Nothing
R/movebank_constants.R
In move2: Processing and Analysing Animal Trajectories
Defines functions
to_download_names
#' @importFrom vroom col_date col_datetime col_double col_factor col_integer col_character col_logical col_big_integer
NULL
# dput(movebank_retrieve("entity_type"='tag_type') ) # nolint: commented_code_linter
movebank_tag_type_table <- structure(list(description = c(
NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Localize tracking devices based on approximated distance to nearby GSM cell towers, WiFi or other network connectors.",
"Localize devices using a global navigation satellite system",
"Data derived from other sensor data", "Time-Depth Recording",
"Location Estimate by ATLAS system"
), external_id = c(
"bird-ring",
"gps", "radio-transmitter", "argos-doppler-shift", "natural-mark",
"acceleration", "solar-geolocator", "accessory-measurements",
"solar-geolocator-raw", "barometer", "magnetometer", "orientation",
"solar-geolocator-twilight", "acoustic-telemetry", "gyroscope",
"heart-rate", "sigfox-geolocation", "proximity", "geolocation-api",
"gnss", "derived", "tdr", "atlas-geolocation"
), id = structure(c(
1.96144061398975e-321,
3.22624866734334e-321, 3.32506179651159e-321, 4.09076473443635e-319,
1.16880220518501e-317, 1.16880269925066e-317, 1.92011745743723e-317,
3.87493413331319e-317, 4.59550368042471e-317, 3.8408856487366e-316,
3.84088619220881e-316, 4.04676003659103e-315, 4.51624043736367e-315,
6.1243104547751e-315, 6.41135836580693e-315, 1.09001844591634e-314,
1.13629901961024e-314, 1.30684843265253e-314, 1.52677095314155e-314,
1.52677095610594e-314, 1.52677095660001e-314, 2.10706387617373e-314,
2.14568681278764e-314
), class = "integer64"), is_location_sensor = c(
TRUE,
TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE,
FALSE, FALSE, TRUE, FALSE, FALSE, TRUE, FALSE, TRUE, TRUE, FALSE,
FALSE, TRUE
), name = structure(1:23, levels = c(
"Bird Ring",
"GPS", "Radio Transmitter", "Argos Doppler Shift", "Natural Mark",
"Acceleration", "Solar Geolocator", "Accessory Measurements",
"Solar Geolocator Raw", "Barometer", "Magnetometer", "Orientation",
"Solar Geolocator Twilight", "Acoustic Telemetry", "Gyroscope",
"Heart Rate", "Sigfox Geolocation", "Proximity", "Geolocation API",
"GNSS", "Derived", "TDR", "ATLAS Geolocation"
), class = "factor")), row.names = c(
NA,
-23L
), spec = structure(list(cols = list(description = structure(list(), class = c(
"collector_character",
"collector"
)), external_id = structure(list(), class = c(
"collector_character",
"collector"
)), id = structure(list(), class = c(
"collector_big_integer",
"collector"
)), is_location_sensor = structure(list(), class = c(
"collector_logical",
"collector"
)), name = structure(list(
levels = NULL, ordered = FALSE,
include_na = FALSE
), class = c("collector_factor", "collector"))), default = structure(list(), class = c(
"collector_guess",
"collector"
)), delim = ","), class = "col_spec"), class = c(
"spec_tbl_df",
"tbl_df", "tbl", "data.frame"
))
movebank_spatial_column_pairs <- list(
lora_gateway_location = c("lora_gateway_longitude", "lora_gateway_latitude"),
argos_location_1 = c("argos_lon1", "argos_lat1"),
argos_location_2 = c("argos_lon2", "argos_lat2"),
birth_location = c("birth_longitude", "birth_latitude"),
animal_birth_hatch_location = c("animal_birth_hatch_longitude", "animal_birth_hatch_latitude"),
animal_mortality_location = c("animal_mortality_longitude", "animal_mortality_latitude"),
mortality_location = c("mortality_longitude", "mortality_latitude"),
capture_location = c("capture_longitude", "capture_latitude"),
location_median = c("long_median", "lat_median"),
location_upper = c("long_upper", "lat_upper"),
location_lower = c("long_lower", "lat_lower"),
main_location = c("main_location_long", "main_location_lat"),
deploy_on_location = c("deploy_on_longitude", "deploy_on_latitude"),
deploy_off_location = c("deploy_off_longitude", "deploy_off_latitude"),
receiver_location = c("receiver_longitude", "receiver_latitude")
)
