-07-23", "genus": "Oncorhynchus", + "gbifdatasetid": "e90a588b-0eed-4077-8a4f-7e61da35b3f8", "order": "Salmoniformes", + "catalognumber": "13434.04", "enddayofyear": "228"}, {"haslifestage": "0", + "month": "8", "decimallongitude": "-119.3297222", "isarch": "0", "startdayofyear": + "222", "networks": "FishNet,HerpNET,MaNIS,ORNIS,VertNet", "vntype": "specimen", + "title": "LACM Vertebrate Collection", "accessrights": "http://vertnet.org/resources/norms.html", + "kingdom": "Animalia", "dctype": "PhysicalObject", "iptrecordid": "03E9A023-4A8B-4EFF-95D3-2345962F0880", + "day": "10", "occurrenceid": "03E9A023-4A8B-4EFF-95D3-2345962F0880", "collectioncode": + "Fish", "verbatimeventdate": "8/10/1978", "gbifdatasetid": "7a25f7aa-03fb-4322-aaeb-66719e1a9527", + "pubdate": "2019-10-03", "infraspecificepithet": "henshawi", "year": "1978", + "wasinvasive": "0", "specificepithet": "clarki", "basisofrecord": "PreservedSpecimen", + "geodeticdatum": "not recorded (forced WGS84)", "occurrenceremarks": "electroshocker, + 2 jars", "highergeography": "North America | USA | California | Mono | | | |", + "continent": "North America", "email": "rfeeney@nhm.org", "orgcountry": "United + States", "source_url": "http://ipt.vertnet.org:8080/ipt/resource.do?r=lacm_verts", + "scientificname": "Oncorhynchus clarki henshawi", "hashid": "695", "hassex": + "0", "language": "en", "institutionid": "http://biocol.org/urn:lsid:biocol:org:34802", + "country": "United States", "hastissue": "0", "genus": "Oncorhynchus", "family": + "Salmonidae", "stateprovince": "California", "rank": 8, "county": "Mono", + "phylum": "Chordata", "references": "http://portal.vertnet.org/o/lacm/fish?id=03e9a023-4a8b-4eff-95d3-2345962f0880", + "taxonrank": "subspecies", "hasmedia": "0", "verbatimlocality": "North America + | USA | California | Mono | East fork Desert Creek trib. to W. Walker River, + below barrier falls", "countrycode": "US", "institutioncode": "LACM", "orgstateprovince": + "California", "occurrencestatus": "present", "hastypestatus": "0", "preparations": + "alcohol", "recordedby": "Eric Gerstong", "georeferenceremarks": "Estimated + latitude/longitude using Encarta World Atlas 2001. No error or extent calculated. Needs better + georeferencing.", "isfossil": "0", "license": "https://creativecommons.org/publicdomain/zero/1.0", + "wascaptive": "0", "dynamicproperties": "{\"length\":\"131.5-197\" }", "georeferenceverificationstatus": + "requires verification", "modified": "2018-10-08", "haslicense": "1", "fieldnumber": + "CF&G Freshwater Fish Collection", "eventdate": "1978-08-10", "individualcount": + "4", "bibliographiccitation": "Natural History Museum of Los Angeles County. + LACM Vertebrate Collection. Record ID: 03E9A023-4A8B-4EFF-95D3-2345962F0880. + Source: http://ipt.vertnet.org:8080/ipt/resource.do?r=lacm_verts (source published + on 2019-10-03)", "citation": "Natural History Museum of Los Angeles County. + LACM Vertebrate Collection. Source: http://ipt.vertnet.org:8080/ipt/resource.do?r=lacm_verts + (source published on 2019-10-03)", "lastindexed": "2019-10-09", "haslength": + "1", "catalognumber": "25128", "emlrights": "http://creativecommons.org/publicdomain/zero/1.0 + and http://vertnet.org/resources/norms.html", "hasmass": "0", "locality": + "East fork Desert Creek trib. to W. Walker River, below barrier falls", "orgname": + "Natural History Museum of Los Angeles County", "keyname": "lacm/fish/03e9a023-4a8b-4eff-95d3-2345962f0880", + "migrator": "2019-10-03", "lengthtype": "total length