Atividade 3
3.1 Acesso a bancos de dados abertos
O acesso pode ser feito de diferentes formas, seja diretamente no website do repositório, utilizando-se pacotes específicos que acessam os repositórios via R ou Python, ou através de API (Application Programming Interface). Nesta última opção, o repositório é acessado por outro aplicativo ou serviço web para automatização de tarefas, seja em servidor local ou remoto, mas requer conhecimento de programação em Java e outras linguagens e não será tratado aqui.
Nesta atividade, temos como objetivo acessar um repositório de dados de ocorrência de espécies, inspecionar os dados, avaliar sua qualidade e fazer um mapa com as ocorrências.
Para iniciar, vamos escolher um repositório e uma espécie de interesse. Vamos iniciar com uma única espécie para facilitar as demais etapas.
O GBIF (Global Biodiversity Information Facility) é o maior repositório de ocorrências da biodiversidade da atualidade, então será nossa opção de repositório. No entanto, o OBIS (Ocean Biodiversity Information System) é um repositório dedicado às espécies marinhas e espelhado no GBIF. Assim, espera-se que algumas ocorrências sejam duplicadas nos dois repositórios.
3.1.1 Exemplo: Finding Dori
A espécie-alvo será o peixe marinho Paracanthurus hepatus, também conhecido como Blue Tang e, mais recentemente como Dori!.
Nosso primeiro exemplor será com as ocorrencias do
GBIF e, para tal, vamos utilizar o pacote
rgbif.
3.1.2 GBIF
Vamos fazer uso do pacote tidyverse para manipular dos
dados, então vamos carregar este pacote e o rgbif.
É importante explorar as funções do pacote e pode-se fazer isto
usando o comando ?rgbif e, para ler sobre uma função em
particular basta colocar ? em frente ao nome da função. Se
o pacote não estiver carregado ou instalada é preciso usar
??.
A função occ_data faz uma busca simplificada das
ocorrências no repositório do GBIF por meio do nome
científico, número de identificação, país e outros. Neste caso, vamos
procurar diretamente pelo nome da espécie-alvo. Outros atributos podem
ser adicionados à função para refinar a busca, leia o material de ajuda
da função para ter uma ideia. Vamos aproveitar alguns destes atributos e
selecionar apenas ocorrências que possuem coordenadas e sem problemas
geoespaciais.
# checar funcoes
?occ_data
# baixar ocorrencias
dori_gbif <- occ_data(scientificName = "Paracanthurus hepatus",
hasCoordinate = TRUE,
hasGeospatialIssue=FALSE)
# dimensoes
dim(dori_gbif)## NULLdim(dori_gbif$data)## [1] 500 147# checar campos
dori_gbif$data %>% names## [1] "key"
## [2] "scientificName"
## [3] "decimalLatitude"
## [4] "decimalLongitude"
## [5] "issues"
## [6] "datasetKey"
## [7] "publishingOrgKey"
## [8] "installationKey"
## [9] "publishingCountry"
## [10] "protocol"
## [11] "lastCrawled"
## [12] "lastParsed"
## [13] "crawlId"
## [14] "hostingOrganizationKey"
## [15] "basisOfRecord"
## [16] "occurrenceStatus"
## [17] "lifeStage"
## [18] "taxonKey"
## [19] "kingdomKey"
## [20] "phylumKey"
## [21] "orderKey"
## [22] "familyKey"
## [23] "genusKey"
## [24] "speciesKey"
## [25] "acceptedTaxonKey"
## [26] "acceptedScientificName"
## [27] "kingdom"
## [28] "phylum"
## [29] "order"
## [30] "family"
## [31] "genus"
## [32] "species"
## [33] "genericName"
## [34] "specificEpithet"
## [35] "taxonRank"
## [36] "taxonomicStatus"
## [37] "iucnRedListCategory"
## [38] "dateIdentified"
## [39] "coordinateUncertaintyInMeters"
## [40] "continent"
## [41] "stateProvince"
## [42] "year"
## [43] "month"
## [44] "day"
## [45] "eventDate"
## [46] "modified"
## [47] "lastInterpreted"
## [48] "references"
## [49] "license"
## [50] "isInCluster"
## [51] "datasetName"
## [52] "recordedBy"
## [53] "identifiedBy"
## [54] "geodeticDatum"
## [55] "countryCode"
## [56] "country"
## [57] "rightsHolder"
## [58] "identifier"
## [59] "http://unknown.org/nick"
## [60] "verbatimEventDate"
## [61] "collectionCode"
## [62] "gbifID"
## [63] "verbatimLocality"
## [64] "occurrenceID"
## [65] "taxonID"
## [66] "catalogNumber"
## [67] "institutionCode"
## [68] "eventTime"
## [69] "http://unknown.org/captive"
## [70] "identificationID"
## [71] "recordNumber"
## [72] "vernacularName"
## [73] "dynamicProperties"
## [74] "http://unknown.org/taxonRankID"
## [75] "taxonConceptID"
## [76] "identificationVerificationStatus"
## [77] "http://unknown.org/species"
## [78] "taxonRemarks"
## [79] "occurrenceRemarks"
## [80] "distanceFromCentroidInMeters"
## [81] "networkKeys"
## [82] "coordinatePrecision"
## [83] "institutionKey"
## [84] "otherCatalogNumbers"
## [85] "samplingProtocol"
## [86] "eventID"
## [87] "acceptedNameUsage"
## [88] "locationRemarks"
## [89] "identificationRemarks"
## [90] "nameAccordingTo"
## [91] "institutionID"
## [92] "higherGeography"
## [93] "locality"
## [94] "language"
## [95] "type"
## [96] "collectionID"
## [97] "higherClassification"
## [98] "elevation"
## [99] "elevationAccuracy"
## [100] "depth"
## [101] "depthAccuracy"
## [102] "datasetID"
## [103] "footprintWKT"
## [104] "originalNameUsage"
## [105] "county"
## [106] "individualCount"
## [107] "waterBody"
## [108] "sampleSizeUnit"
## [109] "sampleSizeValue"
## [110] "habitat"
## [111] "maximumDistanceAboveSurfaceInMeters"
## [112] "dataGeneralizations"
## [113] "georeferencedBy"
## [114] "georeferenceProtocol"
## [115] "islandGroup"
## [116] "island"
## [117] "verbatimDepth"
## [118] "ownerInstitutionCode"
## [119] "rights"
## [120] "georeferenceSources"
## [121] "projectId"
## [122] "programmeAcronym"
## [123] "organismQuantity"
## [124] "organismQuantityType"
## [125] "locationAccordingTo"
## [126] "endDayOfYear"
## [127] "startDayOfYear"
## [128] "samplingEffort"
## [129] "fieldNumber"
## [130] "locationID"
## [131] "eventRemarks"
## [132] "associatedReferences"
## [133] "http://unknown.org/language"
## [134] "verbatimIdentification"
## [135] "collectionKey"
## [136] "materialSampleID"
## [137] "disposition"
## [138] "preparations"
## [139] "municipality"
## [140] "name"
## [141] "bibliographicCitation"
## [142] "identificationReferences"
## [143] "verbatimSRS"
## [144] "georeferenceVerificationStatus"
## [145] "verbatimCoordinateSystem"
## [146] "nomenclaturalCode"
## [147] "parentEventID"Acima, vemos que o conjunto de dados tem ocorrências (uma por linha)
e variáveis. As variáveis podem ser utilizadas para filtrar as
ocorrências de acordo com o objetivo, além de fornecerem diversos dados
a respeito das ocorrências, incluindo dados dos amostradores e
detentores dos direitos. Vale notar que o conjunto de dados retornado
pelo GBIF não é um data frame simples, mas
sim um list que contém um conjunto de
data frames. Para acessar estes data frames é
necessário usar o operador $.
3.2 Problemas reportados
Um dos campos mais úteis dos dados é a coluna issues,
pois ela indica problema já identificados pelo validador automático do
repositório. Os problemas (issues) possuem um código que pode
ser conferido pela função gbif_issues. Ao usar a função não
é preciso indicar nenhum atributo, pois ela retornará um dataframe com
as abreviações usadas e a descrição dos problemas catalogados no
GBIF.
## code issue
## 1 bri BASIS_OF_RECORD_INVALID
## 2 ccm CONTINENT_COUNTRY_MISMATCH
## 3 cdc CONTINENT_DERIVED_FROM_COORDINATES
## 4 conti CONTINENT_INVALID
## 5 cdiv COORDINATE_INVALID
## 6 cdout COORDINATE_OUT_OF_RANGE
## 7 cdrep COORDINATE_REPROJECTED
## 8 cdrepf COORDINATE_REPROJECTION_FAILED
## 9 cdreps COORDINATE_REPROJECTION_SUSPICIOUS
## 10 cdround COORDINATE_ROUNDED
## 11 cucdmis COUNTRY_COORDINATE_MISMATCH
## 12 cudc COUNTRY_DERIVED_FROM_COORDINATES
## 13 cuiv COUNTRY_INVALID
## 14 cum COUNTRY_MISMATCH
## 15 depmms DEPTH_MIN_MAX_SWAPPED
## 16 depnn DEPTH_NON_NUMERIC
## 17 depnmet DEPTH_NOT_METRIC
## 18 depunl DEPTH_UNLIKELY
## 19 elmms ELEVATION_MIN_MAX_SWAPPED
## 20 elnn ELEVATION_NON_NUMERIC
## 21 elnmet ELEVATION_NOT_METRIC
## 22 elunl ELEVATION_UNLIKELY
## 23 gass84 GEODETIC_DATUM_ASSUMED_WGS84
## 24 gdativ GEODETIC_DATUM_INVALID
## 25 iddativ IDENTIFIED_DATE_INVALID
## 26 iddatunl IDENTIFIED_DATE_UNLIKELY
## 27 mdativ MODIFIED_DATE_INVALID
## 28 mdatunl MODIFIED_DATE_UNLIKELY
## 29 muldativ MULTIMEDIA_DATE_INVALID
## 30 muluriiv MULTIMEDIA_URI_INVALID
## 31 preneglat PRESUMED_NEGATED_LATITUDE
## 32 preneglon PRESUMED_NEGATED_LONGITUDE
## 33 preswcd PRESUMED_SWAPPED_COORDINATE
## 34 rdativ RECORDED_DATE_INVALID
## 35 rdatm RECORDED_DATE_MISMATCH
## 36 rdatunl RECORDED_DATE_UNLIKELY
## 37 refuriiv REFERENCES_URI_INVALID
## 38 txmatfuz TAXON_MATCH_FUZZY
## 39 txmathi TAXON_MATCH_HIGHERRANK
## 40 txmatnon TAXON_MATCH_NONE
## 41 typstativ TYPE_STATUS_INVALID
## 42 zerocd ZERO_COORDINATE
## 43 cdpi COORDINATE_PRECISION_INVALID
## 44 cdumi COORDINATE_UNCERTAINTY_METERS_INVALID
## 45 indci INDIVIDUAL_COUNT_INVALID
## 46 interr INTERPRETATION_ERROR
## 47 iccos INDIVIDUAL_COUNT_CONFLICTS_WITH_OCCURRENCE_STATUS
## 48 osiic OCCURRENCE_STATUS_INFERRED_FROM_INDIVIDUAL_COUNT
## 49 osu OCCURRENCE_STATUS_UNPARSABLE
## 50 geodi GEOREFERENCED_DATE_INVALID
## 51 geodu GEOREFERENCED_DATE_UNLIKELY
## 52 ambcol AMBIGUOUS_COLLECTION
## 53 ambinst AMBIGUOUS_INSTITUTION
## 54 colmafu COLLECTION_MATCH_FUZZY
## 55 colmano COLLECTION_MATCH_NONE
## 56 incomis INSTITUTION_COLLECTION_MISMATCH
## 57 inmafu INSTITUTION_MATCH_FUZZY
## 58 inmano INSTITUTION_MATCH_NONE
## 59 osifbor OCCURRENCE_STATUS_INFERRED_FROM_BASIS_OF_RECORD
## 60 diffown DIFFERENT_OWNER_INSTITUTION
## 61 taxmatagg TAXON_MATCH_AGGREGATE
## 62 fpsrsinv FOOTPRINT_SRS_INVALID
## 63 fpwktinv FOOTPRINT_WKT_INVALID
## 64 anm ACCEPTED_NAME_MISSING
## 65 annu ACCEPTED_NAME_NOT_UNIQUE
## 66 anuidi ACCEPTED_NAME_USAGE_ID_INVALID
## 67 aitidinv ALT_IDENTIFIER_INVALID
## 68 bbmn BACKBONE_MATCH_NONE
## 69 basauthm BASIONYM_AUTHOR_MISMATCH
## 70 bibrinv BIB_REFERENCE_INVALID
## 71 chsun CHAINED_SYNOYM
## 72 clasna CLASSIFICATION_NOT_APPLIED
## 73 clasroi CLASSIFICATION_RANK_ORDER_INVALID
## 74 conbascomb CONFLICTING_BASIONYM_COMBINATION
## 75 desinv DESCRIPTION_INVALID
## 76 disinv DISTRIBUTION_INVALID
## 77 hom HOMONYM
## 78 minv MULTIMEDIA_INVALID
## 79 npm NAME_PARENT_MISMATCH
## 80 ns NO_SPECIES
## 81 nsinv NOMENCLATURAL_STATUS_INVALID
## 82 onder ORIGINAL_NAME_DERIVED
## 83 onnu ORIGINAL_NAME_NOT_UNIQUE
## 84 onuidinv ORIGINAL_NAME_USAGE_ID_INVALID
## 85 ov ORTHOGRAPHIC_VARIANT
## 86 pc PARENT_CYCLE
## 87 pnnu PARENT_NAME_NOT_UNIQUE
## 88 pnuidinv PARENT_NAME_USAGE_ID_INVALID
## 89 pp PARTIALLY_PARSABLE
## 90 pbg PUBLISHED_BEFORE_GENUS
## 91 rankinv RANK_INVALID
## 92 relmiss RELATIONSHIP_MISSING
## 93 scina SCIENTIFIC_NAME_ASSEMBLED
## 94 spprinv SPECIES_PROFILE_INVALID
## 95 taxstinv TAXONOMIC_STATUS_INVALID
## 96 taxstmis TAXONOMIC_STATUS_MISMATCH
## 97 unpars UNPARSABLE
## 98 vernnameinv VERNACULAR_NAME_INVALID
## 99 backmatagg BACKBONE_MATCH_AGGREGATE
## description
## 1 The given basis of record is impossible to interpret or seriously different from the recommended vocabulary.
## 2 The interpreted continent and country do not match up.
## 3 The interpreted continent is based on the coordinates, not the verbatim string information.
## 4 Uninterpretable continent values found.
## 5 Coordinate value given in some form but GBIF is unable to interpret it.
## 6 Coordinate has invalid lat/lon values out of their decimal max range.
## 7 The original coordinate was successfully reprojected from a different geodetic datum to WGS84.
## 8 The given decimal latitude and longitude could not be reprojected to WGS84 based on the provided datum.
## 9 Indicates successful coordinate reprojection according to provided datum, but which results in a datum shift larger than 0.1 decimal degrees.