# Columns from movebank with these names are automatically converted to the correct units
mb_column_units <- c(
"acceleration-sampling-frequency-per-axis" = "Hz",
"accelerations" = "m/s^2",
"acceleration-x" = "m/s^2",
"acceleration-y" = "m/s^2",
"acceleration-z" = "m/s^2",
"activity-count" = "count",
"angular-velocity-x" = "arc_degree/s",
"angular-velocity-y" = "arc_degree/s",
"angular-velocity-z" = "arc_degree/s",
"animal-mass" = "g",
"argos:altitude" = "m",
"argos:best-level" = "dB",
"argos:calcul-freq" = "MHz",
"argos:error-radius" = "m",
"argos:gdop" = "m/Hz",
"argos:orientation" = "arc_degree",
"argos:pass-duration" = "s",
"argos:semi-major" = "m",
"argos:semi-minor" = "m",
"atlas:varx" = "m^2",
"atlas:varxy" = "m^2",
"atlas:vary" = "m^2",
"bar:barometric-depth" = "m",
"bar:barometric-height" = "m",
"bar:barometric-pressure" = "mbar",
"barometric-depth" = "m",
"barometric-height" = "m",
"barometric-pressure" = "mbar",
# "bas:compensated-latitude" = , # decimal degrees, WGS84 reference system
"bas:mid-value-secs" = "s",
# "bas:stationary-latitude" = , # decimal degrees, WGS84 reference system
# "bas:transition-1" = , # units GMT
# "bas:transition-2" = , # units GMT
"battery-charge-percent" = "%",
"battery-charging-current" = "mA",
"battery-charging-voltage" = "mV",
"beacon:frequency" = "MHz",
"capture-handling-time" = "s",
"compass-heading" = "degree_north",
"cpu-temperature" = "degree_C",
"ctt:solar-current-since-last-fix" = "mA",
"deltatime" = "s",
# "deploy-off-latitude" = , # decimal degrees, WGS84 reference system
# "deploy-off-longitude" = , # decimal degrees, WGS84 reference system
# "deploy-on-latitude" = , # decimal degrees, WGS84 reference system
# "deploy-on-longitude" = , # decimal degrees, WGS84 reference system
"depth" = "m",
"dive-duration" = "s",
"ecg:sampling-frequency" = "Hz",
"eobs:acceleration-sampling-frequency-per-axis" = "Hz",
"eobs:battery-voltage" = "mV",
"eobs:fix-battery-voltage" = "mV",
"eobs:horizontal-accuracy-estimate" = "m",
"eobs:speed-accuracy-estimate" = "m/s",
"eobs:temperature" = "degree_C",
"eobs:used-time-to-get-fix" = "s",
"error-count" = "count",
"external-temperature" = "degree_C",
"geolocation-station-count" = "count",
"geolocator-sun-elevation-angle" = "arc_degree",
"gmatrix:gps-fix-interval" = "s",
"gnss:dop" = "1",
"gnss:hdop" = "1",
"gnss:maximum-signal-strength" = "dBm",
"gnss:message-count" = "count",
"gnss:pdop" = "1",
"gnss:satellite-count" = "count",
"gnss:time-to-fix" = "s",
"gnss:vdop" = "1",
"gps:activity-count" = "count",
"gps:dop" = "1",
"gps:gdop" = "1",
"gps:hdop" = "1",
"gps:maximum-signal-strength" = "dBm",
"gps:message-count" = "count",
"gps:pdop" = "1",
"gps:satellite-count" = "count",
"gps:speed-accuracy-estimate" = "m/s",
"gps:tdop" = "1",
"gps-time-to-fix" = "s",
"gps:vdop" = "1",
"ground-speed" = "m/s",
# "gsm:gsm-signal-strength" = "ASU", # arbitrary strength units
"gt:sys-week" = "count",
"gt:tx-count" = "count",
"gyroscope-sampling-frequency-per-axis" = "Hz",
"heading" = "degree_north",
"heartrate:ecg-sampling-frequency" = "Hz",
"heartrate:heart-rate" = "1/min", # Units: beats per minute
"heartrate:rr-interval" = "s",
"heartrate:voltage-resolution" = "mV",
"height-above-ellipsoid" = "m",
"height-above-ground-level" = "m",
"height-above-mean-sea-level" = "m",
"height-above-msl" = "m",
"icarus:solar-cell-current" = "mA",
"individual-count" = "count",
"internal-temperature" = "degree_C",
# "lat-lower" = , # decimal degrees, WGS84 reference system
# "lat-upper" = , # decimal degrees, WGS84 reference system
"location-error-3d" = "m",
"location-error-numerical" = "m",
"location-error-percentile" = "%",
# "long-lower" = , # decimal degrees, WGS84 reference system
# "long-upper" = , # decimal degrees, WGS84 reference system
"lora:rssi" = "dBm",
"lora:snr" = "dB",
"lora:uplink-count" = "count",
"lotek:deltatime" = "s",
"lotek-eres" = "1",
"mag:magnetic-field-sampling-frequency-per-axis" = "Hz",
"magnetic-field-sampling-frequency-per-axis" = "Hz",
"magnetic-field-x" = "microtesla",
"magnetic-field-y" = "microtesla",
"magnetic-field-z" = "microtesla",
