Package robis. July 2, 2018

Transcription

1 Package robis July 2, 2018 Title Ocean Biogeographic Information System (OBIS) Client Client for the Ocean Biogeographic Information System (< Includes functions for each of the API methods, including searching for occurrences, creating a checklist, searching for datasets and for visualizing the results. Version Date URL BugReports Depends R (>= 3.1.3) Imports httr, dplyr, jsonlite, leaflet License MIT + file LICENSE Suggests testthat RoxygenNote NeedsCompilation no Author Pieter Provoost [aut], Samuel Bosch [cre, aut], Ward Appeltans [ctb], OBIS [cph] Maintainer Samuel Bosch <mail@samuelbosch.com> Repository CRAN Date/Publication :00:03 UTC R topics documented: area checklist dataset dataset_by_id group leafletmap

2 2 checklist node occurrence qc qcflags robis taxon taxon_common Index 14 area Fetch areas. Fetch areas. area( = FALSE) The areas. occurrence checklist node group dataset taxon checklist Generate checklists. Generate checklists. checklist(scientificname = NULL, year = NULL, obisid = NULL, aphiaid = NULL, groupid = NULL, resourceid = NULL, areaid = NULL, startdate = NULL, enddate = NULL, startdepth = NULL, enddepth = NULL, geometry = NULL, qc = NULL, fields = NULL, = FALSE)

3 checklist 3 scientificname character vector. The full scientific name, with authorship and date information if known. year obisid aphiaid integer vector. The year in which the Event occurred. integer vector. The OBIS identifier of the species. integer vector. The WoRMS identifier of the species. groupid integer. The taxonomic group id. See also group for the list of taxonomic groups. resourceid areaid startdate enddate startdepth enddepth geometry qc fields integer vector. The dataset identifier. See also dataset for querying the list of datasets. integer vector. The OBIS area identifier (country, marine world heritage site, ABNJ, EBSA,...). See also area for the list of areas. The earliest date on which the Event occurred. The latest date on which the Event occurred. The minimum depth below the sea surface. The maximum depth below the sea surface. A wkt geometry string. A vector of quality control flags you want to filter on. List of QC flags. A vector of field names you want to have returned in order, by default all fields with values are returned. The checklist. occurrence dataset area Examples taxa <- checklist(scientificname = c("pterois volitans", "Voluta musica")) taxa <- checklist(aphiaid = , year = 2000:2002, fields = c("species", "records"))

4 4 dataset dataset Fetch dataset metadata. dataset returns dataset metadata based on the id or some query parameters. dataset(id = NULL, scientificname = NULL, q = NULL, obisid = NULL, aphiaid = NULL, groupid = NULL, areaid = NULL, nodeid = NULL, startdate = NULL, enddate = NULL, startdepth = NULL, enddepth = NULL, geometry = NULL, = FALSE) id integer vector. One or more dataset ids, if provided all the other query parameters will be ignored. scientificname character vector. The full scientific name, with authorship and date information if known. q obisid aphiaid character. The search string. integer vector. The OBIS identifier of the species. integer vector. The WoRMS identifier of the species. groupid integer. The taxonomic group id. See also group for the list of taxonomic groups. areaid nodeid startdate enddate startdepth enddepth geometry The dataset metadata records. Examples integer vector. The OBIS area identifier (country, marine world heritage site, ABNJ, EBSA,...). See also area for the list areas. integer vector. The OBIS node identifier. See also node for the list of nodes. The earliest date on which the Event occurred. The latest date on which the Event occurred. The minimum depth below the sea surface. The maximum depth below the sea surface. A wkt geometry string. datasets <- dataset(id = 1) datasets <- dataset(q = "MICROBIS") datasets <- dataset(nodeid = c(0,1))

5 dataset_by_id 5 dataset_by_id Fetch dataset metadata by id. dataset_by_id is an internal method for fetching dataset metadata based on the internal identifier. dataset_by_id(id, = FALSE) id numeric. One or more dataset ids. The dataset metadata records. group Fetch taxonomic groups Fetch taxonomic groups group( = FALSE) The taxonomic groups. occurrence checklist node area dataset taxon

6 6 node leafletmap Create a Leaflet map. Create a Leaflet map. leafletmap(data, popup = NULL) data popup occurrence records you want to map, minimal required fields are decimallongitude and decimallatitude. Column to be used for popups. HTML widget object. occurrence node Fetch nodes Fetch nodes node( = FALSE) The nodes. occurrence checklist group area dataset taxon