## 10 Original coordinate modified by rounding to 5 decimals.
## 11 The interpreted occurrence coordinates fall outside of the indicated country.
## 12 The interpreted country is based on the coordinates, not the verbatim string information.
## 13 Uninterpretable country values found.
## 14 Interpreted country for dwc:country and dwc:countryCode contradict each other.
## 15 Set if supplied min>max
## 16 Set if depth is a non numeric value
## 17 Set if supplied depth is not given in the metric system, for example using feet instead of meters
## 18 Set if depth is larger than 11.000m or negative.
## 19 Set if supplied min > max elevation
## 20 Set if elevation is a non numeric value
## 21 Set if supplied elevation is not given in the metric system, for example using feet instead of meters
## 22 Set if elevation is above the troposphere (17km) or below 11km (Mariana Trench).
## 23 Indicating that the interpreted coordinates assume they are based on WGS84 datum as the datum was either not indicated or interpretable.
## 24 The geodetic datum given could not be interpreted.
## 25 The date given for dwc:dateIdentified is invalid and cant be interpreted at all.
## 26 The date given for dwc:dateIdentified is in the future or before Linnean times (1700).
## 27 A (partial) invalid date is given for dc:modified, such as a non existing date, invalid zero month, etc.
## 28 The date given for dc:modified is in the future or predates unix time (1970).
## 29 An invalid date is given for dc:created of a multimedia object.
## 30 An invalid uri is given for a multimedia object.
## 31 Latitude appears to be negated, e.g. 32.3 instead of -32.3
## 32 Longitude appears to be negated, e.g. 32.3 instead of -32.3
## 33 Latitude and longitude appear to be swapped.
## 34 A (partial) invalid date is given, such as a non existing date, invalid zero month, etc.
## 35 The recording date specified as the eventDate string and the individual year, month, day are contradicting.
## 36 The recording date is highly unlikely, falling either into the future or represents a very old date before 1600 that predates modern taxonomy.
## 37 An invalid uri is given for dc:references.
## 38 Matching to the taxonomic backbone can only be done using a fuzzy, non exact match.
## 39 Matching to the taxonomic backbone can only be done on a higher rank and not the scientific name.
## 40 Matching to the taxonomic backbone cannot be done cause there was no match at all or several matches with too little information to keep them apart (homonyms).
## 41 The given type status is impossible to interpret or seriously different from the recommended vocabulary.
## 42 Coordinate is the exact 0/0 coordinate, often indicating a bad null coordinate.
## 43 Indicates an invalid or very unlikely coordinatePrecision
## 44 Indicates an invalid or very unlikely dwc:uncertaintyInMeters.
## 45 Individual count value not parsable into an integer.
## 46 An error occurred during interpretation, leaving the record interpretation incomplete.
## 47 Example: individual count value > 0, but occurrence status is absent and etc.
## 48 Occurrence status was inferred from the individual count value
## 49 Occurrence status value can't be assigned to OccurrenceStatus
## 50 The date given for dwc:georeferencedDate is invalid and can't be interpreted at all.
## 51 The date given for dwc:georeferencedDate is in the future or before Linnean times (1700).
## 52 The given collection matches with more than 1 GrSciColl collection.
## 53 The given institution matches with more than 1 GrSciColl institution.
## 54 The given collection was fuzzily matched to a GrSciColl collection.
## 55 The given collection couldn't be matched with any GrSciColl collection.
## 56 The collection matched doesn't belong to the institution matched.
## 57 The given institution was fuzzily matched to a GrSciColl institution.
## 58 The given institution couldn't be matched with any GrSciColl institution.
## 59 Occurrence status was inferred from basis of records
## 60 The given owner institution is different than the given institution. Therefore we assume it doesn't belong to the institution and we don't link it to the occurrence.
## 61 Matching to the taxonomic backbone can only be done on a species level, but the occurrence was in fact considered a broader species aggregate/complex.
## 62 The Footprint Spatial Reference System given could not be interpreted
## 63 The Footprint Well-Known-Text given could not be interpreted
## 64 Synonym lacking an accepted name.
## 65 Synonym has a verbatim accepted name which is not unique and refers to several records.
## 66 The value for dwc:acceptedNameUsageID could not be resolved.
## 67 At least one alternative identifier extension record attached to this name usage is invalid.
## 68 Name usage could not be matched to the GBIF backbone.
## 69 The authorship of the original name does not match the authorship in brackets of the actual name.
## 70 At least one bibliographic reference extension record attached to this name usage is invalid.
## 71 If a synonym points to another synonym as its accepted taxon the chain is resolved.
## 72 The denormalized classification could not be applied to the name usage.
## 73 The given ranks of the names in the classification hierarchy do not follow the hierarchy of ranks.
## 74 There have been more than one accepted name in a homotypical basionym group of names.
## 75 At least one description extension record attached to this name usage is invalid.
## 76 At least one distribution extension record attached to this name usage is invalid.
## 77 A not synonymized homonym exists for this name in some other backbone source which have been ignored at build time.
## 78 At least one multimedia extension record attached to this name usage is invalid.
## 79 The (accepted) bi/trinomial name does not match the parent name and should be recombined into the parent genus/species.
## 80 The group (currently only genera are tested) are lacking any accepted species GBIF backbone specific issue.
## 81 dwc:nomenclaturalStatus could not be interpreted
## 82 Record has a original name (basionym) relationship which was derived from name & authorship comparison, but did not exist explicitly in the data.
## 83 Record has a verbatim original name (basionym) which is not unique and refers to several records.
## 84 The value for dwc:originalNameUsageID could not be resolved.
## 85 A potential orthographic variant exists in the backbone.
## 86 The child parent classification resulted into a cycle that needed to be resolved/cut.
## 87 Record has a verbatim parent name which is not unique and refers to several records.
## 88 The value for dwc:parentNameUsageID could not be resolved.
## 89 The beginning of the scientific name string was parsed, but there is additional information in the string that was not understood.
## 90 A bi/trinomial name published earlier than the parent genus was published.
## 91 dwc:taxonRank could not be interpreted
## 92 There were problems representing all name usage relationships, i.e.
## 93 The scientific name was assembled from the individual name parts and not given as a whole string.
## 94 At least one species profile extension record attached to this name usage is invalid.
## 95 dwc:taxonomicStatus could not be interpreted
## 96 no description
## 97 The scientific name string could not be parsed at all, but appears to be a parsable name type, i.e.
## 98 At least one vernacular name extension record attached to this name usage is invalid.
## 99 Name usage could only be matched to a GBIF backbone species, but was in fact a broader species aggregate/complex.
## type
## 1 occurrence
## 2 occurrence
## 3 occurrence
## 4 occurrence
## 5 occurrence
## 6 occurrence
## 7 occurrence
## 8 occurrence
## 9 occurrence
## 10 occurrence
## 11 occurrence
## 12 occurrence
## 13 occurrence
## 14 occurrence
## 15 occurrence
## 16 occurrence
## 17 occurrence
## 18 occurrence
## 19 occurrence
## 20 occurrence
## 21 occurrence
## 22 occurrence
## 23 occurrence
## 24 occurrence
## 25 occurrence
## 26 occurrence
## 27 occurrence
## 28 occurrence
## 29 occurrence
## 30 occurrence
## 31 occurrence
## 32 occurrence
## 33 occurrence
## 34 occurrence
## 35 occurrence
## 36 occurrence
## 37 occurrence
## 38 occurrence
## 39 occurrence
## 40 occurrence
## 41 occurrence
## 42 occurrence
## 43 occurrence
## 44 occurrence
## 45 occurrence
## 46 occurrence
## 47 occurrence
## 48 occurrence
## 49 occurrence
## 50 occurrence
## 51 occurrence
## 52 occurrence
## 53 occurrence
## 54 occurrence
## 55 occurrence
## 56 occurrence
## 57 occurrence
## 58 occurrence
## 59 occurrence
## 60 occurrence
## 61 occurrence
## 62 occurrence
## 63 occurrence
## 64 name
## 65 name
## 66 name
## 67 name
## 68 name
## 69 name
## 70 name
## 71 name
## 72 name
## 73 name
## 74 name
## 75 name
## 76 name
## 77 name
## 78 name
## 79 name
## 80 name
## 81 name
## 82 name
## 83 name
## 84 name
## 85 name
## 86 name
## 87 name
## 88 name
## 89 name
## 90 name
## 91 name
## 92 name
## 93 name
## 94 name
## 95 name
## 96 name
## 97 name
## 98 name
## 99 namePara checar os issues indicados na base baixada é
necessário um pequeno tratamento, uma vez que algumas ocorrências
possuem múltiplos problemas. Assim, utilizamos a função
strsplit para individualizar os issues e poder
conferí-los.
# checar problemas reportados
issues_gbif <- dori_gbif$data$issues %>%
unique() %>%
strsplit(., "[,]") %>%
unlist()
gbif_issues() %>%
data.frame() %>%
filter(code %in% issues_gbif)## code issue
## 1 ccm CONTINENT_COUNTRY_MISMATCH
## 2 cdc CONTINENT_DERIVED_FROM_COORDINATES
## 3 conti CONTINENT_INVALID
## 4 cdreps COORDINATE_REPROJECTION_SUSPICIOUS
## 5 cdround COORDINATE_ROUNDED
## 6 cudc COUNTRY_DERIVED_FROM_COORDINATES
## 7 cum COUNTRY_MISMATCH
## 8 gass84 GEODETIC_DATUM_ASSUMED_WGS84
## 9 gdativ GEODETIC_DATUM_INVALID
## 10 refuriiv REFERENCES_URI_INVALID
## 11 osiic OCCURRENCE_STATUS_INFERRED_FROM_INDIVIDUAL_COUNT
## 12 colmafu COLLECTION_MATCH_FUZZY
## 13 incomis INSTITUTION_COLLECTION_MISMATCH
## 14 inmafu INSTITUTION_MATCH_FUZZY
## description
## 1 The interpreted continent and country do not match up.
## 2 The interpreted continent is based on the coordinates, not the verbatim string information.
## 3 Uninterpretable continent values found.
## 4 Indicates successful coordinate reprojection according to provided datum, but which results in a datum shift larger than 0.1 decimal degrees.
## 5 Original coordinate modified by rounding to 5 decimals.
## 6 The interpreted country is based on the coordinates, not the verbatim string information.
## 7 Interpreted country for dwc:country and dwc:countryCode contradict each other.
## 8 Indicating that the interpreted coordinates assume they are based on WGS84 datum as the datum was either not indicated or interpretable.
## 9 The geodetic datum given could not be interpreted.
## 10 An invalid uri is given for dc:references.
## 11 Occurrence status was inferred from the individual count value
## 12 The given collection was fuzzily matched to a GrSciColl collection.
## 13 The collection matched doesn't belong to the institution matched.
## 14 The given institution was fuzzily matched to a GrSciColl institution.
## type
## 1 occurrence
## 2 occurrence
## 3 occurrence
## 4 occurrence
## 5 occurrence
## 6 occurrence
## 7 occurrence
## 8 occurrence
## 9 occurrence
## 10 occurrence
## 11 occurrence
## 12 occurrence
## 13 occurrence
## 14 occurrenceA maioria dos problemas reportados é relacionado com discrepancias entre informações indicadas pelos autores e as levantadas pelo algoritmo de checagem, mas nenhum parece invalidar as ocorrências, por enquanto.
Prosseguimos selecionando algumas variáveis que serão úteis para a validação dos dados e futuras análises, como coordenadas, profundidade, nome da base de dados etc.
dori_gbif1 <- dori_gbif$data %>%
dplyr::select(scientificName, acceptedScientificName, decimalLatitude, decimalLongitude,
issues, waterBody, basisOfRecord, occurrenceStatus, rightsHolder,
datasetName, recordedBy, depth, locality, habitat) Note que temos 500 ocorrências, no entanto, vamos ver quantas são
únicas aplicando a função distinct do pacote
dplyr.
dori_gbif1 <- dori_gbif1 %>%
distinct() No fim, observamos que ficamos com 377 ocorrências agora, e isso acontece por causa de diferenças em colunas que, neste caso, não serão usadas para o objetivo desta prática.
Para identificar todos os valores únicos presented nos dados, vamos
aplicar a função unique a cada coluna com um loop
na função lapply.