"mw:activity-count" = "count",
"number-of-deployed-locations" = "count",
"number-of-deployments" = "count",
"number-of-events" = "count",
"number-of-individuals" = "count",
"number-of-tags" = "count",
"odba" = "standard_free_fall",
"opencollar:cold-retry" = "count",
"opencollar:hot-retry" = "count",
"opencollar:msg" = "count",
"opencollar:uptime" = "weeks",
"orientation-quaternions-sampling-frequency" = "Hz",
"pitch" = "arc_degree",
"quaternions-sampling-frequency" = "Hz",
"relative-humidity" = "%",
"roll" = "arc_degree",
"rr-interval" = "s",
"sampling-frequency" = "Hz",
"sequence-number" = "count",
"sigfox:computed-location-radius" = "m",
"sigfox:tx-interval" = "min",
"solar-cell-voltage" = "mV",
"solar-voltage-percent" = "%",
"speed-accuracy" = "m/s",
"tag-backup-voltage" = "mV",
"tag-beacon-frequency" = "MHz",
"tag-mass" = "g",
"tag-mass-total" = "g",
"tag-voltage" = "mV",
"tdr:depth" = "m",
# "technosmart:signal-quality" = ,
# MB figure out how to express the carrier to noise density ratio:
# https://en.wikipedia.org/wiki/Carrier-to-noise_ratio#Carrier-to-noise_density_ratio
# Units: dB-Hz (decibel-Hz?)(Wikipedia: dB(Hz) – bandwidth relative to one hertz. E.g., 20 dB‑Hz corresponds to a
# bandwidth of 100 Hz)
"temperature-max" = "degree_C",
"temperature-min" = "degree_C",
"tilt-angle" = "arc_degree", # Units: degrees
"tilt-x" = "standard_free_fall",
"tilt-y" = "standard_free_fall",
"tilt-z" = "standard_free_fall",
"tinyfox:activity-percent-last-24h" = "%",
"tinyfox:pressure-min-last-24h" = "mbar",
"tinyfox:sunny-index-start-voltage" = "mV",
"tinyfox:sunny-index-voltage-increase" = "mV",
"tinyfox:temperature-max-last-24h" = "degree_C",
"tinyfox:temperature-min-last-24h" = "degree_C",
"tinyfox:total-vedba-count" = "count",
"tinyfox:total-vedba" = "m/s^2",
"tinyfox:vedba-00h-ago" = "m/s^2",
"tinyfox:vedba-01h-ago" = "m/s^2",
"tinyfox:vedba-02h-ago" = "m/s^2",
"tinyfox:vedba-03h-ago" = "m/s^2",
"tinyfox:vedba-04h-ago" = "m/s^2",
"tinyfox:vedba-05h-ago" = "m/s^2",
"tinyfox:vedba-06h-ago" = "m/s^2",
"tinyfox:vedba-07h-ago" = "m/s^2",
"tinyfox:vedba-08h-ago" = "m/s^2",
"tinyfox:vedba-09h-ago" = "m/s^2",
"tinyfox:vedba-10h-ago" = "m/s^2",
"tinyfox:vedba-11h-ago" = "m/s^2",
"tinyfox:vedba-12h-ago" = "m/s^2",
"tinyfox:vedba-13h-ago" = "m/s^2",
"tinyfox:vedba-14h-ago" = "m/s^2",
"tinyfox:vedba-15h-ago" = "m/s^2",
"tinyfox:vedba-16h-ago" = "m/s^2",
"tinyfox:vedba-17h-ago" = "m/s^2",
"tinyfox:vedba-18h-ago" = "m/s^2",
"tinyfox:vedba-19h-ago" = "m/s^2",
"tinyfox:vedba-20h-ago" = "m/s^2",
"tinyfox:vedba-21h-ago" = "m/s^2",
"tinyfox:vedba-22h-ago" = "m/s^2",
"tinyfox:vedba-23h-ago" = "m/s^2",
"tinyfox:vedba-burst-sum" = "m/s^2",
"underwater-count" = "count",
"underwater-time" = "s",
"utm-easting" = "m", # Units: meters, WGS84 reference system
"utm-northing" = "m", # Units: meters, WGS84 reference system
"vedba" = "standard_free_fall",
"vertical-error-numerical" = "m",
"vertical-speed" = "m/s",
"voltage-resolution" = "mV",
"wc-residual" = "1",
"weight" = "g",
"wet-count" = "count",
"zero-crossings-steps" = "count",
NULL
)
movebank_column_types <- list(
"<html>" = col_character(),
"acceleration-axes" = col_character(),
"acceleration-raw-x" = col_double(),
"acceleration-raw-y" = col_double(),
"acceleration-raw-z" = col_double(),
"acceleration-sampling-frequency-per-axis" = col_double(),
"accelerations" = col_character(),
"accelerations-raw" = col_character(),
"acceleration-x" = col_double(),
"acceleration-y" = col_double(),
"acceleration-z" = col_double(),
"acknowledgements" = col_character(),
"activity-count" = col_integer(),
"activity-x" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000334/
"activity-y" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000335/
"activity-z" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000336/
"algorithm-marked-outlier" = col_logical(),
"alt-index-id" = col_character(),
"alt-project-id" = col_factor(),
# "ambiguous-detection", # not documented in mb dictionary
"angular-velocities-raw" = col_character(),
"angular-velocity-x" = col_double(),