range", "collectionid": + "http://biocol.org/urn:lsid:biocol:org:34804", "icode": "LACM", "gbifpublisherid": + "493fe050-055d-11d8-b84f-b8a03c50a862", "class": "Actinopterygii", "previousidentifications": + "Salmo clarki henshawi", "decimallatitude": "38.4519444", "mappable": "1", + "othercatalognumbers": "CF&G 610", "nomenclaturalcode": "ICZN", "contact": + "Rick Feeney", "order": "Salmoniformes", "enddayofyear": "222"}, {"haslifestage": + "0", "individualcount": "6", "recordedby": "Wong, Shumway, Pauli, Reid", "bibliographiccitation": + "Natural History Museum of Los Angeles County. LACM Vertebrate Collection. + Record ID: 13CC7991-8A2C-432D-A7BF-FD66CAAC020E. Source: http://ipt.vertnet.org:8080/ipt/resource.do?r=lacm_verts + (source published on 2019-10-03)", "pubdate": "2019-10-03", "wasinvasive": + "0", "accessrights": "http://vertnet.org/resources/norms.html", "stateprovince": + "California", "hastypestatus": "0", "basisofrecord": "PreservedSpecimen", + "rank": 8, "month": "9", "decimallongitude": "-118.7413889", "phylum": "Chordata", + "references": "http://portal.vertnet.org/o/lacm/fish?id=13cc7991-8a2c-432d-a7bf-fd66caac020e", + "haslength": "1", "isarch": "0", "year": "1978", "startdayofyear": "272", + "wascaptive": "0", "taxonrank": "subspecies", "specificepithet": "clarki", + "networks": "FishNet,HerpNET,MaNIS,ORNIS,VertNet", "emlrights": "http://creativecommons.org/publicdomain/zero/1.0 + and http://vertnet.org/resources/norms.html", "hasmass": "0", "vntype": "specimen", + "family": "Salmonidae", "countrycode": "US", "title": "LACM Vertebrate Collection", + "orgname": "Natural History Museum of Los Angeles County", "hasmedia": "0", + "geodeticdatum": "not recorded (forced WGS84)", "occurrenceremarks": "O. clarki + henshawi?", "orgstateprovince": "California", "highergeography": "North America + | USA | California | Mono | | | |", "continent": "North America", "contact": + "Rick Feeney", "verbatimlocality": "North America | USA | California | Mono + | O''Harrel Canyon", "migrator": "2019-10-03", "lengthtype": "total length + range", "email": "rfeeney@nhm.org", "day": "29", "kingdom": "Animalia", "citation": + "Natural History Museum of Los Angeles County. LACM Vertebrate Collection. + Source: http://ipt.vertnet.org:8080/ipt/resource.do?r=lacm_verts (source published + on 2019-10-03)", "collectioncode": "Fish", "collectionid": "http://biocol.org/urn:lsid:biocol:org:34804", + "occurrencestatus": "present", "verbatimeventdate": "9/29/1978", "hassex": + "0", "orgcountry": "United States", "source_url": "http://ipt.vertnet.org:8080/ipt/resource.do?r=lacm_verts", + "institutioncode": "LACM", "dctype": "PhysicalObject", "iptrecordid": "13CC7991-8A2C-432D-A7BF-FD66CAAC020E", + "icode": "LACM", "scientificname": "Oncorhynchus clarki henshawi", "locality": + "O''Harrel Canyon", "gbifpublisherid": "493fe050-055d-11d8-b84f-b8a03c50a862", + "hashid": "4766", "georeferenceremarks": "Estimated latitude/longitude using + Encarta World Atlas 2001. No error or extent calculated. Needs better georeferencing.", + "class": "Actinopterygii", "keyname": "lacm/fish/13cc7991-8a2c-432d-a7bf-fd66caac020e", + "isfossil": "0", "county": "Mono", "decimallatitude": "37.7619444", "occurrenceid": + "13CC7991-8A2C-432D-A7BF-FD66CAAC020E", "language": "en", "license": "https://creativecommons.org/publicdomain/zero/1.0", + "institutionid": "http://biocol.org/urn:lsid:biocol:org:34802", "dynamicproperties": + "{\"length\":\"55-147.5\" }", "mappable": "1", "georeferenceverificationstatus": + "requires