# checar niveis dos fatores
lapply(dori_gbif1, unique)## $scientificName
## [1] "Paracanthurus hepatus (Linnaeus, 1766)"
## [2] "BOLD:AAC3227"
##
## $acceptedScientificName
## [1] "Paracanthurus hepatus (Linnaeus, 1766)"
## [2] "BOLD:AAC3227"
##
## $decimalLatitude
## [1] -30.205483 -27.532258 -8.413278 -16.700000 -30.017840 -5.815955
## [7] 3.441135 -22.492167 -4.696106 7.208062 -1.985980 -33.800169
## [13] -30.202839 -27.400000 -4.289271 -17.071277 -17.075208 -27.465857
## [19] 13.477716 13.480037 4.595825 4.121438 -5.775973 -10.429189
## [25] -14.550000 -17.745759 -27.531884 -5.771697 -5.821940 -5.820498
## [31] -7.670200 1.743368 -24.114077 -24.113960 -5.775017 -22.592943
## [37] -19.949027 -17.070864 -17.054430 -29.479089 -0.556017 -28.611278
## [43] -4.656524 -17.636875 25.015492 2.728201 -4.356636 -6.353158
## [49] 22.075700 28.169633 22.319095 -14.663600 -18.287067 -8.349668
## [55] -13.647350 -24.113935 22.680581 27.404722 22.680278 -8.476267
## [61] -21.057139 -21.654910 -28.196141 26.189035 -2.244373 -8.727807
## [67] -2.204717 -30.204320 -24.113638 15.022028 -5.816751 27.388889
## [73] -5.840112 -28.611482 -24.116345 -17.076469 -17.077753 -10.423094
## [79] -29.927833 -10.393100 -8.481814 -8.612647 1.615687 13.522638
## [85] 13.518570 4.116129 -28.611023 0.186880 0.798243 6.384268
## [91] -16.428461 27.328333 -4.714799 -16.767523 4.109330 -21.151370
## [97] -23.817600 -29.929429 -4.279653 -4.288243 -4.258536 -24.110377
## [103] -0.584608 -17.575953 14.865178 14.838945 13.282353 18.090721
## [109] 18.169705 18.144987 14.108882 14.169204 15.192456 15.274841
## [115] 14.924998 15.052066 14.927633 15.010917 25.752000 -18.158240
## [121] -27.535837 -18.171880 -18.167790 18.093946 18.050178 18.085108
## [127] 15.134210 15.111052 15.113834 16.718400 -2.757490 13.686601
## [133] -5.820478 -18.671667 -21.239710 -21.170370 -21.205960 -21.205150
## [139] -21.035070 -21.233100 -21.073840 -2.260250 -2.249608 -5.775622
## [145] -14.273857 -17.076470 -16.783458 -21.349500 -21.484390 -16.657679
## [151] 30.487778 -5.801525 -25.288066 -8.400000 -21.319020 -4.321165
## [157] 24.306446 -17.068420 -8.689442 -14.235900 -21.370350 -21.366690
## [163] -21.371320 26.291180 1.872135 -17.116486 0.190310 0.187242
## [169] 0.191557 0.820899 0.822466 -17.070283 -17.062497 -14.151863
## [175] -14.224068 -14.278573 -14.279030 -14.241373 -14.285210 -14.273254
## [181] 16.135100 6.382461 -21.660010 -21.991250 -27.532000 24.436835
## [187] -5.611260 -27.525900 -15.484300 -8.475600 -8.537167 -4.530000
## [193] -5.304400 24.472500 -12.872840 23.212100 -4.714922 -21.015540
## [199] -21.015000 6.986900 7.134422 -27.523100 -27.520850 -21.058230
## [205] -17.408093 -4.292379 14.843660 18.149654 14.201462 15.269845
## [211] 15.261225 15.282955 15.275694 15.275189 15.276654 15.281291
## [217] 15.268836 15.256714 15.116363 15.003307 14.934944 -8.636633
## [223] 17.591924 26.237900 -8.459459 24.455000 -8.349183 -23.890883
## [229] -23.322967 -8.277300 13.230371 -8.505400 -24.112880 -8.289789
## [235] 13.522800 -14.529133 -21.160690 -29.447500 -14.681537 -27.529900
## [241] -27.538681 -6.456933 -29.930400 -30.202300 5.550000 -23.247900
## [247] 18.437700 -21.851700 -21.897300 -21.248000 -20.976700 -17.827500
## [253] 11.030300 -8.583764 -16.931600 -12.217000 27.510000 19.292300
## [259] -21.365210 -21.372000 -21.371260 -17.092612 4.500861 -17.100688
## [265] 0.194956 0.190741 0.195480 16.383300 -8.556720 -26.822600
## [271] -6.634620 -8.277000 25.821500 -14.523517 -8.295380 3.352720
## [277] 8.739842 39.284700 -27.524900 -27.533300 -12.085451 -24.111530
## [283] 19.675859 18.049572 15.255971 15.110629 15.105225 15.091283
## [289] 16.710502 14.931544 14.952465 14.864917 14.847157 20.748400
## [295] 15.077733 15.086594 15.069572 15.055609 -29.923100 -30.017600
## [301] -21.150000 16.324900 -23.796683 -23.848667 -23.745917 -21.146900
## [307] -18.846000 0.206550 0.193110 0.190290 -14.652800 -14.652770
## [313] -28.611000 -27.413500 -27.413510 25.034300 -10.429600 -10.428100
## [319] -4.313293 2.285408 -2.244887 -0.580346 20.307600 12.601900
## [325] 5.864600 -29.930440 -30.206662 15.273530
##
## $decimalLongitude
## [1] 153.26693 153.46261 127.31272 145.90000 153.27135 39.38287
## [7] 73.61533 166.44180 39.30214 134.32551 130.51253 151.30166
## [13] 153.26505 153.56667 55.85906 179.10738 179.10387 153.50513
## [19] 144.70608 144.70552 118.86434 118.63332 123.89485 105.66692
## [25] 145.40000 177.13443 123.88753 39.38888 39.38350 125.92338
## [31] 125.15346 152.70885 152.70963 123.89355 167.40760 57.62582
## [37] 179.10844 179.07802 153.36404 130.68908 153.62837 39.36794
## [43] 148.44080 122.00093 72.97009 55.83400 39.30729 121.58082
## [49] 129.29053 114.16936 145.66355 147.69919 116.06586 144.10688
## [55] 152.71469 121.50087 128.53389 121.49028 125.89175 55.21947
## [61] 164.54949 153.57911 127.40389 130.55572 115.54442 130.56772
## [67] 153.26482 152.70748 145.57996 39.38253 128.52111 39.46530
## [73] 153.62856 152.70794 179.11049 179.10984 105.66871 153.38925
## [79] 105.66045 119.52971 158.20064 124.73795 120.97290 120.99116
## [85] 118.63001 153.62923 -176.46176 -176.62003 -162.46472 145.99662
## [91] 128.55778 39.37970 179.94055 118.62500 35.08851 35.40329
## [97] 153.39147 55.72781 55.86531 55.67413 152.71023 130.63281
## [103] 178.98593 145.56811 145.53007 144.76383 145.76129 145.79179
## [109] 145.75369 145.16840 145.28545 145.70396 145.79259 145.64574
## [115] 145.65608 145.63037 145.58553 141.47400 -174.18171 32.67988
## [121] -174.20580 -174.18214 145.74479 145.70588 145.72653 145.67886
## [127] 145.70275 145.69897 145.77638 150.71890 120.91363 39.38162
## [133] -174.07435 55.30145 55.27931 55.27962 55.27898 55.21433
## [139] 55.29266 55.22368 130.64465 130.62375 123.89358 -169.49334
## [145] 179.11049 179.92354 55.46860 35.45493 146.02884 130.15250
## [151] 39.38400 152.90847 119.35000 35.50786 55.86569 124.09048
## [157] 179.10468 119.57251 -178.17400 55.73661 55.65609 55.68264
## [163] 126.78845 -157.42781 179.10813 -176.45731 -176.46102 -176.48886
## [169] -176.62671 -176.62678 179.10590 179.09860 -169.61060 -169.51954
## [175] -170.54882 -170.54739 -170.67885 -170.54548 -170.50510 -61.77100
## [181] -162.42674 35.42359 35.38154 32.68670 123.79669 132.74726
## [187] 32.68540 147.10760 119.55653 119.60195 131.65190 131.99690
## [193] 122.96361 45.27593 -81.18580 39.37488 55.23410 55.23405
## [199] 134.21884 134.22094 32.68600 32.68732 55.21915 -179.05644
## [205] 55.86796 145.56591 145.81155 145.26090 145.78511 145.82889
## [211] 145.80272 145.79354 145.82971 145.82731 145.80069 145.83191
## [217] 145.81463 145.69629 145.67423 145.65172 119.71143 145.81372
## [223] -80.00000 119.57176 -81.85830 116.05110 152.43017 151.98242
## [229] 115.59450 144.64386 157.99209 152.71402 115.60694 120.99300
## [235] 145.58833 55.83662 159.05390 145.43811 32.68800 32.67879
## [241] 71.25228 153.38980 153.26580 73.45000 155.56720 -69.69920
## [247] 153.52120 153.53760 155.76360 154.34530 148.50350 125.72300
## [253] 119.60596 149.99040 123.00390 34.18600 -81.10510 55.53040
## [259] 55.54547 55.54613 179.09921 118.93199 179.12516 -176.48664
## [265] -176.48881 -176.48669 -86.40000 125.50000 32.88350 39.23600
## [271] 115.59400 -77.93170 145.58198 115.61258 72.43150 167.69440
## [277] -76.60830 32.68440 32.68090 96.87765 152.71830 145.40914
## [283] 145.70552 145.72341 145.70190 145.72023 145.75022 145.76719
## [289] 145.63004 145.61942 145.58005 145.56905 -86.88900 145.65842
## [295] 145.65793 145.65610 145.59721 153.38810 153.26920 55.83000
## [301] -86.57990 152.30293 152.38175 152.28250 55.82176 36.32800
## [307] -176.47949 -176.45694 -176.45685 145.45050 153.62830 153.52520
## [313] 153.62831 153.52519 -77.39630 105.66810 105.66580 55.86585
## [319] 118.24362 130.56744 130.54309 -87.01840 -70.05770 95.26880
## [325] 153.38984 153.26605 145.79122
##
## $issues
## [1] "cdc,cdround"
## [2] ""
## [3] "cdround,cudc"
## [4] "cudc"
## [5] "incomis,inmafu"
## [6] "cdc,cdround,gass84,incomis,inmafu"
## [7] "cdc"
## [8] "cum"
## [9] "cdc,cudc,gass84,gdativ,refuriiv"
## [10] "cudc,gass84,gdativ,refuriiv"
## [11] "cdc,cdreps"
## [12] "osiic"
## [13] "cdc,cdround,gass84"
## [14] "gass84,incomis,inmafu"
## [15] "cdc,cum,gass84"
## [16] "cdc,cum"
## [17] "cdc,gass84,incomis,inmafu"
## [18] "cdc,gass84"
## [19] "gass84"
## [20] "cdc,cdround,cudc,gass84,gdativ,refuriiv"
## [21] "cdreps"
## [22] "cdround,gass84"
## [23] "conti,cdround,gass84,osiic,colmafu"
## [24] "ccm"
## [25] "cdc,cudc,gass84,osiic"
## [26] "cdc,cudc"
##
## $waterBody
## [1] NA "North Pacific Ocean" "Celebes Sea"
## [4] "Pacific Ocean" "South Pacific Ocean" "Flores Sea"
## [7] "Pacific" "Caribbean Sea" "Gulf of Mexico"
## [10] "Atlantic Ocean" "Verde Island" "La Caleta"
## [13] "Pacific, Leyte Gulf" "Red Sea" "Carribean"
## [16] "Banda Sea" "Indian Ocean" "IndianOcean"
## [19] "Laut Bali" "Royal Caribbean" "Laccadive Sea"
## [22] "Baltimore, MD"
##
## $basisOfRecord
## [1] "HUMAN_OBSERVATION" "PRESERVED_SPECIMEN" "MATERIAL_SAMPLE"
## [4] "OBSERVATION"
##
## $occurrenceStatus
## [1] "PRESENT"
##
## $rightsHolder
## [1] "divercraig" "Cameron Duchatel" "ulexeuropaeus"
## [4] NA "Joanne" "Emanuele Santarelli"
## [7] "eliotthuguet" "Claire Goiran" "quentindepl"
## [10] "sueinomaha" "Tony Stromberg" "Peter"
## [13] "Jens Sommer-Knudsen" "mdoelling" "Mark Rosenstein"
## [16] "Debra Baker" "Adam Smith" "Motusaga Vaeoso"
## [19] "Marisa Agarwal" "tracc" "Albert Kang"
## [22] "brutledge" "Garth Wimbush" "Dr Elodie Camprasse"
## [25] "Jacek Pietruszewski" "bewambay" "Jonathan Newman"
## [28] "Jean-Paul Boerekamps" "Harry Rosenthal" "Adelma Hills"
## [31] "Ashley Parr" "Steve Smith" "pclark2"
## [34] "Nigel Marsh" "Michal" "Wasini Tour Guide"
## [37] "John Sear" "顏水蛭" "David R"
## [40] "Rafi Amar" "Victor HOYEAU" "呂一起(Lu i-chi)"
## [43] "chloisf" "Hao Sen Liu" "Alastair Freeman"
## [46] "Daniela Kupschus" "Sophie Duc" "riki_paleatus"
## [49] "calvin1976" "ivansls" "Francois Libert"
## [52] "joseph_dibattista" "kfa" "desertnaturalist"
## [55] "Matthew Bokach" "Josh Moloney" "Zack"
## [58] "GF" "Chen Zhi" "warren cameron"
## [61] "hokoonwong" "Robin Laws-Wall" "blackdogto"
## [64] "craigjhowe" "Lesley Clements" "Roxanne Lazarus"
## [67] "mwamlavya" "Diveboard" "Ian Shaw"
## [70] "Sylvain Le Bris" "Geoff Shuetrim" "nahpets"
## [73] "Mathew Zappa" "Tony Strazzari" "Francesco Ricciardi"
## [76] "Joachim Louis" "João D'Andretta" "bja2800dk"
## [79] "Wayne and Pam Osborn" "Michael Long" "Franco Colnago"
## [82] "Geir Drange" "Christian Doedt" "Carmelo López Abad"
## [85] "cindyjay" "RLS" "Ewout Knoester"
## [88] "Paolo Mazzei" "uwkwaj" "rowanwattpringle"
## [91] "jeyre" "brudermann" "msr"
## [94] "lappuggla" "Karen Willshaw" "gernotkunz"
## [97] "ninjawil" "Richard Ling"
##
## $datasetName
## [1] "iNaturalist research-grade observations"
## [2] NA
## [3] "NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands"
## [4] "Diveboard - Scuba diving citizen science"
## [5] "Instituto Nacional de Investigação Pesqueira"
## [6] "Tonga Reef survey data 2016-2018"
## [7] "NMNH Material Samples (USNM)"
## [8] "NMNH Extant Biology"
## [9] "NOAA Pacific Islands Fisheries Science Center, Ecosystem Science Division Coral Reef Ecosystem Program, Rapid Ecological Assessments of Fish Belt Transect Surveys (BLT) at Coral Reef Sites across the Pacific Ocean from 2000 to 2009"
##
## $recordedBy
## [1] "divercraig"
## [2] "Cameron Duchatel"
## [3] "ulexeuropaeus"
## [4] "<a href='https://bee.questagame.com/#/profile/46905?questagame_user_id=46905'> DJWitherall|questagame.com</a>"
## [5] "Joanne"
## [6] "Emanuele Santarelli"
## [7] "eliotthuguet"
## [8] "Claire Goiran"
## [9] "quentindepl"
## [10] "sueinomaha"
## [11] "Tony Stromberg"
## [12] "Peter"
## [13] "Jens Sommer-Knudsen"
## [14] "mdoelling"
## [15] "Mark Rosenstein"
## [16] "Debra Baker"
## [17] "Adam Smith"
## [18] "Motusaga Vaeoso"
## [19] "Marisa Agarwal"
## [20] "tracc"
## [21] "Albert Kang"
## [22] "brutledge"
## [23] "Garth Wimbush"
## [24] "Dr Elodie Camprasse"
## [25] "Jacek Pietruszewski"
## [26] "bewambay"
## [27] "Jonathan Newman"
## [28] "Jean-Paul Boerekamps"
## [29] "Harry Rosenthal"
## [30] "Adelma Hills"
## [31] "Ashley Parr"
## [32] "Steve Smith"
## [33] "pclark2"
## [34] "Nigel Marsh"
## [35] "Michal"
## [36] "Wasini Tour Guide"
## [37] "John Sear"
## [38] "顏水蛭"
## [39] "David R"
## [40] "Rafi Amar"
## [41] "Victor HOYEAU"
## [42] "呂一起(Lu i-chi)"
## [43] "chloisf"
## [44] "Hao Sen Liu"
## [45] "Alastair Freeman"
## [46] "Daniela Kupschus"
## [47] "Sophie Duc"
## [48] NA
## [49] "riki_paleatus"
## [50] "calvin1976"
## [51] "ivansls"
## [52] "Francois Libert"
## [53] "ALLIER Serge (FFESSM)"
## [54] "joseph_dibattista"
## [55] "kfa"
## [56] "desertnaturalist"
## [57] "Matthew Bokach"
## [58] "Josh Moloney"
## [59] "Zack"
## [60] "GF"
## [61] "Chen Zhi"
## [62] "warren cameron"
## [63] "hokoonwong"
## [64] "Robin Laws-Wall"
## [65] "blackdogto"
## [66] "craigjhowe"
## [67] "Lesley Clements"
## [68] "Roxanne Lazarus"
## [69] "Diver initials CC"
## [70] "Diver initials TCW"
## [71] "Diver initials LMG"
## [72] "Diver initials JWM"
## [73] "mwamlavya"