"angular-velocity-y" = col_double(),
"angular-velocity-z" = col_double(),
"animal-birth-hatch-latitude" = col_double(),
"animal-birth-hatch-longitude" = col_double(),
"animal-comments" = col_character(),
"animal-death-comments" = col_character(),
"animal-earliest-date-born" = col_datetime(),
"animal-exact-date-of-birth" = col_datetime(),
"animal-group-id" = col_factor(),
"animal-id" = col_factor(),
"animal-latest-date-born" = col_datetime(),
"animal-life-stage" = col_factor(),
"animal-marker-id" = col_factor(),
"animal-mass" = col_double(),
"animal-mates" = col_factor(),
"animal-mortality-date" = col_date(),
"animal-mortality-latitude" = col_double(),
"animal-mortality-longitude" = col_double(),
"animal-mortality-type" = col_factor(
levels = c(
"bycatch", "capture", "electrocution", "harvest", "disease",
"natural-death", "other", "parasites", "poison", "predation",
"starvation", "unknown", "vehicle-collision"
)
),
"animal-nickname" = col_factor(),
"animal-offspring" = col_factor(),
"animal-parents" = col_factor(),
"animal-reproductive-condition" = col_factor(),
"animal-ring-id" = col_factor(),
"animal-sex" = col_factor(levels = c("m", "f", "u")),
"animal-siblings" = col_factor(),
"animal-taxon" = col_factor(),
"animal_taxon_detail" = col_factor(),
"argos:altitude" = col_double(),
"argos:best-level" = col_double(),
"argos:calcul-freq" = col_double(),
"argos:error-radius" = col_double(),
"argos:gdop" = col_double(),
"argos:iq" = col_factor(
levels = c(apply(expand.grid(0:6, 0:8), 1, paste0, collapse = ""), 0:8, "99")
), # MB argos:iq 99 is not in the documentation but does occur in study 1420256397
"argos:lat1" = col_double(),
"argos:lat2" = col_double(),
"argos:lc" = col_factor(levels = c("G", 3:0, "A", "B", "Z"), ordered = TRUE),
"argos:location-algorithm" = col_factor(levels = c("least-squares", "Kalman")),
"argos:lon1" = col_double(),
"argos:lon2" = col_double(),
"argos:nb-mes-120" = col_integer(),
"argos:nb-mes" = col_integer(),
# "argos:nb-mes-identical", # not documented in mb dictionary
"argos:nopc" = col_factor(ordered = TRUE, levels = as.character(c(0:4, 9))), # MB argos:nopc 9 is not in the documentation but does occur in study 1420256397
"argos:orientation" = col_double(),
"argos:pass-duration" = col_double(),
"argos:sat-id" = col_factor(),
"argos:semi-major" = col_double(),
"argos:semi-minor" = col_double(),
"argos:sensor-1" = col_integer(),
"argos:sensor-2" = col_integer(),
"argos:sensor-3" = col_integer(),
"argos:sensor-4" = col_integer(),
"argos:transmission-timestamp" = col_datetime(),
"argos:valid-location-algorithm" = col_factor(levels = as.character(1L:2L)),
"argos:valid-location-manual" = col_factor(levels = as.character(1L:2L)),
"atlas:varx" = col_double(),
"atlas:varxy" = col_double(),
"atlas:vary" = col_double(),
"attachment-body-part" = col_factor(),
"attachment-comments" = col_character(),
"attachment-type" = col_factor(
levels = c(
"backpack-harness", "collar", "ear-tag", "fin mount", "glue",
"harness", "implant", "leg-band", "leg-loop-harness", "none",
"other", "subcutaneous-anchor", "suction-cup", "sutures", "tape"
)
),
"awt:alarms-battery" = col_logical(),
"awt:alarms-cbit" = col_logical(),
"awt:alarms-coverage" = col_logical(),
"awt:alarms-geofence" = col_logical(),
"awt:alarms-memory" = col_logical(),
"awt:alarms-movement" = col_logical(),
"awt:alarms-tamperfoil" = col_logical(),
"awt:alarms-track-mode" = col_logical(),
"awt:log-interval" = col_factor(
levels = c(
"every 10 minutes", "every 30 minutes", "every 1 hour",
"every 2 hours", "every 3 hours", "every 4 hours",
"every 5 hours", "every 6 hours", "every 8 hours",
"every 12 hours", "every 24 hours", "every 48 hours", "off"
), ordered = TRUE
),
"bar:barometric-depth" = col_double(),
"bar:barometric-height" = col_double(),
"bar:barometric-pressure" = col_double(),
"barometric-depth" = col_double(),
"barometric-height" = col_double(),
"barometric-pressure" = col_double(),
"bas:compensated-latitude" = col_double(),
"bas:confidence" = col_factor(), # MB only integer values allowed?
