Finalizing ATN to OBIS-USA notebook

.gitignore

@@ -4,4 +4,13 @@
 .DS_Store
 .Rhistory
 *.ipynb_checkpoints*
-.idea
+.idea
+datasets/atn_satellite_telemetry/data/src/
+datasets/atn_satellite_telemetry/data/dwc/*
+!datasets/atn_satellite_telemetry/data/dwc/137491/
+!datasets/atn_satellite_telemetry/data/dwc/137494/
+!datasets/atn_satellite_telemetry/data/dwc/38553/
+!datasets/atn_satellite_telemetry/data/dwc/atn_137491_spotted-seal_trajectory_20180418-20180526/
+!datasets/atn_satellite_telemetry/data/dwc/atn_137494_ribbon-seal_trajectory_20140426-20140426/
+!datasets/atn_satellite_telemetry/data/dwc/atn_38553_bearded-seal_trajectory_20110618-20120314/
+datasets/atn_satellite_telemetry/.env

datasets/atn_satellite_telemetry/atn_satellite_telemetry_netCDF2DwC.qmd

@@ -202,7 +202,7 @@ platform_id_tbl <- metadata %>% dplyr::filter(variable == "NC_GLOBAL") %>% dplyr
 platform_id <- chartr(" ", "_", platform_id_tbl$value)
 occurrencedf$organismID <- paste(platform_id , common_name, sep = "_") 
 
-# occurrenceID - {eventDate}_{depth}_{common_name}
+# occurrenceID - ioos_atn_{eventDate}_{depth}_{common_name}
 occurrencedf$occurrenceID <- sub(" ", "_", paste("ioos_atn", occurrencedf$eventDate, atn_tbl$z, common_name, sep = "_"))
 
 # geodeticDatum
@@ -285,13 +285,17 @@ The next step below this, we filter out only the first observation of the hour.
 occurrencedf <- occurrencedf %>% arrange(eventDate)
 
 occurrencedf <- occurrencedf %>%
+
     mutate(eventDateHrs = format(as.POSIXct(eventDate, format="%Y-%m-%dT%H:%M:%SZ"),"%Y-%m-%dT%H")
            ) %>%
+
     add_count(eventDateHrs) %>%
+
     mutate(dataGeneralizations = case_when(n == 1 ~ "",
                                            TRUE ~ paste("first of ", n ,"records")
                                            )
            ) %>%
+
     select(-n)
 
 occurrencedf
@@ -431,6 +435,7 @@ emof_data <- #var_names %>%
     c("animal_length",
       "animal_length_2",
       "animal_weight") %>%
+
     purrr::map_df(function(x) {
         list(measurementValue = ncvar_get( nc, x),
              measurementType = ncatt_get( nc, x)$long_name,
@@ -442,8 +447,11 @@ emof_data <- #var_names %>%
 
 
 emofdf <- occurrencedf %>%
+
     filter(basisOfRecord == 'HumanObservation') %>%
+
     select(organismID, eventID, occurrenceID) %>%
+
     cbind(emof_data)
 
 str(emofdf)

datasets/atn_satellite_telemetry/data/dwc/atn_137491_spotted-seal_trajectory_20180418-20180526/atn_137491_spotted-seal_trajectory_20180418-20180526_emof.csv