verification", "infraspecificepithet": "henshawi", "modified": "2018-10-08", + "eventdate": "1978-09-29", "nomenclaturalcode": "ICZN", "haslicense": "1", + "hastissue": "0", "country": "United States", "lastindexed": "2019-10-09", + "genus": "Oncorhynchus", "gbifdatasetid": "7a25f7aa-03fb-4322-aaeb-66719e1a9527", + "order": "Salmoniformes", "catalognumber": "45788-1", "enddayofyear": "272"}, + {"haslifestage": "0", "month": "10", "decimallongitude": "-119.3377778", "isarch": + "0", "startdayofyear": "289", "networks": "FishNet,HerpNET,MaNIS,ORNIS,VertNet", + "vntype": "specimen", "title": "LACM Vertebrate Collection", "accessrights": + "http://vertnet.org/resources/norms.html", "kingdom": "Animalia", "dctype": + "PhysicalObject", "iptrecordid": "CBFFB7A5-81F8-48D1-AC9E-BEE944BE03D2", "day": + "16", "occurrenceid": "CBFFB7A5-81F8-48D1-AC9E-BEE944BE03D2", "collectioncode": + "Fish", "verbatimeventdate": "10/16/1974", "gbifdatasetid": "7a25f7aa-03fb-4322-aaeb-66719e1a9527", + "pubdate": "2019-10-03", "infraspecificepithet": "henshawi", "year": "1974", + "wasinvasive": "0", "specificepithet": "clarki", "basisofrecord": "PreservedSpecimen", + "geodeticdatum": "not recorded (forced WGS84)", "highergeography": "North + America | USA | California | Mono | | | |", "continent": "North America", + "email": "rfeeney@nhm.org", "orgcountry": "United States", "source_url": "http://ipt.vertnet.org:8080/ipt/resource.do?r=lacm_verts", + "scientificname": "Oncorhynchus clarki henshawi", "hashid": "677", "hassex": + "0", "language": "en", "institutionid": "http://biocol.org/urn:lsid:biocol:org:34802", + "country": "United States", "hastissue": "0", "genus": "Oncorhynchus", "family": + "Salmonidae", "stateprovince": "California", "rank": 8, "county": "Mono", + "phylum": "Chordata", "references": "http://portal.vertnet.org/o/lacm/fish?id=cbffb7a5-81f8-48d1-ac9e-bee944be03d2", + "taxonrank": "subspecies", "hasmedia": "0", "verbatimlocality": "North America + | USA | California | Mono | By-day Creek, 2.0 miles upstream from Buckeye + Rd.", "countrycode": "US", "institutioncode": "LACM", "orgstateprovince": + "California", "occurrencestatus": "present", "hastypestatus": "0", "preparations": + "alcohol", "recordedby": "J. Deinstadt", "georeferenceremarks": "Estimated + latitude/longitude using Encarta World Atlas 2001. No error or extent calculated. Needs better + georeferencing.", "isfossil": "0", "license": "https://creativecommons.org/publicdomain/zero/1.0", + "wascaptive": "0", "dynamicproperties": "{\"length\":\"84.5-141\" }", "georeferenceverificationstatus": + "requires verification", "modified": "2018-10-08", "haslicense": "1", "fieldnumber": + "CF&G Freshwater Fish Collection", "eventdate": "1974-10-16", "individualcount": + "11", "bibliographiccitation": "Natural History Museum of Los Angeles County. + LACM Vertebrate Collection. Record ID: CBFFB7A5-81F8-48D1-AC9E-BEE944BE03D2. + Source: http://ipt.vertnet.org:8080/ipt/resource.do?r=lacm_verts (source published + on 2019-10-03)", "citation": "Natural History Museum of Los Angeles County. + LACM Vertebrate Collection. Source: http://ipt.vertnet.org:8080/ipt/resource.do?r=lacm_verts + (source published on 2019-10-03)", "lastindexed": "2019-10-09", "haslength": + "1", "catalognumber": "24997", "emlrights": "http://creativecommons.org/publicdomain/zero/1.0 + and http://vertnet.org/resources/norms.html", "hasmass": "0", "locality": + "By-day Creek, 2.0 miles upstream from Buckeye Rd.", "orgname": "Natural History + Museum of Los Angeles County", "keyname": "lacm/fish/cbffb7a5-81f8-48d1-ac9e-bee944be03d2", + "migrator": "2019-10-03", "lengthtype": "total length