## [74] "Thomas Chardon"
## [75] "Simão Elias Mupengo"
## [76] "Açúrcio Belmiro Cumbane"
## [77] "Ian Shaw"
## [78] "539637721"
## [79] "Sylvain Le Bris"
## [80] "Geoff Shuetrim"
## [81] "nahpets"
## [82] "Diver initials VAB"
## [83] "Diver initials RMW"
## [84] "Diver initials PMA"
## [85] "Diver initials JPZ"
## [86] "Diver initials KDG"
## [87] "Diver initials ARP"
## [88] "Karen Stone"
## [89] "Mathew Zappa"
## [90] "Heather Kramp"
## [91] "Tony Strazzari"
## [92] "Francesco Ricciardi"
## [93] "Joachim Louis"
## [94] "Patrick Smallhorn-West"
## [95] "João D'Andretta"
## [96] "Nicet J.B., Pinault M.,Wickel J., Bigot L.,C. Bourmaud,Mulochau T., Zubia M., Conand C., Poupin,M. Schleyer,Benon P., G. Malfait"
## [97] "RNMR, IRD, université de La Réunion"
## [98] "Rangel de Jesus"
## [99] "bja2800dk"
## [100] "Wayne and Pam Osborn"
## [101] "xavier, tristan (haustral plongée)"
## [102] "Jorge Fichane Zibane"
## [103] "Michael Long"
## [104] "Franco Colnago"
## [105] "Foster, Kenneth"
## [106] "Sebastien Rezzonico"
## [107] "Herculano Patricio"
## [108] "Geir Drange"
## [109] "Isaias Jeckson Elija"
## [110] "J. Williams & S. Planes"
## [111] "Nicet JB., Pinault M., Wickel J., Bigot L., Mulochau T., Zubia M., Conand C., Poupin J., Barrère A., Quod, J.P., Benon P"
## [112] "Christian Doedt"
## [113] "Diver initials AEG"
## [114] "Diver initials JMA"
## [115] "Diver initials JMM"
## [116] "Diver initials KCL"
## [117] "Diver initials KS"
## [118] "Diver initials EMD"
## [119] "Marie"
## [120] "Diver initials EC"
## [121] "Gil Zaqueu Maquene"
## [122] "Silva Carlos Mondlane"
## [123] "Sam Hansen"
## [124] "Carmelo López Abad"
## [125] "cindyjay"
## [126] "lisa hengelein"
## [127] "JS"
## [128] "JPS"
## [129] "TPC"
## [130] "Maguelone GRATEAU, Henri GRATEAU (ESSOR)"
## [131] "David Bishop"
## [132] "Ewout Knoester"
## [133] "Pieterjl"
## [134] "seastung"
## [135] "angelique tourret (o sea bleu)"
## [136] "Paolo Mazzei"
## [137] "Diver initials KSM"
## [138] "Diver initials IDW"
## [139] "Morgan"
## [140] "Jyore"
## [141] "IVS"
## [142] "Viriato José Mutelecanamba"
## [143] "uwkwaj"
## [144] "Christina Estrup"
## [145] "RSS"
## [146] "Hoggett, Anne"
## [147] "rowanwattpringle"
## [148] "jeyre"
## [149] "Rowan Watt-Pringle"
## [150] "Gaither, Michelle R.; Wagner, Daniel"
## [151] "NAD"
## [152] "brudermann"
## [153] "WCB"
## [154] "Breezy"
## [155] "GJE"
## [156] "RJE"
## [157] "GER"
## [158] "J. Williams, K. Carpenter, A. Lizano & A. Macaspac"
## [159] "msr"
## [160] "AJG"
## [161] "Ilya Bychkov"
## [162] "Alf"
## [163] "lappuggla"
## [164] "Diver initials MON"
## [165] "Sean Shrum"
## [166] "Joao Sarmento"
## [167] "Cam"
## [168] "Shiko"
## [169] "Ryan Lee"
## [170] "Steven Lawson"
## [171] "Haydee Osorio"
## [172] "Bruno Amim"
## [173] "Anonymous"
## [174] "Sea Escapes"
## [175] "Elodie"
## [176] "Karen Willshaw"
## [177] "Diver initials SCM"
## [178] "Diver initials MF"
## [179] "Diver initials MKM"
## [180] "()"
## [181] "João Luís Dramane"
## [182] "Diver initials JLG"
## [183] "Diver initials KMO"
## [184] "TJA"
## [185] "AS"
## [186] "Rémi Forget"
## [187] "MLD"
## [188] "gernotkunz"
## [189] "ninjawil"
## [190] "Mike"
## [191] "JWG"
## [192] "AR"
## [193] "Richard Ling"
##
## $depth
## [1] NA 15.000 20.700 5.450 10.600 20.000 11.745 13.500 15.400 16.500
## [11] 11.400 20.600 24.400 23.700 14.200 24.850 9.300 9.700 4.800 9.200
## [21] 8.650 20.150 12.800 12.700 14.650 14.550 6.000 11.300 5.000 23.400
## [31] 21.300 21.350 12.250 21.000 16.200 15.600 21.900 22.650 7.000 9.100
## [41] 12.540 1.250 8.750 18.950 19.200 23.000 6.350 6.850 15.950 17.800
## [51] 18.000 9.000 8.500 13.000 9.400 9.500 22.200 10.770 9.900 9.600
## [61] 10.000 22.000 21.950 11.600 11.200 21.200 21.500 11.000 19.400 5.300
## [71] 5.500 7.200 8.800 21.600 17.050 19.500 8.990 5.330 12.000 14.480
## [81] 8.735 12.500 9.070 8.000 4.900 6.095 2.285 25.700 27.000 7.470
## [91] 19.000 4.420 13.715 8.840
##
## $locality
## [1] NA
## [2] "Taminazaki, Tamina, China, Oshima-gun, Okinoerabu-jima island, Amami Islands, Kagoshima, Japan"
## [3] "west of Tamina, China, Oshima-gun, Okinoerabu-jima island, Amami Islands, Kagoshima, Japan"
## [4] "off Yakomo, China, Oshima-gun, Okinoerabu-jima island, Amami Islands, Kagoshima, Japan"
## [5] "Hanging Gardens"
## [6] "Govuro Mar Aberto"
## [7] "Jangamo Estuário"
## [8] "Curieuse Island"
## [9] "Japan, Ogasawara Is., Kazan Is. (Volcano Is.), Kita-Iwo-jima I., northeastern coast"
## [10] "Toku"
## [11] "Hunga"
## [12] "Maxixe Estuário"
## [13] "Inhassoro MAI"
## [14] "Urasoko, Kuchierabujima,Yakushima, Kumage-gun, Kuchierabu-jima island, Osumi Islands, Kagoshima, Japan"
## [15] "3 Pulgul St, Urangan QLD 4655, Australia"
## [16] "Crystal Rock, Komodo National Park"
## [17] "Inhassoro MAII"
## [18] "Morrumbene Estuário"
## [19] "Futuna, Wallis and Futuna, Futuna Island, exposed rocks of"
## [20] "Wallis and Futuna, Futuna Island, exposed rocks off north point, exposed rocky reef and channels."
## [21] "Aquarium"
## [22] "Vilankulo MA II"
## [23] "Sodwana Bay, Bikini South"
## [24] "Sodwana Bay, Caves & Overhangs"
## [25] "Bougainville Reef Lagoon East"
## [26] "Pulau Kasiui SW"
## [27] "Kanar Yapas"
## [28] "Umabana, Yonaguni, Yonaguni, Yaeyama-gun, Yonaguni-jima island, Yaeyama Islands, Okinawa, Japan"
## [29] "Claraboyas Reef"
## [30] "Sodwana Bay"
## [31] "Bikini"
## [32] "Sunkist Reef"
## [33] "Rock Key (Reef)"
## [34] "Paradise House reef"
## [35] "Vilankulo MA I"
## [36] "The Atoll"
## [37] "Wreck 1"
## [38] "Lizard Island, Queensland"
## [39] "Sodwana Bay, Bikini"
## [40] "Chagos Archipelago, Great Chagos Bank"
## [41] "Elbow Cave Mooring N Solitary Is"
## [42] "South Boulder Wall"
## [43] "Cato East"
## [44] "Los Paisanitos"
## [45] "Saumarez SW Islet"
## [46] "Saumarez SW reef cay"
## [47] "Kenn Reef rubble"
## [48] "Frederick Ridge Rock"
## [49] "Flinders Reef Bommie"
## [50] "Philippines, Guiuan, Guiuan Market"
## [51] "Chilcott Islet SW inner reef"
## [52] "Surge Crest East"
## [53] "Temple"
## [54] "Playing Field"
## [55] "40 Foot Wall"
## [56] "Dili Rock East"
## [57] "Steps"
## [58] "Sistersreef"
## [59] "Coral Garden"
## [60] "Coco Cay"
## [61] "Rangali Madivaru"
## [62] "National Aquarium"
## [63] "Bikini, Sodwana"
## [64] "1, Sodwana Main Road"
## [65] "Cerebros"
## [66] "Anemone Bay N Solitary Is"
## [67] "Manta Mooring NW Solitary Is"
## [68] "Overheat Reef"
## [69] "Gazelas Mar Aberto"
## [70] "Turtle Beach"
## [71] "Anemone mooring Julien Rocks"
## [72] "Shag Rock"
## [73] "Flying Fish Cove Boat Ramp"
## [74] "Smith Point"
## [75] "Columbia"
## [76] "Antilla Wreck"
## [77] "Lhok Weng"
##
## $habitat
## [1] NA
## [2] "Forereef : ROB : Rock/Boulder"
## [3] "Forereef : SAG : Spur and Groove"
## [4] "Protected Slope : AGR : Aggregate Reef"
## [5] "Forereef : AGR : Aggregate Reef"
## [6] "Forereef : PSC : Pavement with Sand Channels"
## [7] "Forereef : PAV : Pavement"
## [8] "Forereef : PPR : Pavement with Patch Reefs"
## [9] "ZZZ"
## [10] "Exposed Wall"
## [11] "Forereef : RRB : Reef Rubble"
## [12] "Coral Reef"
## [13] "Forereef : MIX : Mixed Habitats"
## [14] "Shallow coral reef : Forereef"
## [15] "Forereef : UNK : Unknown"3.3 Problemas não reportados
Agora iniciamos o processo de checagem mais fina que não é realizada
pelo algoritmo, por apresentar especificidades que vão além de sua
programação. Inicialmente, podemos verificar se as coordenadas são
válidas (e.g., latitudes > 90 ou longitude > 180) utilizando
funções dos pacotes CoordinateCleaner
e bcd.
Clicando nos links dos pacotes vocês podem checar diversas outras
funcionalidades oferecidas.
library(bdc)
library(CoordinateCleaner)
# checar coordenadas válidas
check_pf <-
bdc::bdc_coordinates_outOfRange(
data = dori_gbif1,
lat = "decimalLatitude",
lon = "decimalLongitude")
# checar coordenadas válidas e próximas a capitais (muitas vezes as coordenadas são erroneamente associadas a capitais dos países)
cl <- dori_gbif1 %>%
select(acceptedScientificName, decimalLatitude, decimalLongitude) %>%
rename(decimallongitude = decimalLongitude,
decimallatitude = decimalLatitude,
scientificName = acceptedScientificName) %>%
as_tibble() %>%
mutate(val = cc_val(., value = "flagged"),
sea = cc_sea(., value = "flagged"),
capital = cc_cap(., value = "flagged"))Na imagem abaixo podemos dar uma rápida conferida nos alertas indicados pelas funções. Não tivemos nenhuma coordenada inválida, mas algumas ocorrências parecem estar muito próximas a capitais. No entanto, todas as capitais estão em terra e, nesse caso, temos que investigar se as ocorrências estão em terra (lembre-se a Dori vive no mar!) ou apenas próximas a países insulares.
# verificar coordenadas com flags
# capitais (padrão é um raio de 10km)
cl %>%
rename(decimalLongitude = decimallongitude,
decimalLatitude = decimallatitude) %>%
bdc::bdc_quickmap(., col_to_map = "capital") 
cl %>%
rename(decimalLongitude = decimallongitude,
decimalLatitude = decimallatitude) %>%
bdc::bdc_quickmap(., col_to_map = "sea") 
Uma maneira fácil de excluir dados em terra é checar a distribuição
das ocorrências em relação às regiões oceanográficas indicadas nos dados
(waterBody). Isso vale apenas para o OBIS, mas se o
objetivo é avaliar espécies terrestres, basta excluir as espécies com
flags TRUE na coluna sea criada pela
função cc_sea.
# investigar niveis suspeitos
dori_gbif1 %>%
distinct(waterBody) %>%
pull()## [1] NA "North Pacific Ocean" "Celebes Sea"
## [4] "Pacific Ocean" "South Pacific Ocean" "Flores Sea"
## [7] "Pacific" "Caribbean Sea" "Gulf of Mexico"
## [10] "Atlantic Ocean" "Verde Island" "La Caleta"
## [13] "Pacific, Leyte Gulf" "Red Sea" "Carribean"
## [16] "Banda Sea" "Indian Ocean" "IndianOcean"
## [19] "Laut Bali" "Royal Caribbean" "Laccadive Sea"
## [22] "Baltimore, MD"# waterBody
dori_gbif1 %>%
group_by(waterBody) %>%
summarise(occ = length(scientificName)) %>%
ggplot(aes(occ, y=waterBody)) +
geom_bar(stat = 'identity') 
Aparentemente, esta espécie tem sido reportada no mundo todo. Com o sucesso da animação Procurando Nemo, já temos uma ideia de que a Dori tem ocorrência nas águas Australianas, mas podemos acessar bancos de dados especializados para checar estas informações. No caso de peixes (Osteichthyes e Chondrichthyes) o FishBase é a fonte mais atualizada de informações deste grupo. Depois desta confirmação, podemos suspeitar das ocorrências indicadas no Atlântico e, o tratamento mais rigoroso é a exclusão de qualquer ocorrência suspeita.
# fonte das regioes erradas
dori_gbif1 %>%
filter(waterBody %in% c("Atlantic Ocean", "Carribean", "Royal Caribbean", "Carribean Sea", "Bonaire")) %>%
distinct(datasetName)## # A tibble: 1 × 1
## datasetName
## <chr>
## 1 Diveboard - Scuba diving citizen scienceAlguma característica destas ocorrências do Atlântico podem dar pistas de como continuar filtrando os resultados. Neste caso, abaixo podemos ver que, ao investigarmos um programa de ciência específico de identificação realizada por mergulhadores amadores, notamos que este concentra a maior parte das suspeitas. Assim, é melhor ser conservador e remover todas as ocorrências associadas a tal programa.
# 25 ocorrencias
dori_gbif1 %>%
filter(datasetName %in% c("Diveboard - Scuba diving citizen science"))## # A tibble: 24 × 14
## scientificName accep…¹ decim…² decim…³ issues water…⁴ basis…⁵ occur…⁶ right…⁷
## <chr> <chr> <dbl> <dbl> <chr> <chr> <chr> <chr> <chr>
## 1 Paracanthurus… Paraca… 4.11 119. cdc,c… Celebe… HUMAN_… PRESENT Divebo…
## 2 Paracanthurus… Paraca… -8.4 119. cdc,c… Flores… HUMAN_… PRESENT Divebo…
## 3 Paracanthurus… Paraca… 16.1 -61.8 cdc,c… Caribb… HUMAN_… PRESENT Divebo…
## 4 Paracanthurus… Paraca… 23.2 -81.2 cdc,c… Gulf o… HUMAN_… PRESENT Divebo…
## 5 Paracanthurus… Paraca… 26.2 -80 cdreps Atlant… HUMAN_… PRESENT Divebo…
## 6 Paracanthurus… Paraca… 24.5 -81.9 cdreps Gulf o… HUMAN_… PRESENT Divebo…
## 7 Paracanthurus… Paraca… 13.5 121. cdc,c… Verde … HUMAN_… PRESENT Divebo…
## 8 Paracanthurus… Paraca… 18.4 -69.7 cdc,c… La Cal… HUMAN_… PRESENT Divebo…
## 9 Paracanthurus… Paraca… 27.5 34.2 cdreps Red Sea HUMAN_… PRESENT Divebo…
## 10 Paracanthurus… Paraca… 19.3 -81.1 cdc,c… Caribb… HUMAN_… PRESENT Divebo…
## # … with 14 more rows, 5 more variables: datasetName <chr>, recordedBy <chr>,
## # depth <dbl>, locality <chr>, habitat <chr>, and abbreviated variable names
## # ¹acceptedScientificName, ²decimalLatitude, ³decimalLongitude, ⁴waterBody,
## # ⁵basisOfRecord, ⁶occurrenceStatus, ⁷rightsHolder# filtrar todas do dataset suspeito
dori_gbif_ok <- dori_gbif1 %>%
filter(!datasetName %in% c("Diveboard - Scuba diving citizen science"))Agora não vemos mais nenhuma ocorrência no Atlântico!
library(ggmap)
library(maps)
library(mapdata)
world <- map_data('world')
# checar pontos
ggplot() +
geom_polygon(data = world, aes(x = long, y = lat, group = group)) +
coord_fixed() +
theme_classic() +
geom_point(data = dori_gbif_ok, aes(x = decimalLongitude, y = decimalLatitude), color = "red") +
labs(x = "longitude", y = "latitude", title = expression(italic("Paracanthurus hepatus")))
Podemos usar a profundidade como outro critério, pois esta espécie é associada apenas a recifes rasos segundo o FishBase. E parece tudo ok.