@@ -0,0 +1,7 @@
+eventID,occurrenceID,measurementValue,measurementType,measurementTypeID,measurementMethod,measurementUnit,measurementUnitID
+atn_137491_spotted-seal_trajectory_20180418-20180526,ioos_atn_137491_2018-04-18T04:45:00Z_0.0_spotted_seal,69.0,animal_weight: mass of the animal as measured or estimated at deployment,http://vocab.nerc.ac.uk/collection/MVB/current/MVB000019,69.0 (kg),kg,http://vocab.nerc.ac.uk/collection/P06/current/KGXX/
+atn_137491_spotted-seal_trajectory_20180418-20180526,ioos_atn_137491_2018-04-18T04:45:00Z_0.0_spotted_seal,129.0,animal_length: length of the animal as measured or estimated at deployment,http://vocab.nerc.ac.uk/collection/P01/current/TL01XX01/,129.0 (cm) standard length,cm,http://vocab.nerc.ac.uk/collection/P06/current/ULCM/
+atn_137491_spotted-seal_trajectory_20180418-20180526,ioos_atn_137491_2018-04-18T04:45:00Z_0.0_spotted_seal,16U2111,tag serial number,http://vocab.nerc.ac.uk/collection/MVB/current/MVB000189/,,,
+atn_137491_spotted-seal_trajectory_20180418-20180526,ioos_atn_137491_2018-04-18T04:45:00Z_0.0_spotted_seal,Wildlife Computers,tag manufacturer,http://vocab.nerc.ac.uk/collection/MVB/current/MVB000183/,,,
+atn_137491_spotted-seal_trajectory_20180418-20180526,ioos_atn_137491_2018-04-18T04:45:00Z_0.0_spotted_seal,SPOT,tag make and model,http://vocab.nerc.ac.uk/collection/MVB/current/MVB000185/,,,
+atn_137491_spotted-seal_trajectory_20180418-20180526,ioos_atn_137491_2018-04-18T04:45:00Z_0.0_spotted_seal,flipper,tag attachment location,http://vocab.nerc.ac.uk/collection/MVB/current/MVB000395/,,,

datasets/atn_satellite_telemetry/data/dwc/atn_137491_spotted-seal_trajectory_20180418-20180526/atn_137491_spotted-seal_trajectory_20180418-20180526_occurrence.csv