range", "collectionid": + "http://biocol.org/urn:lsid:biocol:org:34804", "icode": "LACM", "gbifpublisherid": + "493fe050-055d-11d8-b84f-b8a03c50a862", "class": "Actinopterygii", "previousidentifications": + "Salmo clarki henshawi", "decimallatitude": "38.2702778", "mappable": "1", + "othercatalognumbers": "CF&G 466", "nomenclaturalcode": "ICZN", "contact": + "Rick Feeney", "order": "Salmoniformes", "enddayofyear": "289"}, {"haslifestage": + "1", "scientificnameid": "urn:lsid:biosci.ohio-state.edu:osuc_names:297783", + "bibliographiccitation": "Ohio State University. Ohio State University Fish + Division (OSUM). Record ID: urn:lsid:biosci.ohio-state.edu:osuc_occurrences:OSUM__74567. + Source: http://hymfiles.biosci.ohio-state.edu:8080/ipt/resource.do?r=osum-fish + (source published on 2015-05-22)", "pubdate": "2015-05-22", "individualcount": + "1", "wasinvasive": "0", "stateprovince": "Washington", "hastypestatus": "0", + "lifestage": "adult", "rank": 8, "sex": "undetermined", "decimallongitude": + "-120.5015", "fieldnotes": "ACC:1988-VII - 4; preparation:Skeleton; length:1; + det_comments:~298 mm", "phylum": "Chordata", "references": "http://osuc.biosci.ohio-state.edu/Fishes/spmInfo.html?id=OSUM%2074567", + "dateidentified": "2011", "year": "1988", "startdayofyear": "151", "wascaptive": + "0", "specificepithet": "clarkii", "networks": "FishNet,VertNet", "recordedby": + "Varney, G. (Gilbert), McAllister, B. (Bob) & Beezley, C. 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Source: http://hymfiles.biosci.ohio-state.edu:8080/ipt/resource.do?r=osum-fish + (source published on 2015-05-22)", "georeferencesources": "Unknown", "samplingprotocol": + "none specified", "hassex": "1", "underivedlifestage": "adult", "source_url": + "http://hymfiles.biosci.ohio-state.edu:8080/ipt/resource.do?r=osum-fish", + "institutioncode": "Ohio State University - Fish Division, Columbus, OH (OSUM)", + "dctype": "PhysicalObject", "iptrecordid": "urn:lsid:biosci.ohio-state.edu:osuc_occurrences:OSUM__74567", + "icode": "OSUM", "scientificname": "Salmo clarki henshawi", "orgcountry": + "United States", "gbifpublisherid": "5ffa575c-fcd4-4583-9611-545f67b04316", + "hashid": "2928", "georeferenceremarks": "Locality: Fish", "month": "5", "class": + "Actinopterygii", "keyname": "osum/fishes/urn-lsid-biosci-ohio-state-edu-osuc-occurrences-osum-74567", + "isfossil": "0", "county": "Okanogan", "decimallatitude": "47.5001", "genus": + "Oncorhynchus", "occurrenceid": "urn:lsid:biosci.ohio-state.edu:osuc_occurrences:OSUM__74567", + "language": "en", "basisofrecord": "PreservedSpecimen", "country": "United + States", "mappable": "1", "title": "Ohio State University Fish Division (OSUM)", + "collectioncode": "Fishes", "modified": "2015-02-09T15:43:03Z", "eventdate": + "1988-05-30", "identifiedby": "Cavender, T. (Ted)", "haslicense": "0", "fieldnumber": + "GEV 88-40", "lengthunitsinferred": "1", "underivedsex": "undetermined", "lastindexed": + "2016-08-11", "enddayofyear": "151", "gbifdatasetid": "813b435e-f762-11e1-a439-00145eb45e9a", + "order": "Salmoniformes", "catalognumber": "OSUM 74567", "haslength": "1"}, + {"haslifestage": "0", "individualcount": "6", "recordedby": "Russell Wickwire, + California Dept. of Fish and Gam", "bibliographiccitation": "Natural History + Museum of Los Angeles County. LACM Vertebrate Collection. Record ID: B680B656-13B6-48BD-AC09-D63484013461. + Source: http://ipt.vertnet.org:8080/ipt/resource.do?r=lacm_verts (source published + on 