7 occurrence 7 occurrence Find occurrences. Find occurrences. occurrence(scientificname = NULL, year = NULL, obisid = NULL, aphiaid = NULL, groupid = NULL, resourceid = NULL, nodeid = NULL, areaid = NULL, startdate = NULL, enddate = NULL, startdepth = NULL, enddepth = NULL, geometry = NULL, qc = NULL, fields = NULL, = FALSE) scientificname character vector. The full scientific name, with authorship and date information if known. year obisid aphiaid integer vector. The year in which the Event occurred. integer vector. The OBIS identifier of the species. integer vector. The WoRMS identifier of the species. groupid integer. The taxonomic group id. See also group for the list of taxonomic groups. resourceid nodeid areaid startdate enddate startdepth enddepth geometry qc fields The occurrence records. integer vector. The dataset identifier. See also dataset for querying the list of datasets. integer vector. The OBIS node identifier. See also node for the list of nodes. integer vector. The OBIS area identifier (country, marine world heritage site, ABNJ, EBSA,...). See also area for the list of areas. The earliest date on which the Event occurred. The latest date on which the Event occurred. The minimum depth below the sea surface. The maximum depth below the sea surface. A wkt geometry string. A vector of quality control flags you want to filter on. List of QC flags. A vector of field names you want to have returned in order, by default all fields with values are returned.

8 8 qc leafletmap qcflags checklist dataset area node group Examples records <- occurrence(scientificname = "Abra sibogai") records <- occurrence(aphiaid = , startdate = as.date(" ")) records <- occurrence(aphiaid = , geometry = "POLYGON ((0 0, 0 45, 45 45, 45 0, 0 0))") records <- occurrence(scientificname = "Abra sibogai", qc = c(1:6, 27)) records <- occurrence(scientificname = "Abra sibogai", fields = c("species", "decimallongitude", "decimallatitude")) qc Quality control flags Details Quality control flags At the moment there are 29 QC flags, numbered from 1 to 30 with disabled flag (qc 8, 9 and 20). 1. OBIS data format: are the required fields from the OBIS Schema completed? 2. Taxonomy: is the taxon name matched to WoRMS? 3. Taxonomy: is the taxon level genus or lower? 4. Geography (lat/lon): are the latitude/longitude values different from zero? 5. Geography (lat/lon): are the latitude/longitude values within their possible boundaries? (world coordinates) 6. Geography (lat/lon): are the coordinates situated in sea or along the coastline (20 km buffer)? 7. Completeness (date/time): is the sampling year (start/end) completed and valid? 10. OBIS data format: is the Basis of Record documented, and is an existing OBIS code used? 11. Completeness (date/time): is the sampling date (year/month/day; start/end) valid? 12. Completeness (date/time): if a start and end date are given, is the start before the end? 13. Completeness (date/time): if a sampling time is given, is this valid and is the time zone completed? 14. Completeness (presence/abundance/biomass): is the value of the field ObservedIndividualCount empty or >0? 15. Completeness (presence/abundance/biomass): is the value of the field Observedweight empty or >0? 16. Completeness (presence/abundance/biomass): is the field SampleSize completed if the field ObservedIndividualCount is >0?

9 qcflags 9 References 17. OBIS data format: is the value of the field Sex empty or is an existing OBIS code used? 18. Geography (depth): is minimum depth <= maximum depth? 19. Geography (depth): is the sampling depth possible when compared with GEBCO depth map (incl. margin)? 21. Species outliers (environment/depth): is the observation within six MADs from the median depth of this taxon? 22. Species outliers (environment/depth): is the observation within three IQRs from the first & third quartile depth of this taxon? 23. Species outliers (environment/sss): is the observation within six MADs from the median sea surface salinity (SSS) of this taxon? 24. Species outliers (environment/sss): is the observation within three IQRs from the first & third quartile sea surface salinity (SSS) of this taxon? 25. Species outliers (environment/sst): is the observation within six MADs from the median sea surface temperature (SST) of this taxon? 26. Species outliers (environment/sst): is the observation within three IQRs from the first & third quartile sea surface temperature (SST) of this taxon? 27. Species outliers (geography): is the observation within six MADs from the distance to the geographic centroid of this taxon? 28. Species outliers (geography): is the observation within three IQRs from the first & third quartile distance to the geographic centroid of this taxon? 29. Dataset outliers (geography): is the observation within six MADs from the distance to the geographic centroid of this dataset? 30. Dataset outliers (geography): is the observation within three IQRs from the first & third quartile distance to the geographic centroid of this dataset? Vandepitte, L., Bosch, S., Tyberghein, L., Waumans, F., Vanhoorne, B., Hernandez, F.,??? Mees, J. (2015). Fishing for data and sorting the catch: assessing the data quality, completeness and fitness for use of data in marine biogeographic databases. Database, 2015, bau125???bau125. doi: /database/bau125 qcflags qcflags Count QC flags set. Count QC flags set.