@@ -0,0 +1,6 @@
+eventID,occurrenceID,occurrenceStatus,basisOfRecord,organismID,eventDate,decimalLatitude,decimalLongitude,geodeticDatum,scientificName,scientificNameID,samplingProtocol,kingdom,taxonRank,lifeStage,sex,associatedReferences,coordinateUncertaintyInMeters,minimumDepthInMeters,maximumDepthInMeters,dataGeneralizations,bibliographicCitation,occurrenceRemarks
+atn_137491_spotted-seal_trajectory_20180418-20180526,ioos_atn_137491_2018-04-18T04:45:00Z_0.0_spotted_seal,present,HumanObservation,255021_spotted_seal,2018-04-18T04:45:00Z,63.6222,-165.0651,EPSG:4326,Phoca largha,urn:lsid:marinespecies.org:taxname:255021,satellite telemetry,Animalia,Species,adult,female,https://doi.org/10.25921/wp4e-ph20; https://www.ncei.noaa.gov/archive/accession/0305177; https://doi.org/10.24431/rw1k8er,0,0.0,0.0,,"London, Josh; Koslovsky, Stacie; Cameron, Michael; Boveng, Peter; Ziel, Heather. (2025). Spotted seal (Phoca largha) location data from a satellite telemetry tag (ptt id 137491) deployed in the Bering Sea from 2018-04-18 to 2018-05-26, deployment id 5ad6ce42efec72080c898c77. [Dataset]. US Integrated Ocean Observing System (IOOS) Animal Telemetry Network (ATN).",This is a representative occurrence from a full deployment. For the complete dataset please see https://www.ncei.noaa.gov/archive/accession/0305177.
+atn_137491_spotted-seal_trajectory_20180418-20180526,ioos_atn_137491_2018-04-18T06:09:20Z_0.0_spotted_seal,present,MachineObservation,255021_spotted_seal,2018-04-18T06:09:20Z,63.6399,-165.0595,EPSG:4326,Phoca largha,urn:lsid:marinespecies.org:taxname:255021,satellite telemetry,Animalia,Species,adult,female,https://doi.org/10.25921/wp4e-ph20; https://www.ncei.noaa.gov/archive/accession/0305177; https://doi.org/10.24431/rw1k8er,1500,0.0,0.0,first of 3 records for this hour.,"London, Josh; Koslovsky, Stacie; Cameron, Michael; Boveng, Peter; Ziel, Heather. (2025). Spotted seal (Phoca largha) location data from a satellite telemetry tag (ptt id 137491) deployed in the Bering Sea from 2018-04-18 to 2018-05-26, deployment id 5ad6ce42efec72080c898c77. [Dataset]. US Integrated Ocean Observing System (IOOS) Animal Telemetry Network (ATN).",This is a representative occurrence from a full deployment. For the complete dataset please see https://www.ncei.noaa.gov/archive/accession/0305177.
+atn_137491_spotted-seal_trajectory_20180418-20180526,ioos_atn_137491_2018-04-29T07:05:19Z_0.0_spotted_seal,present,MachineObservation,255021_spotted_seal,2018-04-29T07:05:19Z,60.0415,-164.4277,EPSG:4326,Phoca largha,urn:lsid:marinespecies.org:taxname:255021,satellite telemetry,Animalia,Species,adult,female,https://doi.org/10.25921/wp4e-ph20; https://www.ncei.noaa.gov/archive/accession/0305177; https://doi.org/10.24431/rw1k8er,1500,0.0,0.0,first of 4 records for this hour.,"London, Josh; Koslovsky, Stacie; Cameron, Michael; Boveng, Peter; Ziel, Heather. (2025). Spotted seal (Phoca largha) location data from a satellite telemetry tag (ptt id 137491) deployed in the Bering Sea from 2018-04-18 to 2018-05-26, deployment id 5ad6ce42efec72080c898c77. [Dataset]. US Integrated Ocean Observing System (IOOS) Animal Telemetry Network (ATN).",This is a representative occurrence from a full deployment. For the complete dataset please see https://www.ncei.noaa.gov/archive/accession/0305177.
+atn_137491_spotted-seal_trajectory_20180418-20180526,ioos_atn_137491_2018-05-13T20:07:00Z_0.0_spotted_seal,present,MachineObservation,255021_spotted_seal,2018-05-13T20:07:00Z,63.365,-164.0013,EPSG:4326,Phoca largha,urn:lsid:marinespecies.org:taxname:255021,satellite telemetry,Animalia,Species,adult,female,https://doi.org/10.25921/wp4e-ph20; https://www.ncei.noaa.gov/archive/accession/0305177; https://doi.org/10.24431/rw1k8er,10000,0.0,0.0,first of 3 records for this hour.,"London, Josh; Koslovsky, Stacie; Cameron, Michael; Boveng, Peter; Ziel, Heather. (2025). Spotted seal (Phoca largha) location data from a satellite telemetry tag (ptt id 137491) deployed in the Bering Sea from 2018-04-18 to 2018-05-26, deployment id 5ad6ce42efec72080c898c77. [Dataset]. US Integrated Ocean Observing System (IOOS) Animal Telemetry Network (ATN).",This is a representative occurrence from a full deployment. For the complete dataset please see https://www.ncei.noaa.gov/archive/accession/0305177.
+atn_137491_spotted-seal_trajectory_20180418-20180526,ioos_atn_137491_2018-05-20T19:26:36Z_0.0_spotted_seal,present,MachineObservation,255021_spotted_seal,2018-05-20T19:26:36Z,64.6676,-161.5203,EPSG:4326,Phoca largha,urn:lsid:marinespecies.org:taxname:255021,satellite telemetry,Animalia,Species,adult,female,https://doi.org/10.25921/wp4e-ph20; https://www.ncei.noaa.gov/archive/accession/0305177; https://doi.org/10.24431/rw1k8er,10000,0.0,0.0,,"London, Josh; Koslovsky, Stacie; Cameron, Michael; Boveng, Peter; Ziel, Heather. (2025). Spotted seal (Phoca largha) location data from a satellite telemetry tag (ptt id 137491) deployed in the Bering Sea from 2018-04-18 to 2018-05-26, deployment id 5ad6ce42efec72080c898c77. [Dataset]. US Integrated Ocean Observing System (IOOS) Animal Telemetry Network (ATN).",This is a representative occurrence from a full deployment. For the complete dataset please see https://www.ncei.noaa.gov/archive/accession/0305177.