# checar profundidade
dori_gbif_ok %>%
ggplot(aes(x = depth, fill = waterBody)) +
geom_histogram() 
3.3.1 OBIS
Agora vamos fazer os mesmos procedimentos com os dados do
OBIS, utilizando o pacote robis e a função
occurrence deste pacote.
- Baixar as ocorrências
## OBIS
dori_obis <- robis::occurrence("Paracanthurus hepatus")- Checar os dados
Temos variáveis com os mesmos nomes, pois ambos usam o sistema
DwC, mas os problemas reportados neste caso são indicados
na coluna flags.
# checar dados
names(dori_obis)## [1] "rightsHolder"
## [2] "infraphylum"
## [3] "country"
## [4] "scientificNameID"
## [5] "scientificName"
## [6] "individualCount"
## [7] "dropped"
## [8] "gigaclassid"
## [9] "aphiaID"
## [10] "decimalLatitude"
## [11] "subclassid"
## [12] "type"
## [13] "gigaclass"
## [14] "infraphylumid"
## [15] "phylumid"
## [16] "familyid"
## [17] "catalogNumber"
## [18] "occurrenceStatus"
## [19] "basisOfRecord"
## [20] "terrestrial"
## [21] "id"
## [22] "parvphylum"
## [23] "order"
## [24] "recordNumber"
## [25] "dataset_id"
## [26] "locality"
## [27] "decimalLongitude"
## [28] "collectionCode"
## [29] "speciesid"
## [30] "occurrenceID"
## [31] "license"
## [32] "genus"
## [33] "collectionID"
## [34] "eventDate"
## [35] "brackish"
## [36] "coordinateUncertaintyInMeters"
## [37] "absence"
## [38] "genusid"
## [39] "originalScientificName"
## [40] "marine"
## [41] "subphylumid"
## [42] "institutionCode"
## [43] "wrims"
## [44] "class"
## [45] "orderid"
## [46] "kingdom"
## [47] "recordedBy"
## [48] "classid"
## [49] "phylum"
## [50] "species"
## [51] "subphylum"
## [52] "subclass"
## [53] "family"
## [54] "kingdomid"
## [55] "parvphylumid"
## [56] "node_id"
## [57] "flags"
## [58] "sss"
## [59] "shoredistance"
## [60] "sst"
## [61] "bathymetry"
## [62] "scientificNameAuthorship"
## [63] "identifiedBy"
## [64] "waterBody"
## [65] "institutionID"
## [66] "year"
## [67] "fieldNumber"
## [68] "language"
## [69] "modified"
## [70] "acceptedNameUsage"
## [71] "higherGeography"
## [72] "georeferencedBy"
## [73] "month"
## [74] "acceptedNameUsageID"
## [75] "ownerInstitutionCode"
## [76] "identificationID"
## [77] "continent"
## [78] "eventID"
## [79] "taxonRank"
## [80] "preparations"
## [81] "locationRemarks"
## [82] "countryCode"
## [83] "georeferenceVerificationStatus"
## [84] "verbatimSRS"
## [85] "geodeticDatum"
## [86] "specificEpithet"
## [87] "previousIdentifications"
## [88] "locationID"
## [89] "date_year"
## [90] "day"
## [91] "date_end"
## [92] "date_start"
## [93] "samplingProtocol"
## [94] "samplingEffort"
## [95] "date_mid"
## [96] "footprintWKT"
## [97] "startDayOfYear"
## [98] "datasetID"
## [99] "habitat"
## [100] "references"
## [101] "maximumDepthInMeters"
## [102] "verbatimEventDate"
## [103] "sampleSizeUnit"
## [104] "maximumDistanceAboveSurfaceInMeters"
## [105] "island"
## [106] "stateProvince"
## [107] "islandGroup"
## [108] "taxonID"
## [109] "minimumDepthInMeters"
## [110] "vernacularName"
## [111] "dataGeneralizations"
## [112] "georeferenceProtocol"
## [113] "datasetName"
## [114] "verbatimDepth"
## [115] "depth"
## [116] "occurrenceRemarks"
## [117] "sampleSizeValue"
## [118] "organismQuantity"
## [119] "organismQuantityType"
## [120] "coordinatePrecision"
## [121] "verbatimLatitude"
## [122] "higherClassification"
## [123] "verbatimLongitude"
## [124] "nomenclaturalCode"
## [125] "parentNameUsageID"
## [126] "organismID"
## [127] "eventRemarks"
## [128] "taxonomicStatus"
## [129] "associatedSequences"
## [130] "parentEventID"
## [131] "dynamicProperties"
## [132] "lifeStage"
## [133] "georeferenceRemarks"
## [134] "minimumElevationInMeters"
## [135] "maximumElevationInMeters"
## [136] "eventTime"
## [137] "municipality"
## [138] "otherCatalogNumbers"
## [139] "typeStatus"
## [140] "dateIdentified"
## [141] "associatedReferences"
## [142] "county"
## [143] "endDayOfYear"
## [144] "footprintSRS"
## [145] "bibliographicCitation"
## [146] "georeferencedDate"
## [147] "namePublishedInID"
## [148] "disposition"
## [149] "originalNameUsage"
## [150] "accessRights"
## [151] "sex"
## [152] "associatedMedia"
## [153] "verbatimCoordinates"dori_obis1 <- dori_obis %>%
dplyr::select(scientificName, decimalLatitude, decimalLongitude, bathymetry,
flags, waterBody, basisOfRecord, occurrenceStatus, rightsHolder,
datasetName, recordedBy, depth, locality, habitat) %>%
distinct()
# check problemas reportados (flags)
dori_obis1 %>%
distinct(flags)## # A tibble: 7 × 1
## flags
## <chr>
## 1 NO_DEPTH
## 2 NO_DEPTH,ON_LAND
## 3 <NA>
## 4 ON_LAND
## 5 ON_LAND,NO_DEPTH
## 6 DEPTH_EXCEEDS_BATH
## 7 DEPTH_EXCEEDS_BATH,ON_LAND# check NA em datasetName
dori_obis1 %>%
filter(!flags %in% c("no_depth,on_land", "on_land", "on_land,depth_exceeds_bath", "depth_exceeds_bath,on_land"),
is.na(datasetName)) %>%
distinct(waterBody)## # A tibble: 13 × 1
## waterBody
## <chr>
## 1 <NA>
## 2 Oceania
## 3 Pacific Ocean
## 4 Asia
## 5 Africa
## 6 indien
## 7 Caribbean Sea
## 8 North America Atlantic
## 9 Pacific
## 10 pacifique
## 11 atlantique
## 12 Indian
## 13 North AmericaAqui usamos as flags para filtrar ocorrências em terra,
além de remover dados sem nome de dataset (não temos como
checar a origem adequadamente, então podemos tratar como suspeitos),
filtrar ocorrências no Atlântico e verificar a profundidade
reportada.
# depth ok
dori_obis1 %>%
filter(!flags %in% c("no_depth,on_land", "on_land", "on_land,depth_exceeds_bath", "depth_exceeds_bath,on_land"),
!is.na(datasetName),
!waterBody %in% c("North America", "North America Atlantic", "atlantique")) %>%
ggplot(aes(x = depth, fill = waterBody)) +
geom_histogram() 
# checar niveis
dori_obis1 %>%
filter(!flags %in% c("no_depth,on_land", "on_land", "on_land,depth_exceeds_bath", "depth_exceeds_bath,on_land"),
!is.na(datasetName),
!waterBody %in% c("North America", "North America Atlantic", "atlantique")) %>%
lapply(., unique)## $scientificName
## [1] "Paracanthurus hepatus"
##
## $decimalLatitude
## [1] 15.2612250 15.0777326 20.9260006 14.9315443 15.2735300 0.1868800
## [7] 0.1915569 14.8471569 18.1697050 -6.0790000 13.2303711 0.1902900
## [13] 18.0501780 -18.6716667 14.8436598 15.2812907 -14.2790305 15.0695718
## [19] 15.1052253 0.2065500 14.2014619 15.2688078 0.1872420 15.0865944
## [25] 15.0033074 15.1110520 0.1949556 15.0520660 15.2829550 14.9524648
## [31] 15.1924560 15.0912826 14.1692040 14.1088820 15.1760200 0.7982430
## [37] -14.2738570 18.1449870 14.8649172 -14.1518635 -8.4156407 -0.0235591
## [43] 14.9276330 15.1138340 16.7184000 -18.1677900 13.2823530 15.1163631
## [49] -14.2240685 14.9249980 2.1641140 15.2766544 -18.1582400 15.0042435
## [55] 15.2748410 0.1903102 18.0939460 14.8389450 0.8208993 -18.1486000
## [61] 14.2460003 15.2542167 15.2567141 7.1170001 -18.1718800 14.9349439
## [67] -8.4180000 15.1342100 -6.8000000 6.3842680 -14.2413730 15.2688363
## [73] 0.1970000 15.0556089 0.8224659 -14.2785729 15.2756939 -8.4465079
## [79] 18.0907210 15.2698445 0.1907412 15.2751892 16.7105020 15.2559710
## [85] 18.1496535 15.0109170 24.8008330 18.8112216 6.3824613 14.8651780
## [91] 0.1989000 -14.2732544 0.1931100 -11.6506000 -3.7833333 11.7946000
## [97] -8.6047191 0.1954804 -8.3627887 24.7975000 18.0851080 17.6075300
## [103] -14.2852098 19.6758593 15.1106289 0.1882000 18.0495721 0.1908500
## [109] 17.5919243 -17.1836910 17.5869300
##
## $decimalLongitude
## [1] 145.8289 145.6584 -156.4530 145.6300 145.7912 -176.4618 -176.4889
## [8] 145.5690 145.7918 106.8370 144.6439 -176.4569 145.7059 -174.0744
## [15] 145.5659 145.8007 -170.5474 145.6561 145.7202 -176.4795 145.2609
## [22] 145.8322 -176.4610 145.6579 145.6742 145.7028 -176.4866 145.6561
## [29] 145.8027 145.6194 145.7040 145.7502 145.2855 145.1684 145.7876
## [36] -176.6200 -169.4933 145.7537 145.5800 -169.6106 127.3111 37.9062
## [43] 145.6304 145.6990 145.7764 -174.1821 144.7638 145.6963 -169.5195
## [50] 145.6457 118.6458 145.8273 -174.1817 145.5867 145.7926 -176.4573
## [57] 145.7448 145.5301 -176.6267 178.3790 120.4790 145.7518 145.8146
## [64] 79.8080 -174.2058 145.6517 127.3090 145.6789 39.2500 -162.4647
## [71] -170.6789 145.8319 -176.4862 145.5972 -176.6268 -170.5488 145.7935
## [78] 127.3203 145.7613 145.7851 -176.4888 145.8297 145.7672 145.7234
## [85] 145.8115 145.5855 141.2858 145.6768 -162.4267 145.5681 -176.4850
## [92] -170.5051 -176.4569 43.2572 128.1250 -66.8902 125.2193 -176.4867
## [99] 127.1033 141.2908 145.7265 145.8153 -170.5455 145.4091 145.7019
## [106] -176.4827 145.7055 -176.4889 145.8137 146.2910 145.8181
##
## $bathymetry
## [1] 35.00 75.00 29.00 -17.00 -4.00 33.00 266.00 91.00 1.00
## [10] 9.00 181.00 264.00 47.00 81.00 -61.00 -109.00 -10.00 -2.00
## [19] 122.00 52.00 -16.00 -15.00 -42.00 -1.00 -28.00 17.00 7.00
## [28] 141.00 -27.00 170.00 -7.00 -26.00 -842.00 56.00 111.00 432.00
## [37] 28.00 -3.00 132.00 55.00 63.00 198.00 -24.00 -72.00 -12.00
## [46] 26.00 322.00 292.00 3.00 -19.00 15.00 251.00 88.00 -37.00
## [55] 14.00 -22.00 2.00 38.00 -8.00 -13.00 -52.00 19.00 96.00
## [64] -71.00 218.00 151.00 126.00 3.12 -66.00
##
## $flags
## [1] NA "NO_DEPTH" "ON_LAND"
## [4] "DEPTH_EXCEEDS_BATH" "NO_DEPTH,ON_LAND"
##
## $waterBody
## [1] "North Pacific Ocean"
## [2] "Pacific Ocean"
## [3] "South China and Eastern Archipelagic Seas"
## [4] "South Pacific Ocean"
## [5] "Indian"
## [6] NA
## [7] "Indian Ocean"
## [8] "Caribbean Sea"
## [9] "Coral Sea"
##
## $basisOfRecord
## [1] "HumanObservation" "PreservedSpecimen"
##
## $occurrenceStatus
## [1] "present" NA "Present"
##
## $rightsHolder
## [1] NA "Bernice Pauahi Bishop Museum"
## [3] "Canadian Museum of Nature"
##
## $datasetName
## [1] "NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands"
## [2] "Ocean Genome Legacy Collection"
## [3] "NOAA Pacific Islands Fisheries Science Center, Ecosystem Science Division Coral Reef Ecosystem Program, Rapid Ecological Assessments of Fish Belt Transect Surveys (BLT) at Coral Reef Sites across the Pacific Ocean from 2000 to 2009"
## [4] "Tonga Reef survey data 2016-2018"
## [5] "Kenya Marine and Fisheries Research Institute - Marine Species"
## [6] "Asia-Pacific Dataset"
## [7] "Bishop Museum Fish Specimens"
## [8] "Fish"
## [9] "Pacific Reef Assessment and Monitoring Program: Rapid Ecological Assessments of Fish Large-Area Stationary Point Count Surveys (SPC) at Coral Reef Sites across the Pacific Ocean from 2000 to 2007"
## [10] "Fish collection of National Museum of Nature and Science"
## [11] "MMM_ALR_FISH"
##
## $recordedBy
## [1] "Diver initials KSM" "Diver initials EMD"
## [3] NA "Diver initials VAB"
## [5] "Diver initials TCW" "Diver initials LMG"
## [7] "Diver initials MF" "Diver initials PMA"
## [9] "Diver initials KMO" "Diver initials RMW"
## [11] "Patrick Smallhorn-West" "Diver initials EC"
## [13] "Diver initials IDW" "Diver initials MKM"
## [15] "Diver initials SCM" "Diver initials JLG"
## [17] "Diver initials KDG" "Diver initials MON"
## [19] "Diver initials JMM" "Diver initials JPZ"
## [21] "Diver initials KCL" "Karen Stone"
## [23] "Diver initials KS" "Diver initials CC"
## [25] "Diver initials AEG" "Diver initials JMA"
## [27] "Macaulay, A.J." "Diver initials JWM"
## [29] "Diver initials ARP" "Youngman, Dr. Philip Merrill"
## [31] "F. Martin" "Diver initials BDS"
## [33] "Heather Kramp" "Jamie Hopkins"
##
## $depth
## [1] 15.60 13.00 NA 11.00 10.00 20.70 6.35 23.70 12.00 19.00 21.30 7.00
## [13] 22.00 21.00 11.20 23.00 20.00 21.60 16.20 12.80 15.40 27.00 11.60 4.80
## [25] 25.70 9.30 24.85 15.00 5.45 9.10 14.20 17.80 2.70 13.50 21.90 22.65
## [37] 5.00 9.70 11.40 8.80 9.00 20.15 6.00 3.00 9.20 18.95 23.40 1.80
## [49] 7.20 5.50 17.05 4.60 10.60 9.40 19.40 9.60 6.85 8.65 15.95 8.50
## [61] 19.20 18.00 5.30 10.15 20.60 21.20 21.50 12.70 12.50 21.95 14.55 9.90
## [73] 14.65 22.20 3.10 21.35 9.75 24.40 14.00 11.30 12.25 9.50 16.50 19.50
## [85] 17.00
##
## $locality
## [1] NA
## [2] "Hunga"
## [3] "Kenya"
## [4] "Toku"
## [5] "the lagoon in Tanjung Duwata"
## [6] "Viti Levu Island; W of Rat-Tail Passage"
## [7] "Manila, Philippines"
## [8] "Kochchikade, Sri Lanka"
## [9] "Fungu Yasini, southwest reef, 8 kilometres north of north tip of Bongovo Island"
## [10] "offshore reef, Io-sima"
## [11] "South Indian Ocean, 700 metres north of Hantsambu, off Itsandra"
## [12] "Indoneshia Ambon I. S coast Latsuhalat"
## [13] "Gran Roque. Archipielago Los Roques"
## [14] "East of Kangokuiwa, Io-sima"
## [15] "Flora Reef, Coral Sea"
##
## $habitat
## [1] "Forereef : SAG : Spur and Groove"
## [2] "Forereef : PAV : Pavement"
## [3] NA
## [4] "Shallow coral reef : Forereef"
## [5] "Forereef : ROB : Rock/Boulder"
## [6] "Forereef : AGR : Aggregate Reef"
## [7] "Forereef : UNK : Unknown"
## [8] "Exposed Wall"
## [9] "Forereef : MIX : Mixed Habitats"
## [10] "Forereef : RRB : Reef Rubble"
## [11] "Forereef : PPR : Pavement with Patch Reefs"
## [12] "Forereef : PSC : Pavement with Sand Channels"
## [13] "ZZZ"
## [14] "Protected Slope : AGR : Aggregate Reef"
## [15] "Forereef : SCR : Sand with Scattered Coral/Rock"# ok
dori_obis_ok <- dori_obis1 %>%
filter(!flags %in% c("no_depth,on_land", "on_land", "on_land,depth_exceeds_bath", "depth_exceeds_bath,on_land"),
!is.na(datasetName),
!waterBody %in% c("North America", "North America Atlantic", "atlantique", NA)) Podemos usar um mapa para verificar melhor as ocorrências também.