"bas:fix-type" = col_factor(levels = c("noon", "midnight")),
"bas:mid-value-secs" = col_double(),
"bas:stationary-latitude" = col_double(),
"bas:transition-1" = col_double(),
"bas:transition-2" = col_double(),
"battery-charge-percent" = col_integer(), # integer in study
"battery-charging-current" = col_double(),
"battery-charging-voltage" = col_logical(),
"beacon:frequency" = col_double(),
"behavior-according-to" = col_character(),
"behavioural-classification" = col_factor(),
"breed-stage" = col_character(),
"canonical-name" = col_factor(),
"capture-handling-time" = col_double(),
"capture-latitude" = col_double(),
"capture-longitude" = col_double(),
"capture-method" = col_character(),
"capture-timestamp" = col_datetime(),
"citation" = col_character(),
"comments" = col_character(),
"compass-heading" = col_double(),
"conductivity" = col_double(),
"contact-person" = col_character(),
"contact-person-id" = col_factor(),
"contact-person-name" = col_factor(),
"cpu-temperature" = col_double(),
"ctt:solar-current-since-last-fix" = col_integer(),
"data-decoding-software" = col_factor(),
"data-processing-software" = col_factor(),
"dba-comments" = col_character(),
"death-comments" = col_character(),
"deltatime" = col_integer(),
"deployment-comments" = col_character(),
"deployment-end-comments" = col_character(),
"deployment-end-type" = col_factor(
levels = c(
"captured", "dead", "dead/fall-off",
"equipment-failure", "fall-off", "other", "released",
"removal", "transmission-end", "unknown"
)
),
"deployment-id" = col_big_integer(), # deployment id now can be a given name defined by de user and, in its absence a large integer created by movebank
"deployment-image" = col_character(),
"deploy-off-date" = col_datetime(),
"deploy-off-latitude" = col_double(),
"deploy-off-longitude" = col_double(),
"deploy-off-measurements" = col_character(),
"deploy-off-person" = col_character(),
"deploy-off-sampling" = col_character(),
"deploy-off-timestamp" = col_datetime(),
"deploy-on-date" = col_datetime(),
"deploy-on-latitude" = col_double(),
"deploy-on-longitude" = col_double(),
"deploy-on-measurements" = col_character(),
"deploy-on-person" = col_character(),
"deploy-on-sampling" = col_character(),
"deploy-on-timestamp" = col_datetime(),
"depth" = col_double(),
"dive-duration" = col_integer(),
"druid:alert" = col_factor(levels = 1),
"druid:data-source" = col_factor(
levels = c("[1]", "[2]", "[4]", "[8]", "[10]", "[100]", "[101]")
),
"duty-cycle" = col_character(),
"earliest-date-born" = col_datetime(), # seems to be undocumented api name
"ecg:raw" = col_double(),
"ecg:sampling-frequency" = col_double(),
"ecgs:raw" = col_character(),
"end-timestamp" = col_datetime(),
"eobs:acceleration-axes" = col_factor(),
"eobs:acceleration-sampling-frequency-per-axis" = col_double(),
"eobs:accelerations-raw" = col_character(),
"eobs:activity" = col_integer(),
"eobs:activity-samples" = col_integer(),
"eobs:battery-voltage" = col_integer(),
"eobs:fix-battery-voltage" = col_integer(),
"eobs:horizontal-accuracy-estimate" = col_double(),
"eobs:key-bin-checksum" = col_big_integer(),
"eobs:speed-accuracy-estimate" = col_double(),
"eobs:start-timestamp" = col_datetime(),
"eobs:status" = col_factor(ordered = TRUE, levels = LETTERS[1L:4L]),
"eobs:temperature" = col_integer(),
"eobs:type-of-fix" = col_factor(), # MB galapagos albatrosses have a type of fix 0 for eobs:type-of-fix I expect either 2 or 3 : http://vocab.nerc.ac.uk/collection/MVB/current/MVB000100/
"eobs:used-time-to-get-fix" = col_integer(),
"error-count" = col_integer(),
"event-group-id" = col_factor(),
"event-id" = col_big_integer(),
"exact-date-of-birth" = col_datetime(), # seems to be undocumented api name
"external-temperature" = col_double(),
"flt:switch" = col_factor(
levels = c(as.character(c(0L, 6L, 48L, 49L, 64L, 69L, 72L, 77L, 112L))), ordered = TRUE
), # MB check if ordered
"format-type" = col_character(),