10 10 qcflags qcflags(qc, id) qc id The QC value as returned from the occurrence method. The QC flag ids. Details At the moment there are 27 QC flags, numbered from 1 to 30 with disabled flag (qc 8, 9 and 20). 1. OBIS data format: are the required fields from the OBIS Schema completed? 2. Taxonomy: is the taxon name matched to WoRMS? 3. Taxonomy: is the taxon level genus or lower? 4. Geography (lat/lon): are the latitude/longitude values different from zero? 5. Geography (lat/lon): are the latitude/longitude values within their possible boundaries? (world coordinates) 6. Geography (lat/lon): are the coordinates situated in sea or along the coastline (20 km buffer)? 7. Completeness (date/time): is the sampling year (start/end) completed and valid? 10. OBIS data format: is the Basis of Record documented, and is an existing OBIS code used? 11. Completeness (date/time): is the sampling date (year/month/day; start/end) valid? 12. Completeness (date/time): if a start and end date are given, is the start before the end? 13. Completeness (date/time): if a sampling time is given, is this valid and is the time zone completed? 14. Completeness (presence/abundance/biomass): is the value of the field ObservedIndividualCount empty or >0? 15. Completeness (presence/abundance/biomass): is the value of the field Observedweight empty or >0? 16. Completeness (presence/abundance/biomass): is the field SampleSize completed if the field ObservedIndividualCount is >0? 17. OBIS data format: is the value of the field Sex empty or is an existing OBIS code used? 18. Geography (depth): is minimum depth <= maximum depth? 19. Geography (depth): is the sampling depth possible when compared with GEBCO depth map (incl. margin)? 21. Species outliers (environment/depth): is the observation within six MADs from the median depth of this taxon? 22. Species outliers (environment/depth): is the observation within three IQRs from the first & third quartile depth of this taxon? 23. Species outliers (environment/sss): is the observation within six MADs from the median sea surface salinity (SSS) of this taxon?

11 robis Species outliers (environment/sss): is the observation within three IQRs from the first & third quartile sea surface salinity (SSS) of this taxon? 25. Species outliers (environment/sst): is the observation within six MADs from the median sea surface temperature (SST) of this taxon? 26. Species outliers (environment/sst): is the observation within three IQRs from the first & third quartile sea surface temperature (SST) of this taxon? 27. Species outliers (geography): is the observation within six MADs from the distance to the geographic centroid of this taxon? 28. Species outliers (geography): is the observation within three IQRs from the first & third quartile distance to the geographic centroid of this taxon? 29. Dataset outliers (geography): is the observation within six MADs from the distance to the geographic centroid of this dataset? 30. Dataset outliers (geography): is the observation within three IQRs from the first & third quartile distance to the geographic centroid of this dataset? Number of QC flags set. References Vandepitte, L., Bosch, S., Tyberghein, L., Waumans, F., Vanhoorne, B., Hernandez, F.,??? Mees, J. (2015). Fishing for data and sorting the catch: assessing the data quality, completeness and fitness for use of data in marine biogeographic databases. Database, 2015, bau125???bau125. http: //dx.doi.org/ /database/bau125 occurrence leafletmap robis robis: R client for the OBIS API Work in progress

12 12 taxon_common taxon Fetch one taxon. taxon fetches information for a specific taxon. taxon(obisid = NULL, aphiaid = NULL, scientificname = NULL, = FALSE) obisid integer. The OBIS identifier of the species. aphiaid integer. The WoRMS identifier of the species. scientificname character. The full scientific name, with authorship and date information if known. The areas. taxon_common occurrence checklist node area dataset group taxon_common Fetch common names. Fetch common names. taxon_common(obisid, = FALSE) obisid numeric. OBIS identifier for the taxon. The areas.

13 taxon_common 13 taxon_common occurrence checklist node area dataset group

14 Index area, 2, 3 8, 12, 13 checklist, 2, 2, 5, 6, 8, 12, 13 dataset, 2, 3, 4, 5 8, 12, 13 dataset_by_id, 5 group, 2 4, 5, 6 8, 12, 13 leafletmap, 6, 8, 11 node, 2, 4, 5, 6, 7, 8, 12, 13 occurrence, 2, 3, 5, 6, 7, qc, 8 QC flags, 3, 7 qcflags, 8, 9, 9 robis, 11 robis-package (robis), 11 taxon, 2, 5, 6, 12 taxon_common, 12, 12, 13 14