# check
ggplot() +
geom_polygon(data = world, aes(x = long, y = lat, group = group)) +
coord_fixed() +
theme_classic() +
geom_point(data = dori_obis_ok, aes(x = decimalLongitude, y = decimalLatitude, color = waterBody)) +
labs(x = "longitude", y = "latitude", title = expression(italic("Paracanthurus hepatus")))
Parece tudo ok, e chegamos a 146 ocorrências potenciais.
Por fim, vamos unir todas as ocorrências, checar se existem duplicatas e plotar o resultado final.
# unir GBIF e OBIS
# ver diferencas
setdiff(names(dori_gbif_ok), names(dori_obis_ok))## [1] "acceptedScientificName" "issues"setdiff(names(dori_obis_ok), names(dori_gbif_ok))## [1] "bathymetry" "flags"all_data <- bind_rows(dori_gbif_ok %>%
mutate(repo = paste0("gbif", row.names(.))),
dori_obis_ok %>%
mutate(repo = paste0("obis", row.names(.)))) %>%
column_to_rownames("repo") %>%
dplyr::select(decimalLongitude, decimalLatitude, depth) %>%
distinct() %>%
rownames_to_column("occ") %>%
separate(col = "occ", into = c("datasetName", "rn"), sep = 4) %>%
mutate(scientificName = "Paracanthurus hepatus") %>%
dplyr::select(-rn)
# mapear ocorrencias
ggplot() +
geom_polygon(data = world, aes(x = long, y = lat, group = group)) +
coord_fixed() +
theme_classic() +
geom_point(data = all_data, aes(x = decimalLongitude, y = decimalLatitude, color = datasetName)) +
#theme(legend.title = element_blank()) +
labs(x = "longitude", y = "latitude", title = expression(italic("Paracanthurus hepatus")))
O último passo é guardarmos os dados baixados e tratados para economizar tempo no próximo uso, mas o mais importante já está registrado, o passo-a-passo de como chegamos até os dados usados nas análises.
write.csv(all_data, "data/occ_GBIF-OBIS_par_hepa.csv", row.names = FALSE)3.3.2 EXTRA: Classificação automática de pontos
3.3.2.1 Função ‘caseira’
Podemos usar outras ferramentas mais refinadas para nos ajudar a
detectar ocorrências suspeitas, como as encontradas nos pacotes
CoordinateCleaner, obistools,
scrubr e biogeo. Além disso, podemos criar
nossas próprias funções para auxiliar nessa tarefa.
Abaixo, vamos utilizar os dados baixados do GBIF antes
da limpeza já realizada acima. Aqui vou começar a exemplificar com uma
função simples criada por mim. Esta função utiliza as coordenadas para
calcular o centróide (ponto médio de todas as ocorrências) e, a partir
dele, a distância de cada ponto até o centróide. Esse princípio se
baseia em propriedades de conectividade de populações contíguas, então
quanto mais distantes (neste caso as muito distantes) maior a chance de
termos uma ocorrência suspeita da mesma espécie. Atenção: isso é
apenas uma ferramenta para classificar as ocorrências! A decisão de
filtrar ou não os pontos suspeitos vai depender do seu conhecimento ou
da literatura a respeito dos habitats e regiões de ocorrência da
espécie-alvo.
Inicialmente, vamos carregar a função flag_outlier. E,
em seguida, aplicaremos a função e vamos plotar um mapa para avaliar as
ocorrências com flag de outlier.
# funcao para classificar ocorrencias suspeitas
flag_outlier <- function(df, species){
# funcao para classificar ocorrencias suspeitas
# baseada no calculo do centroide de todas ocorrencias
# indica como 'check' as ocorrencias que tem distancias até o centroide
# acima do 90th quantil (default) das distancias calculadas
dados <- df %>%
dplyr::filter(scientificName == species);
dados2 <- geosphere::distVincentyEllipsoid(
dados %>%
summarise(centr_lon = median(decimalLongitude),
centr_lat = median(decimalLatitude)),
dados %>%
dplyr::select(decimalLongitude, decimalLatitude)
) %>%
bind_cols(dados) %>%
rename(dist_centroid = '...1') %>%
mutate(flag = ifelse(dist_centroid < quantile(dist_centroid, probs = 0.9), "OK",
ifelse(dist_centroid >= quantile(dist_centroid, probs = 0.90) & dist_centroid < quantile(dist_centroid, probs = 0.95), "check > Q90",
ifelse(dist_centroid >= quantile(dist_centroid, probs = 0.95), "check > Q95", "OK"))))
# mutate(flag = ifelse(dist_centroid > quantile(dist_centroid, probs = prob), "check", "OK"))
print(dados2)
}# classificar ocorrências
marcados <- dori_gbif$data %>%
data.frame() %>%
dplyr::select(scientificName, decimalLongitude, decimalLatitude, datasetName) %>%
distinct() %>%
flag_outlier(., "Paracanthurus hepatus (Linnaeus, 1766)")## dist_centroid scientificName decimalLongitude
## 1 3764546.3 Paracanthurus hepatus (Linnaeus, 1766) 153.26693
## 2 3601973.3 Paracanthurus hepatus (Linnaeus, 1766) 153.46261
## 3 196707.8 Paracanthurus hepatus (Linnaeus, 1766) 127.31272
## 4 2309485.9 Paracanthurus hepatus (Linnaeus, 1766) 145.90000
## 5 3751926.8 Paracanthurus hepatus (Linnaeus, 1766) 153.27135
## 6 9716638.1 Paracanthurus hepatus (Linnaeus, 1766) 39.38287
## 7 6070404.8 Paracanthurus hepatus (Linnaeus, 1766) 73.61533
## 8 4547164.5 Paracanthurus hepatus (Linnaeus, 1766) 166.44180
## 9 9739402.1 Paracanthurus hepatus (Linnaeus, 1766) 39.30214
## 10 1717430.9 Paracanthurus hepatus (Linnaeus, 1766) 134.32551
## 11 624776.9 Paracanthurus hepatus (Linnaeus, 1766) 130.51253
## 12 3892731.0 Paracanthurus hepatus (Linnaeus, 1766) 151.30166
## 13 3764221.6 Paracanthurus hepatus (Linnaeus, 1766) 153.26505
## 14 3602006.4 Paracanthurus hepatus (Linnaeus, 1766) 153.56667
## 15 7916476.8 Paracanthurus hepatus (Linnaeus, 1766) 55.85906
## 16 5743098.4 Paracanthurus hepatus (Linnaeus, 1766) 179.10738
## 17 5742764.0 Paracanthurus hepatus (Linnaeus, 1766) 179.10387
## 18 3601189.7 Paracanthurus hepatus (Linnaeus, 1766) 153.50513
## 19 2940073.9 Paracanthurus hepatus (Linnaeus, 1766) 144.70608
## 20 2940224.8 Paracanthurus hepatus (Linnaeus, 1766) 144.70552
## 21 1556778.3 Paracanthurus hepatus (Linnaeus, 1766) 118.86434
## 22 1531331.1 Paracanthurus hepatus (Linnaeus, 1766) 118.63332
## 23 389994.0 Paracanthurus hepatus (Linnaeus, 1766) 123.89485
## 24 2419012.0 Paracanthurus hepatus (Linnaeus, 1766) 105.66692
## 25 2162534.9 Paracanthurus hepatus (Linnaeus, 1766) 145.40000
## 26 5541886.9 Paracanthurus hepatus (Linnaeus, 1766) 177.13443
## 27 3601949.5 Paracanthurus hepatus (Linnaeus, 1766) 153.46261
## 28 390896.1 Paracanthurus hepatus (Linnaeus, 1766) 123.88753
## 29 9715902.6 Paracanthurus hepatus (Linnaeus, 1766) 39.38888
## 30 9716512.1 Paracanthurus hepatus (Linnaeus, 1766) 39.38350
## 31 191486.9 Paracanthurus hepatus (Linnaeus, 1766) 125.92338
## 32 956989.9 Paracanthurus hepatus (Linnaeus, 1766) 125.15346
## 33 3331044.5 Paracanthurus hepatus (Linnaeus, 1766) 152.70885
## 34 3331105.4 Paracanthurus hepatus (Linnaeus, 1766) 152.70963
## 35 390159.1 Paracanthurus hepatus (Linnaeus, 1766) 123.89355
## 36 4645651.4 Paracanthurus hepatus (Linnaeus, 1766) 167.40760
## 37 7645179.0 Paracanthurus hepatus (Linnaeus, 1766) 57.62582
## 38 5743207.1 Paracanthurus hepatus (Linnaeus, 1766) 179.10844
## 39 5739820.7 Paracanthurus hepatus (Linnaeus, 1766) 179.07802
## 40 3722203.3 Paracanthurus hepatus (Linnaeus, 1766) 153.36404
## 41 769671.7 Paracanthurus hepatus (Linnaeus, 1766) 130.68908
## 42 3684958.8 Paracanthurus hepatus (Linnaeus, 1766) 153.62837
## 43 9732639.1 Paracanthurus hepatus (Linnaeus, 1766) 39.36794
## 44 2597901.7 Paracanthurus hepatus (Linnaeus, 1766) 148.44080
## 45 3548431.6 Paracanthurus hepatus (Linnaeus, 1766) 122.00093
## 46 6126904.2 Paracanthurus hepatus (Linnaeus, 1766) 72.97009
## 47 7918526.6 Paracanthurus hepatus (Linnaeus, 1766) 55.83400
## 48 9718332.7 Paracanthurus hepatus (Linnaeus, 1766) 39.30729
## 49 3236808.3 Paracanthurus hepatus (Linnaeus, 1766) 121.58082
## 50 3856755.0 Paracanthurus hepatus (Linnaeus, 1766) 129.29053
## 51 3508772.5 Paracanthurus hepatus (Linnaeus, 1766) 114.16936
## 52 2193571.2 Paracanthurus hepatus (Linnaeus, 1766) 145.66355
## 53 2559674.7 Paracanthurus hepatus (Linnaeus, 1766) 147.69919
## 54 1255702.0 Paracanthurus hepatus (Linnaeus, 1766) 116.06586
## 55 1995932.1 Paracanthurus hepatus (Linnaeus, 1766) 144.10688
## 56 3331543.3 Paracanthurus hepatus (Linnaeus, 1766) 152.71469
## 57 3304062.8 Paracanthurus hepatus (Linnaeus, 1766) 121.50087
## 58 3768423.7 Paracanthurus hepatus (Linnaeus, 1766) 128.53389
## 59 3304251.4 Paracanthurus hepatus (Linnaeus, 1766) 121.49028
## 60 257046.1 Paracanthurus hepatus (Linnaeus, 1766) 125.89175
## 61 7896746.8 Paracanthurus hepatus (Linnaeus, 1766) 55.21947
## 62 4333429.7 Paracanthurus hepatus (Linnaeus, 1766) 164.54949
## 63 3653994.3 Paracanthurus hepatus (Linnaeus, 1766) 153.57911
## 64 3631442.2 Paracanthurus hepatus (Linnaeus, 1766) 127.40389
## 65 604299.9 Paracanthurus hepatus (Linnaeus, 1766) 130.55572
## 66 1318724.8 Paracanthurus hepatus (Linnaeus, 1766) 115.54442
## 67 608621.9 Paracanthurus hepatus (Linnaeus, 1766) 130.56772
## 68 3764307.1 Paracanthurus hepatus (Linnaeus, 1766) 153.26482
## 69 3330900.2 Paracanthurus hepatus (Linnaeus, 1766) 152.70748
## 70 3130448.4 Paracanthurus hepatus (Linnaeus, 1766) 145.57996
## 71 9716665.4 Paracanthurus hepatus (Linnaeus, 1766) 39.38253
## 72 3766622.7 Paracanthurus hepatus (Linnaeus, 1766) 128.52111
## 73 9707268.4 Paracanthurus hepatus (Linnaeus, 1766) 39.46530
## 74 3684987.0 Paracanthurus hepatus (Linnaeus, 1766) 153.62856
## 75 3331096.0 Paracanthurus hepatus (Linnaeus, 1766) 152.70794
## 76 5743478.4 Paracanthurus hepatus (Linnaeus, 1766) 179.11049
## 77 5743421.7 Paracanthurus hepatus (Linnaeus, 1766) 179.10984
## 78 2418722.0 Paracanthurus hepatus (Linnaeus, 1766) 105.66871
## 79 3754679.8 Paracanthurus hepatus (Linnaeus, 1766) 153.38925
## 80 2419144.6 Paracanthurus hepatus (Linnaeus, 1766) 105.66045
## 81 882834.6 Paracanthurus hepatus (Linnaeus, 1766) 119.52971
## 82 3414324.0 Paracanthurus hepatus (Linnaeus, 1766) 158.20064
## 83 956114.3 Paracanthurus hepatus (Linnaeus, 1766) 124.73795
## 84 2336748.0 Paracanthurus hepatus (Linnaeus, 1766) 120.97290
## 85 2335715.1 Paracanthurus hepatus (Linnaeus, 1766) 120.99116
## 86 1531107.3 Paracanthurus hepatus (Linnaeus, 1766) 118.63001
## 87 3685009.9 Paracanthurus hepatus (Linnaeus, 1766) 153.62923
## 88 6289906.8 Paracanthurus hepatus (Linnaeus, 1766) -176.46176
## 89 6282171.6 Paracanthurus hepatus (Linnaeus, 1766) -176.62003
## 90 7931685.0 Paracanthurus hepatus (Linnaeus, 1766) -162.46472
## 91 2305444.8 Paracanthurus hepatus (Linnaeus, 1766) 145.99662
## 92 3760056.2 Paracanthurus hepatus (Linnaeus, 1766) 128.55778
## 93 9730618.6 Paracanthurus hepatus (Linnaeus, 1766) 39.37970
## 94 5828748.9 Paracanthurus hepatus (Linnaeus, 1766) 179.94055
## 95 1530875.1 Paracanthurus hepatus (Linnaeus, 1766) 118.62500
## 96 9982422.0 Paracanthurus hepatus (Linnaeus, 1766) 35.08851
## 97 9914279.7 Paracanthurus hepatus (Linnaeus, 1766) 35.40329
## 98 3754957.6 Paracanthurus hepatus (Linnaeus, 1766) 153.39147
## 99 7931081.5 Paracanthurus hepatus (Linnaeus, 1766) 55.72781
## 100 7915796.9 Paracanthurus hepatus (Linnaeus, 1766) 55.86531
## 101 7937238.5 Paracanthurus hepatus (Linnaeus, 1766) 55.67413
## 102 3330950.8 Paracanthurus hepatus (Linnaeus, 1766) 152.71023
## 103 763874.9 Paracanthurus hepatus (Linnaeus, 1766) 130.63281
## 104 5735364.5 Paracanthurus hepatus (Linnaeus, 1766) 178.98593
## 105 3116594.3 Paracanthurus hepatus (Linnaeus, 1766) 145.56811
## 106 3111707.2 Paracanthurus hepatus (Linnaeus, 1766) 145.53007
## 107 2928220.0 Paracanthurus hepatus (Linnaeus, 1766) 144.76383
## 108 3404005.8 Paracanthurus hepatus (Linnaeus, 1766) 145.76129
## 109 3412874.0 Paracanthurus hepatus (Linnaeus, 1766) 145.79179
## 110 3408232.9 Paracanthurus hepatus (Linnaeus, 1766) 145.75369
## 111 3025441.6 Paracanthurus hepatus (Linnaeus, 1766) 145.16840
## 112 3038848.7 Paracanthurus hepatus (Linnaeus, 1766) 145.28545
## 113 3153410.5 Paracanthurus hepatus (Linnaeus, 1766) 145.70396
## 114 3166545.0 Paracanthurus hepatus (Linnaeus, 1766) 145.79259
## 115 3127087.8 Paracanthurus hepatus (Linnaeus, 1766) 145.64574
## 116 3138354.2 Paracanthurus hepatus (Linnaeus, 1766) 145.65608
## 117 3126208.9 Paracanthurus hepatus (Linnaeus, 1766) 145.63037
## 118 3129921.4 Paracanthurus hepatus (Linnaeus, 1766) 145.58553
## 119 3896744.5 Paracanthurus hepatus (Linnaeus, 1766) 141.47400
## 120 6462261.4 Paracanthurus hepatus (Linnaeus, 1766) -174.18171
## 121 10131504.3 Paracanthurus hepatus (Linnaeus, 1766) 32.67988
## 122 6459807.8 Paracanthurus hepatus (Linnaeus, 1766) -174.20580
## 123 6462279.3 Paracanthurus