"geolocation-station-count" = col_integer(),
"geolocator-calibration" = col_character(),
"geolocator-fix-type" = col_factor(),
"geolocator-light-threshold" = col_double(),
"geolocator-rise" = col_logical(),
"geolocator-sensor-comments" = col_character(),
"geolocator-sun-elevation-angle" = col_double(),
"geolocator-twilight3" = col_datetime(),
"georeference-protocol" = col_factor(),
"gls:light-level" = col_double(),
"gls:twilight" = col_integer(),
"gmatrix:alert" = col_integer(),
"gmatrix:alert-message" = col_factor(),
"gmatrix:device-type" = col_factor(),
"gmatrix:event" = col_factor(levels = as.character(c(16L, 48L, 49L, 50L, 51L, 52L, 80L))),
"gmatrix:firmware-version" = col_factor(),
"gmatrix:gps-event" = col_factor(levels = as.character(c(0L:5L))),
"gmatrix:gps-event-text" = col_factor(
levels = c("Unknown location", "Alert", "Panic", "Timed", "Fall", "Heartbeat")
),
"gmatrix:gps-fix-interval" = col_integer(),
"gmatrix:gps-fix-interval-text" = col_factor(),
"gmatrix:hardware-version" = col_factor(),
"gmatrix:is-moving" = col_factor(levels = c("A1", "0")),
"gmatrix:is-moving-text" = col_factor(levels = c("MOVING", "STATIC")),
"gmatrix:last-location" = col_factor(levels = c("null", "0", "1")),
"gmatrix:last-location-text" = col_factor(
levels = c("not available", "new location", "last known location")
),
"gmatrix:mode" = col_factor(levels = as.character(c(0:6))),
"gmatrix:mode-text" = col_factor(
levels = c(
"reserved", "help me", "press it", "track it",
"guard it", "monitor it", "don't lose it"
)
),
"gmatrix:packet-type" = col_factor(), # MB check with Sarah if can be integer
"gnss:dop" = col_double(),
"gnss:fix-type" = col_factor(ordered = TRUE, levels = 1L:3L),
"gnss:fix-type-raw" = col_factor(),
"gnss:hdop" = col_double(),
"gnss:maximum-signal-strength" = col_double(),
"gnss:message-count" = col_integer(),
"gnss:pdop" = col_double(),
"gnss:satellite-count" = col_integer(),
"gnss:time-to-fix" = col_double(),
"gnss:vdop" = col_double(),
"go_public_date" = col_datetime(),
"gps:activity-count" = col_integer(),
"gps:dop" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000115/
"gps:fix-type" = col_factor(
levels = as.character(0:3), ordered = TRUE
), # MB 0 not in vocabulary for fix type but in study 619097045
"gps:fix-type-raw" = col_factor(),
"gps:gdop" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000360/
"gps:hdop" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000118/
"gps:maximum-signal-strength" = col_double(),
"gps:message-count" = col_integer(),
"gps:pdop" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000284/
"gps:satellite-count" = col_integer(),
"gps:speed-accuracy-estimate" = col_double(),
"gps:tdop" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000361/
"gps-time-to-fix" = col_double(),
"gps:twilight" = col_factor(),
"gps:vdop" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000122/
"grants-used" = col_character(),
"ground-speed" = col_double(),
"gsat:charge-mode" = col_factor(
levels = c("Discharge", "ChargeSlow", "ChargeMedium", "ChargeHigh"), ordered = TRUE
),
"gsat:low-power-mode" = col_logical(),
"gsat:orientation" = col_factor(
levels = c("XPositive", "XNegative", "YPositive", "YNegative", "ZPositive", "Znegative")
),
"gsm:gsm-signal-strength" = col_integer(),
"gsm:mcc-mnc" = col_integer(),
# "gt:activity-count", # not documented in mb dictionary
"gt:sys-week" = col_integer(),
"gt:tx-count" = col_integer(),
"guaternions-raw" = col_character(),
"gundi-urn" = col_character(),
"gyroscope-axes" = col_factor(),
"gyroscope-sampling-frequency-per-axis" = col_double(),
"habitat-according-to" = col_character(),
"habitat" = col_factor(),
"heading" = col_double(),
"heartrate:ecg-raw" = col_integer(),
"heartrate:ecg-sampling-frequency" = col_double(),
"heartrate:ecgs-raw" = col_character(),
"heartrate:heart-rate" = col_double(),
"heartrate:rr-interval" = col_double(),
"heartrate:voltage-resolution" = col_double(),