2019-10-03)", "pubdate": "2019-10-03", "accessrights": "http://vertnet.org/resources/norms.html", + "stateprovince": "California", "hastypestatus": "0", "basisofrecord": "PreservedSpecimen", + "rank": 5, "infraspecificepithet": "henshawi x o. mykiss", "decimallongitude": + "-120.0919444", "phylum": "Chordata", "references": "http://portal.vertnet.org/o/lacm/fish?id=b680b656-13b6-48bd-ac09-d63484013461", + "haslength": "1", "isarch": "0", "wasinvasive": "0", "wascaptive": "0", "taxonrank": + "subspecies", "specificepithet": "clarki", "continent": "North America", "emlrights": + "http://creativecommons.org/publicdomain/zero/1.0 and http://vertnet.org/resources/norms.html", + "hasmass": "0", "vntype": "specimen", "preparations": "alcohol", "family": + "Salmonidae", "countrycode": "US", "title": "LACM Vertebrate Collection", + "orgname": "Natural History Museum of Los Angeles County", "hasmedia": "0", + "geodeticdatum": "not recorded (forced WGS84)", "orgstateprovince": "California", + "highergeography": "North America | USA | California | El Dorado | | | |", + "networks": "FishNet,HerpNET,MaNIS,ORNIS,VertNet", "contact": "Rick Feeney", + "verbatimlocality": "North America | USA | California | El Dorado | Cascade + Lake", "migrator": "2019-10-03", "lengthtype": "total length range", "hastissue": + "0", "email": "rfeeney@nhm.org", "kingdom": "Animalia", "citation": "Natural + History Museum of Los Angeles County. LACM Vertebrate Collection. Source: + http://ipt.vertnet.org:8080/ipt/resource.do?r=lacm_verts (source published + on 2019-10-03)", "collectionid": "http://biocol.org/urn:lsid:biocol:org:34804", + "occurrencestatus": "present", "hassex": "0", "orgcountry": "United States", + "source_url": "http://ipt.vertnet.org:8080/ipt/resource.do?r=lacm_verts", + "institutioncode": "LACM", "dctype": "PhysicalObject", "iptrecordid": "B680B656-13B6-48BD-AC09-D63484013461", + "icode": "LACM", "scientificname": "Oncorhynchus clarki henshawi x o. mykiss", + "locality": "Cascade Lake", "gbifpublisherid": "493fe050-055d-11d8-b84f-b8a03c50a862", + "hashid": "2101", "georeferenceremarks": "Estimated latitude/longitude using + Encarta World Atlas 2001. No error or extent calculated. 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Record ID: urn:catalog:CAS:SU + (ICH):37970. Source: http://ipt.calacademy.org:8080/ipt/resource.do?r=ich + (source published on 2019-07-15)", "waterbody": "Upper Blue Lake", "genus": + "Oncorhynchus", "gbifdatasetid": "5d6c10bd-ea31-4363-8b79-58c96d859f5b", "order": + "Salmoniformes", "catalognumber": "37970", "collectioncode": "SU"}], "matching_records": + 60, "api_version": "api.py 2017-11-24T12:16-03:00"}' + recorded_at: 2020-08-10 20:24:27 GMT + recorded_with: vcr/0.5.4, webmockr/0.6.2 diff --git a/tests/testthat/test-vertsummary.R b/tests/testthat/test-vertsummary.R index ed9fd98..f06dbe9 100644 --- a/tests/testthat/test-vertsummary.R +++ b/tests/testthat/test-vertsummary.R @@ -5,8 +5,7 @@ test_that("vertsummary works with vertsearch input", { vcr::use_cassette("vertsummary_prep_vertsearch", { vs1 <- vertsearch("Junco hyemalis", messages = FALSE, limit = 10) - vs2 <- vertsearch("Oncorhynchus clarki henshawi", messages = FALSE, - limit = 10) + vs2 <- vertsearch("Oncorhynchus clarki henshawi", messages = FALSE) }) vs1_summ <- vertsummary(vs1) vs2_summ <- vertsummary(vs2) @@ -25,7 +24,7 @@ test_that("vertsummary works with vertsearch input", { expect_is(vs2_summ, "vertsummary") expect_is(vs2_summ$country, "table") expect_is(vs2_summ$taxon, "table") - expect_equal(vs2_summ$recs, 10) + expect_gt(vs2_summ$recs, 10) }) test_that("vertsummary works with searchbytem input", {