hepatus (Linnaeus, 1766) -174.18214
## 124 3403207.1 Paracanthurus hepatus (Linnaeus, 1766) 145.74479
## 125 3396853.8 Paracanthurus hepatus (Linnaeus, 1766) 145.70588
## 126 3401244.2 Paracanthurus hepatus (Linnaeus, 1766) 145.72653
## 127 3146791.1 Paracanthurus hepatus (Linnaeus, 1766) 145.67886
## 128 3146567.5 Paracanthurus hepatus (Linnaeus, 1766) 145.70275
## 129 3146529.6 Paracanthurus hepatus (Linnaeus, 1766) 145.69897
## 130 3286844.3 Paracanthurus hepatus (Linnaeus, 1766) 145.77638
## 131 2631411.6 Paracanthurus hepatus (Linnaeus, 1766) 150.71890
## 132 2355981.1 Paracanthurus hepatus (Linnaeus, 1766) 120.91363
## 133 9716719.7 Paracanthurus hepatus (Linnaeus, 1766) 39.38162
## 134 6477124.1 Paracanthurus hepatus (Linnaeus, 1766) -174.07435
## 135 7888260.7 Paracanthurus hepatus (Linnaeus, 1766) 55.30145
## 136 7890544.5 Paracanthurus hepatus (Linnaeus, 1766) 55.27931
## 137 7890519.3 Paracanthurus hepatus (Linnaeus, 1766) 55.27962
## 138 7890585.6 Paracanthurus hepatus (Linnaeus, 1766) 55.27898
## 139 7897279.9 Paracanthurus hepatus (Linnaeus, 1766) 55.21433
## 140 7889171.6 Paracanthurus hepatus (Linnaeus, 1766) 55.29266
## 141 7896310.7 Paracanthurus hepatus (Linnaeus, 1766) 55.22368
## 142 608829.4 Paracanthurus hepatus (Linnaeus, 1766) 130.64465
## 143 608362.8 Paracanthurus hepatus (Linnaeus, 1766) 130.62375
## 144 390139.1 Paracanthurus hepatus (Linnaeus, 1766) 123.89358
## 145 6951391.0 Paracanthurus hepatus (Linnaeus, 1766) -169.49334
## 146 5743478.3 Paracanthurus hepatus (Linnaeus, 1766) 179.11049
## 147 5827080.1 Paracanthurus hepatus (Linnaeus, 1766) 179.92354
## 148 7870954.0 Paracanthurus hepatus (Linnaeus, 1766) 55.46860
## 149 9940195.4 Paracanthurus hepatus (Linnaeus, 1766) 35.45493
## 150 2319696.2 Paracanthurus hepatus (Linnaeus, 1766) 146.02884
## 151 4119005.5 Paracanthurus hepatus (Linnaeus, 1766) 130.15250
## 152 9716692.0 Paracanthurus hepatus (Linnaeus, 1766) 39.38400
## 153 3417205.4 Paracanthurus hepatus (Linnaeus, 1766) 152.90847
## 154 900216.5 Paracanthurus hepatus (Linnaeus, 1766) 119.35000
## 155 9936954.8 Paracanthurus hepatus (Linnaeus, 1766) 35.50786
## 156 7915403.4 Paracanthurus hepatus (Linnaeus, 1766) 55.86569
## 157 3440710.7 Paracanthurus hepatus (Linnaeus, 1766) 124.09048
## 158 5742784.2 Paracanthurus hepatus (Linnaeus, 1766) 179.10468
## 159 883655.4 Paracanthurus hepatus (Linnaeus, 1766) 119.57251
## 160 6014741.6 Paracanthurus hepatus (Linnaeus, 1766) -178.17400
## 161 6014741.6 Paracanthurus hepatus (Linnaeus, 1766) -178.17400
## 162 7843167.8 Paracanthurus hepatus (Linnaeus, 1766) 55.73661
## 163 7851516.5 Paracanthurus hepatus (Linnaeus, 1766) 55.65609
## 164 7848765.7 Paracanthurus hepatus (Linnaeus, 1766) 55.68264
## 165 3643185.9 Paracanthurus hepatus (Linnaeus, 1766) 126.78845
## 166 8414228.2 Paracanthurus hepatus (Linnaeus, 1766) -157.42781
## 167 5743618.9 Paracanthurus hepatus (Linnaeus, 1766) 179.10813
## 168 6290450.6 Paracanthurus hepatus (Linnaeus, 1766) -176.45731
## 169 6289993.8 Paracanthurus hepatus (Linnaeus, 1766) -176.46102
## 170 6286991.5 Paracanthurus hepatus (Linnaeus, 1766) -176.48886
## 171 6281804.1 Paracanthurus hepatus (Linnaeus, 1766) -176.62671
## 172 6281822.1 Paracanthurus hepatus (Linnaeus, 1766) -176.62678
## 173 5742931.3 Paracanthurus hepatus (Linnaeus, 1766) 179.10590
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## 179 6823460.4 Paracanthurus hepatus (Linnaeus, 1766) -170.67885
## 180 6837862.8 Paracanthurus hepatus (Linnaeus, 1766) -170.54548
## 181 6842217.3 Paracanthurus hepatus (Linnaeus, 1766) -170.50510
## 182 18574819.0 Paracanthurus hepatus (Linnaeus, 1766) -61.77100
## 183 7935801.1 Paracanthurus hepatus (Linnaeus, 1766) -162.42674
## 184 9941068.3 Paracanthurus hepatus (Linnaeus, 1766) 35.42359
## 185 9940945.6 Paracanthurus hepatus (Linnaeus, 1766) 35.38154
## 186 10130897.1 Paracanthurus hepatus (Linnaeus, 1766) 32.68670
## 187 3458440.4 Paracanthurus hepatus (Linnaeus, 1766) 123.79669
## 188 612084.3 Paracanthurus hepatus (Linnaeus, 1766) 132.74726
## 189 10131119.8 Paracanthurus hepatus (Linnaeus, 1766) 32.68540
## 190 2371572.2 Paracanthurus hepatus (Linnaeus, 1766) 147.10760
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## 192 876475.0 Paracanthurus hepatus (Linnaeus, 1766) 119.60195
## 193 534106.4 Paracanthurus hepatus (Linnaeus, 1766) 131.65190
## 194 539077.2 Paracanthurus hepatus (Linnaeus, 1766) 131.99690
## 195 3473488.4 Paracanthurus hepatus (Linnaeus, 1766) 122.96361
## 196 8995048.5 Paracanthurus hepatus (Linnaeus, 1766) 45.27593
## 197 16466646.3 Paracanthurus hepatus (Linnaeus, 1766) -81.18580
## 198 9731148.6 Paracanthurus hepatus (Linnaeus, 1766) 39.37488
## 199 7895223.8 Paracanthurus hepatus (Linnaeus, 1766) 55.23410
## 200 7895228.9 Paracanthurus hepatus (Linnaeus, 1766) 55.23405
## 201 1690289.5 Paracanthurus hepatus (Linnaeus, 1766) 134.21884
## 202 1704929.7 Paracanthurus hepatus (Linnaeus, 1766) 134.22094
## 203 10131104.9 Paracanthurus hepatus (Linnaeus, 1766) 32.68600
## 204 10131011.1 Paracanthurus hepatus (Linnaeus, 1766) 32.68732
## 205 7896780.3 Paracanthurus hepatus (Linnaeus, 1766) 55.21915
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## 207 7915460.1 Paracanthurus hepatus (Linnaeus, 1766) 55.86796
## 208 3114655.0 Paracanthurus hepatus (Linnaeus, 1766) 145.56591
## 209 3412420.9 Paracanthurus hepatus (Linnaeus, 1766) 145.81155
## 210 3039734.6 Paracanthurus hepatus (Linnaeus, 1766) 145.26090
## 211 3165598.8 Paracanthurus hepatus (Linnaeus, 1766) 145.78511
## 212 3167994.6 Paracanthurus hepatus (Linnaeus, 1766) 145.82889
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## 225 16404254.6 Paracanthurus hepatus (Linnaeus, 1766) -80.00000
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## 227 16342259.4 Paracanthurus hepatus (Linnaeus, 1766) -81.85830
## 228 1257305.2 Paracanthurus hepatus (Linnaeus, 1766) 116.05110
## 229 3293967.2 Paracanthurus hepatus (Linnaeus, 1766) 152.43017
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## 246 3764241.1 Paracanthurus hepatus (Linnaeus, 1766) 153.26580
## 247 6134070.7 Paracanthurus hepatus (Linnaeus, 1766) 73.45000
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## 249 17764755.2 Paracanthurus hepatus (Linnaeus, 1766) -69.69920
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## 62 <NA>
## 63 iNaturalist research-grade observations
## 64 iNaturalist research-grade observations
## 65 iNaturalist research-grade observations
## 66 iNaturalist research-grade observations
## 67 iNaturalist research-grade observations
## 68 iNaturalist research-grade observations
## 69 iNaturalist research-grade observations
## 70 iNaturalist research-grade observations
## 71 iNaturalist research-grade observations
## 72 <NA>
## 73 iNaturalist research-grade observations
## 74 iNaturalist research-grade observations
## 75 iNaturalist research-grade observations
## 76 iNaturalist research-grade observations
## 77 iNaturalist research-grade observations
## 78 iNaturalist research-grade observations
## 79 iNaturalist research-grade observations
## 80 iNaturalist research-grade observations
## 81 iNaturalist research-grade observations
## 82 iNaturalist research-grade observations
## 83 iNaturalist research-grade observations
## 84 iNaturalist research-grade observations
## 85 iNaturalist research-grade observations
## 86 iNaturalist research-grade observations
## 87 iNaturalist research-grade observations
## 88 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 89 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 90 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 91 iNaturalist research-grade observations
## 92 <NA>
## 93 iNaturalist research-grade observations
## 94 iNaturalist research-grade observations
## 95 Diveboard - Scuba diving citizen science
## 96 Instituto Nacional de Investigação Pesqueira
## 97 Instituto Nacional de Investigação Pesqueira
## 98 iNaturalist research-grade observations
## 99 <NA>
## 100 iNaturalist research-grade observations
## 101 iNaturalist research-grade observations
## 102 iNaturalist research-grade observations
## 103 iNaturalist research-grade observations
## 104 iNaturalist research-grade observations
## 105 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 106 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 107 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 108 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 109 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 110 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 111 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 112 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 113 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 114 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 115 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 116 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 117 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 118 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 119 <NA>
## 120 Tonga Reef survey data 2016-2018
## 121 iNaturalist research-grade observations
## 122 Tonga Reef survey data 2016-2018
## 123 Tonga Reef survey data 2016-2018
## 124 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 125 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 126 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 127 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 128 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 129 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 130 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 131 iNaturalist research-grade observations
## 132 iNaturalist research-grade observations
## 133 iNaturalist research-grade observations
## 134 Tonga Reef survey data 2016-2018
## 135 <NA>
## 136 <NA>
## 137 <NA>
## 138 <NA>
## 139 <NA>
## 140 <NA>
## 141 <NA>
## 142 iNaturalist research-grade observations
## 143 iNaturalist research-grade observations
## 144 iNaturalist research-grade observations
## 145 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 146 iNaturalist research-grade observations
## 147 iNaturalist research-grade observations
## 148 <NA>
## 149 Instituto Nacional de Investigação Pesqueira
## 150 iNaturalist research-grade observations
## 151 <NA>
## 152 iNaturalist research-grade observations
## 153 <NA>
## 154 Diveboard - Scuba diving citizen science
## 155 Instituto Nacional de Investigação Pesqueira
## 156 iNaturalist research-grade observations
## 157 iNaturalist research-grade observations
## 158 iNaturalist research-grade observations
## 159 iNaturalist research-grade observations
## 160 NMNH Material Samples (USNM)
## 161 NMNH Extant Biology
## 162 <NA>
## 163 <NA>
## 164 <NA>
## 165 iNaturalist research-grade observations
## 166 iNaturalist research-grade observations
## 167 iNaturalist research-grade observations
## 168 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 169 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 170 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 171 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 172 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 173 iNaturalist research-grade observations
## 174 iNaturalist research-grade observations
## 175 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 176 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 177 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 178 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 179 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 180 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 181 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 182 Diveboard - Scuba diving citizen science
## 183 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 184 Instituto Nacional de Investigação Pesqueira
## 185 Instituto Nacional de Investigação Pesqueira
## 186 <NA>
## 187 iNaturalist research-grade observations
## 188 iNaturalist research-grade observations
## 189 <NA>
## 190 <NA>
## 191 iNaturalist research-grade observations
## 192 iNaturalist research-grade observations
## 193 <NA>
## 194 <NA>
## 195 <NA>
## 196 <NA>
## 197 Diveboard - Scuba diving citizen science
## 198 iNaturalist research-grade observations
## 199 <NA>
## 200 <NA>
## 