"height-above-ellipsoid" = col_double(),
"height-above-ground-level" = col_double(),
"height-above-mean-sea-level" = col_double(),
"height-above-msl" = col_double(),
"height-raw" = col_character(),
"i-am-collaborator" = col_logical(),
"i-am-owner" = col_logical(),
"i-can-see-data" = col_logical(),
"icarus:solar-cell-current" = col_double(),
"id" = col_big_integer(),
"i-have-download-access" = col_logical(),
"import-marked-outlier" = col_logical(),
"individual-count" = col_integer(),
"individual-id" = col_big_integer(),
"individual-local-identifier" = col_factor(),
"individual-taxon-canonical-name" = col_factor(),
"internal-temperature" = col_double(),
"is-location-sensor" = col_logical(),
"is-test" = col_logical(),
"latest-date-born" = col_datetime(), # seems to be undocumented api name
"lat-lower" = col_double(),
"lat-median" = col_double(),
"lat-sd" = col_double(),
"lat-upper" = col_double(),
"license-terms" = col_character(),
"license-type" = col_factor(levels = c("CC_BY", "CC_BY_NC", "CC_0", "CUSTOM")),
"light-level" = col_double(),
"local-identifier" = col_factor(), # needed because api does not append tag_ / individual_ when downloading the specific info
"locality-according-to" = col_character(),
"locality" = col_factor(),
"location-accuracy-comments" = col_character(), # deployment property
"location-error-3d" = col_double(),
"location-error-numerical" = col_double(),
"location-error-percentile" = col_double(),
"location-error-text" = col_character(),
"location-lat" = col_double(),
"location-long" = col_double(),
"long-lower" = col_double(),
"long-median" = col_double(),
"long-sd" = col_double(),
"long-upper" = col_double(),
"lora:data-rate" = col_double(),
"lora:gateway-id" = col_factor(),
"lora:gateway-latitude" = col_double(),
"lora:gateway-longitude" = col_double(),
"lora:payload" = col_character(),
"lora:port" = col_integer(),
"lora:rssi" = col_double(),
"lora:snr" = col_integer(),
"lora:spreading-factor" = col_double(),
"lora:uplink-count" = col_integer(),
"lot:crc-status" = col_factor(levels = c("G", "E", "F")),
"lot:crc-status-text" = col_factor(levels = c("OK", "Fail", "OK(corrected)")), # might be outdated
"lotek:deltatime" = col_integer(),
"lotek-eres" = col_double(),
# "lotek-fix-status", # not documented in mb dictionary
"mag:magnetic-field-axes" = col_factor(),
"mag:magnetic-field-raw-x" = col_double(),
"mag:magnetic-field-raw-y" = col_double(),
"mag:magnetic-field-raw-z" = col_double(),
"mag:magnetic-field-sampling-frequency-per-axis" = col_double(),
"mag:magnetic-fields-raw" = col_character(),
"magnetic-field-sampling-frequency-per-axis" = col_double(),
"magnetic-field-x" = col_double(),
"magnetic-field-y" = col_double(),
"magnetic-field-z" = col_double(),
"main-location-lat" = col_double(),
"main-location-long" = col_double(),
"manipulation-comments" = col_character(),
"manipulation-status" = col_factor(),
"manipulation-type" = col_factor(
levels = c(
"confined", "domesticated", "manipulated-other",
"none", "reintroduction", "relocated"
)
), # MB see https://github.com/movebank/movebank-api-doc/issues/16 about manipulated-other
"manually-marked-outlier" = col_logical(),
"manually-marked-valid" = col_logical(),
"manufacturer-name" = col_factor(),
"migration-stage" = col_factor(),
"migration-stage-standard" = col_factor(
levels = c(
"altitudinal-migration", "breeding-grounds", "fall-migration",
"foraging-grounds", "foraging-migration", "irruptive-migration",
"latitudinal-migration", "migration-to-molt-site", "molt-site",
"natal-area", "nomadic-migration", "other-seasonal-migration",
"removal-migration", "reproductive-migration", "spawning-grounds",
"spring-migration", "stopover", "summer-non-breeding",
"vertical-migration-(aquatic)", "wintering-grounds"
)
),
"model" = col_factor(), # = tag_model
"modelled" = col_logical(),
"mortality-status" = col_factor(),
# "motus:batch-id", # not documented in mb dictionary
"mw:activity-count" = col_double(), # in study 108391885