201 iNaturalist research-grade observations
## 202 iNaturalist research-grade observations
## 203 <NA>
## 204 <NA>
## 205 <NA>
## 206 iNaturalist research-grade observations
## 207 iNaturalist research-grade observations
## 208 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 209 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 210 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 211 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 212 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 213 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 214 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 215 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 216 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 217 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 218 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 219 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 220 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 221 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 222 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 223 iNaturalist research-grade observations
## 224 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 225 Diveboard - Scuba diving citizen science
## 226 iNaturalist research-grade observations
## 227 Diveboard - Scuba diving citizen science
## 228 iNaturalist research-grade observations
## 229 <NA>
## 230 <NA>
## 231 <NA>
## 232 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 233 iNaturalist research-grade observations
## 234 iNaturalist research-grade observations
## 235 iNaturalist research-grade observations
## 236 Diveboard - Scuba diving citizen science
## 237 <NA>
## 238 <NA>
## 239 <NA>
## 240 <NA>
## 241 iNaturalist research-grade observations
## 242 iNaturalist research-grade observations
## 243 <NA>
## 244 <NA>
## 245 <NA>
## 246 <NA>
## 247 iNaturalist research-grade observations
## 248 <NA>
## 249 Diveboard - Scuba diving citizen science
## 250 <NA>
## 251 <NA>
## 252 <NA>
## 253 <NA>
## 254 <NA>
## 255 NMNH Material Samples (USNM)
## 256 NMNH Extant Biology
## 257 iNaturalist research-grade observations
## 258 <NA>
## 259 <NA>
## 260 Diveboard - Scuba diving citizen science
## 261 Diveboard - Scuba diving citizen science
## 262 <NA>
## 263 <NA>
## 264 <NA>
## 265 iNaturalist research-grade observations
## 266 iNaturalist research-grade observations
## 267 iNaturalist research-grade observations
## 268 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 269 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 270 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 271 Diveboard - Scuba diving citizen science
## 272 Diveboard - Scuba diving citizen science
## 273 Diveboard - Scuba diving citizen science
## 274 Diveboard - Scuba diving citizen science
## 275 Diveboard - Scuba diving citizen science
## 276 Diveboard - Scuba diving citizen science
## 277 <NA>
## 278 iNaturalist research-grade observations
## 279 Diveboard - Scuba diving citizen science
## 280 iNaturalist research-grade observations
## 281 Diveboard - Scuba diving citizen science
## 282 <NA>
## 283 <NA>
## 284 iNaturalist research-grade observations
## 285 iNaturalist research-grade observations
## 286 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 287 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 288 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 289 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 290 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 291 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 292 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 293 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 294 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 295 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 296 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 297 Diveboard - Scuba diving citizen science
## 298 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 299 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 300 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 301 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 302 <NA>
## 303 <NA>
## 304 <NA>
## 305 Diveboard - Scuba diving citizen science
## 306 <NA>
## 307 <NA>
## 308 <NA>
## 309 <NA>
## 310 Instituto Nacional de Investigação Pesqueira
## 311 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 312 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 313 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## 314 <NA>
## 315 <NA>
## 316 <NA>
## 317 <NA>
## 318 <NA>
## 319 <NA>
## 320 Diveboard - Scuba diving citizen science
## 321 <NA>
## 322 <NA>
## 323 iNaturalist research-grade observations
## 324 iNaturalist research-grade observations
## 325 iNaturalist research-grade observations
## 326 iNaturalist research-grade observations
## 327 Diveboard - Scuba diving citizen science
## 328 Diveboard - Scuba diving citizen science
## 329 <NA>
## 330 <NA>
## 331 iNaturalist research-grade observations
## 332 NOAA Pacific Islands Fisheries Science Center, Ecosystem Science Division Coral Reef Ecosystem Program, Rapid Ecological Assessments of Fish Belt Transect Surveys (BLT) at Coral Reef Sites across the Pacific Ocean from 2000 to 2009
## 333 NOAA Pacific Islands Fisheries Science Center, Ecosystem Sciences Division, National Coral Reef Monitoring Program: Stratified random surveys (StRS) of reef fish in the U.S. Pacific Islands
## flag
## 1 OK
## 2 OK
## 3 OK
## 4 OK
## 5 OK
## 6 OK
## 7 OK
## 8 OK
## 9 check > Q90
## 10 OK
## 11 OK
## 12 OK
## 13 OK
## 14 OK
## 15 OK
## 16 OK
## 17 OK
## 18 OK
## 19 OK
## 20 OK
## 21 OK
## 22 OK
## 23 OK
## 24 OK
## 25 OK
## 26 OK
## 27 OK
## 28 OK
## 29 OK
## 30 OK
## 31 OK
## 32 OK
## 33 OK
## 34 OK
## 35 OK
## 36 OK
## 37 OK
## 38 OK
## 39 OK
## 40 OK
## 41 OK
## 42 OK
## 43 OK
## 44 OK
## 45 OK
## 46 OK
## 47 OK
## 48 OK
## 49 OK
## 50 OK
## 51 OK
## 52 OK
## 53 OK
## 54 OK
## 55 OK
## 56 OK
## 57 OK
## 58 OK
## 59 OK
## 60 OK
## 61 OK
## 62 OK
## 63 OK
## 64 OK
## 65 OK
## 66 OK
## 67 OK
## 68 OK
## 69 OK
## 70 OK
## 71 OK
## 72 OK
## 73 OK
## 74 OK
## 75 OK
## 76 OK
## 77 OK
## 78 OK
## 79 OK
## 80 OK
## 81 OK
## 82 OK
## 83 OK
## 84 OK
## 85 OK
## 86 OK
## 87 OK
## 88 OK
## 89 OK
## 90 OK
## 91 OK
## 92 OK
## 93 OK
## 94 OK
## 95 OK
## 96 check > Q90
## 97 check > Q90
## 98 OK
## 99 OK
## 100 OK
## 101 OK
## 102 OK
## 103 OK
## 104 OK
## 105 OK
## 106 OK
## 107 OK
## 108 OK
## 109 OK
## 110 OK
## 111 OK
## 112 OK
## 113 OK
## 114 OK
## 115 OK
## 116 OK
## 117 OK
## 118 OK
## 119 OK
## 120 OK
## 121 check > Q95
## 122 OK
## 123 OK
## 124 OK
## 125 OK
## 126 OK
## 127 OK
## 128 OK
## 129 OK
## 130 OK
## 131 OK
## 132 OK
## 133 OK
## 134 OK
## 135 OK
## 136 OK
## 137 OK
## 138 OK
## 139 OK
## 140 OK
## 141 OK
## 142 OK
## 143 OK
## 144 OK
## 145 OK
## 146 OK
## 147 OK
## 148 OK
## 149 check > Q90
## 150 OK
## 151 OK
## 152 OK
## 153 OK
## 154 OK
## 155 check > Q90
## 156 OK
## 157 OK
## 158 OK
## 159 OK
## 160 OK
## 161 OK
## 162 OK
## 163 OK
## 164 OK
## 165 OK
## 166 OK
## 167 OK
## 168 OK
## 169 OK
## 170 OK
## 171 OK
## 172 OK
## 173 OK
## 174 OK
## 175 OK
## 176 OK
## 177 OK
## 178 OK
## 179 OK
## 180 OK
## 181 OK
## 182 check > Q95
## 183 OK
## 184 check > Q90
## 185 check > Q90
## 186 check > Q90
## 187 OK
## 188 OK
## 189 check > Q90
## 190 OK
## 191 OK
## 192 OK
## 193 OK
## 194 OK
## 195 OK
## 196 OK
## 197 check > Q95
## 198 OK
## 199 OK
## 200 OK
## 201 OK
## 202 OK
## 203 check > Q90
## 204 check > Q90
## 205 OK
## 206 OK
## 207 OK
## 208 OK
## 209 OK
## 210 OK
## 211 OK
## 212 OK
## 213 OK
## 214 OK
## 215 OK
## 216 OK
## 217 OK
## 218 OK
## 219 OK
## 220 OK
## 221 OK
## 222 OK
## 223 OK
## 224 OK
## 225 check > Q95
## 226 OK
## 227 check > Q95
## 228 OK
## 229 OK
## 230 OK
## 231 OK
## 232 OK
## 233 OK
## 234 OK
## 235 OK
## 236 OK
## 237 OK
## 238 OK
## 239 OK
## 240 OK
## 241 check > Q90
## 242 check > Q95
## 243 check > Q90
## 244 OK
## 245 OK
## 246 OK
## 247 OK
## 248 OK
## 249 check > Q95
## 250 OK
## 251 OK
## 252 OK
## 253 OK
## 254 OK
## 255 OK
## 256 OK
## 257 OK
## 258 OK
## 259 OK
## 260 check > Q95
## 261 check > Q95
## 262 OK
## 263 OK
## 264 OK
## 265 OK
## 266 OK
## 267 OK
## 268 OK
## 269 OK
## 270 OK
## 271 check > Q95
## 272 OK
## 273 check > Q90
## 274 OK
## 275 OK
## 276 check > Q95
## 277 OK
## 278 OK
## 279 OK
## 280 OK
## 281 check > Q95
## 282 check > Q90
## 283 check > Q90
## 284 OK
## 285 OK
## 286 OK
## 287 OK
## 288 OK
## 289 OK
## 290 OK
## 291 OK
## 292 OK
## 293 OK
## 294 OK
## 295 OK
## 296 OK
## 297 check > Q95
## 298 OK
## 299 OK
## 300 OK
## 301 OK
## 302 OK
## 303 OK
## 304 OK
## 305 check > Q95
## 306 OK
## 307 OK
## 308 OK
## 309 OK
## 310 check > Q90
## 311 OK
## 312 OK
## 313 OK
## 314 OK
## 315 OK
## 316 OK
## 317 OK
## 318 OK
## 319 OK
## 320 check > Q95
## 321 OK
## 322 OK
## 323 OK
## 324 OK
## 325 OK
## 326 OK
## 327 check > Q95
## 328 check > Q95
## 329 OK
## 330 OK
## 331 OK
## 332 OK
## 333 OK# mapa
ggplot() +
geom_polygon(data = world, aes(x = long, y = lat, group = group)) +
coord_fixed() +
theme_classic() +
geom_point(data = marcados,
aes(x = decimalLongitude, y = decimalLatitude,
color = flag)) +
theme(legend.title = element_blank()) +
labs(x = "longitude", y = "latitude",
title = expression(italic("Paracanthurus hepatus")))
Podemos notar no mapa acima que as ocorrencias acima do 90ésimo
quantil são muito similares às já filtradas acima com base no
waterBody, mas se já não tivéssemos a informação da
ocorrência restrita da espécie ao Indo-Pacífico, já poderíamos
desconfiar destas ocorrências tão longe, os outliers.
Investigando o datasetName destas ocorrências com flags também
chegaríamos a mesma conclusão de excluir os dados associados ao
Diveboard - Scuba diving citizen science e sem valor de
datasetName.
3.3.2.2 pacote
obistools
Vale lembrar que o OBIS é um repositório de dados
marinhos, então as ferramentas tem melhor uso para dados desta natureza.
Inclusive uma das funções do pacote (check_onland) checa
coordenadas em terra, sejam ilhas ou continentes. Aqui vamos testar a
função check_outliers_species que tem um princípio
semelhante à nossa função caseira flag_outliers, mas é
baseada no median absolute deviation (MAD) e no
interquartile range (IQR), parâmetros que podem ser
ajustados na função. OBS: Algumas vezes pode ocorrer uma falha de
conexão com o servidor, então deve-se insistir um pouco.
Um pequeno detalhe. Muitas vezes os pacotes não são atualizados na
mesma velocidade que o R e acabam ficando incompatíveis, ou os pacotes
não são enviados ao CRAN e, usando a função
install.packages o pacote não é encontrado. Quando isso
acontece, podemos ir direto no repositório do pacote. Basta dar uma
pesquisada do Google como “nome do pacote e from source”. Abaixo segue o
exemplo de como instalar direto da fonte usando o pacote
devtools.
install.packages(“devtools”)
devtools::install_github(“iobis/obistools”)
library(obistools)
# dori_obis %>%
# dplyr::select(decimalLongitude, decimalLatitude, scientificNameID) %>%
# distinct() %>%
# check_outliers_species(., report=TRUE)
# usando essa configuração chegamos a valores próximos aos da limpeza manual
dori_obis %>%
dplyr::select(decimalLongitude, decimalLatitude, scientificNameID) %>%
distinct() %>%
check_outliers_dataset(., report = FALSE, iqr_coef = 1, mad_coef = 5) %>%
dim()## [1] 28 3Em seguida, verificamos os outliers.
ggplot() +
geom_polygon(data = world, aes(x = long, y = lat, group = group)) +
coord_fixed() +
theme_classic() +
geom_point(data = marcados %>%
filter(flag != "OK"),
aes(x = decimalLongitude, y = decimalLatitude,
color = datasetName)) +
theme(legend.title = element_blank()) +
labs(x = "longitude", y = "latitude",
title = expression(italic("Paracanthurus hepatus")))
Por fim, vamos testar o pacote CoordinateCleaner. Nele
devemos especificar os campos correspondentes na função
clean_coordinates.
flags <-
clean_coordinates(
x = marcados,
lon = "decimalLongitude",
lat = "decimalLatitude",
species = "scientificName",
tests = c("equal", "gbif",
"zeros", "seas")
)Neste caso, nenhuma ocorrência foi marcada como suspeita. Moral da história, sempre temos que conferir todos os dados, mas as ferramentas ajudam muito nesta tarefa! ***
Colabore, compartilhe, e cite as fontes!