"mw:show-in-kml" = col_logical(),
"mw:show-in-KML" = col_logical(),
"name" = col_factor(), # = study name
"nick-name" = col_factor(),
"number-of-deployed-locations" = col_integer(),
"number-of-deployments" = col_integer(),
"number-of-events" = col_integer(),
"number-of-individuals" = col_integer(),
"number-of-tags" = col_integer(),
"observer" = col_factor(),
"odba" = col_double(),
"opencollar:active-tracking" = col_logical(),
"opencollar:cold-retry" = col_integer(),
"opencollar:error-acc" = col_logical(),
"opencollar:error-bat" = col_logical(),
"opencollar:error-ble" = col_logical(),
"opencollar:error-flash" = col_logical(),
"opencollar:error-lr" = col_logical(),
"opencollar:error-lr-join" = col_logical(),
"opencollar:error-ublox" = col_logical(),
"opencollar:error-ublox-fix" = col_logical(),
"opencollar:hot-retry" = col_integer(),
"opencollar:locked" = col_logical(),
"opencollar:msg" = col_integer(),
"opencollar:payload-type" = col_factor(),
"opencollar:reset" = col_integer(),
"opencollar:uptime" = col_double(),
"opencollar:ver-fw-major" = col_factor(),
"opencollar:ver-fw-minor" = col_factor(),
"opencollar:ver-fw-type" = col_factor(),
"orientation:quaternion-raw-w" = col_double(),
"orientation:quaternion-raw-x" = col_double(),
"orientation:quaternion-raw-y" = col_double(),
"orientation:quaternion-raw-z" = col_double(),
"orientation-quaternions-raw" = col_character(),
"orientation-quaternions-sampling-frequency" = col_double(),
"orn:transmission-protocol" = col_factor(levels = c("GPRS", "SMS")),
"outlier-comments" = col_character(),
"pitch" = col_double(),
"principal-investigator-address" = col_character(),
"principal-investigator" = col_character(),
"principal-investigator-email" = col_character(),
"principal-investigator-name" = col_character(),
# "processing-type" = col_character(), # currently not used
"proofed" = col_logical(),
"provider-update-ts" = col_datetime(),
"prox-id" = col_factor(),
"prox-signal-strength" = col_double(),
"quaternion-raw-w" = col_double(),
"quaternion-raw-x" = col_double(),
"quaternion-raw-y" = col_double(),
"quaternion-raw-z" = col_double(),
"quaternions-sampling-frequency" = col_double(),
"raptor-workshop:behaviour" = col_factor(levels = c("Nesting", "Roosting")),
"raptor-workshop:deployment-special-event" = col_factor(
levels = c("BiologicallyIrrelecant", "Death", "ReleaseSite", "TagFailure")
),
"raptor-workshop:migration-state" = col_factor(
levels = c(
"BreedingGrounds", "FallMigration", "Migration", "NatalArea",
"NonBreedingGrounds", "SpringMigration", "StopOver", "SummerNonBreeding"
)
),
"receiver-deployment-id" = col_factor(),
"receiver-detector-id" = col_factor(),
"receiver-id" = col_factor(),
"receiver-latitude" = col_double(),
"receiver-longitude" = col_double(),
"relative-humidity" = col_double(),
"roll" = col_double(),
"rr-interval" = col_double(),
"sampling-frequency" = col_double(),
"savannah:alarm-type" = col_factor(),
"savannah:record-type" = col_factor(levels = c("P", "A")),
"scheduled-detachment-date" = col_date(),
"sensolus:fix-type" = col_character(),
"sensolus:location-source" = col_character(),
"sensor-type" = col_factor(levels = movebank_tag_type_table$`external_id`),
"sensor-type-id" = col_big_integer(),
"sensor-type-ids" = col_character(),
"sequence-number-burst" = col_character(),
"sequence-number" = col_integer(),
"serial_no" = col_factor(),
"sigfox:computed-location-radius" = col_double(),
"sigfox:computed-location-source" = col_factor(levels = as.character(c(1L, 2L, 6L))),
"sigfox:computed-location-status" = col_factor(levels = c("00", "01", "02", "20"), include_na = T),
"sigfox:country" = col_factor(),
"sigfox:device-type" = col_factor(),
"sigfox:duplicates" = col_character(),
"sigfox:format-character" = col_factor(levels = c(0:9, LETTERS[1L:6L]), ordered = TRUE),
"sigfox:link-quality" = col_factor(levels = as.character(c(0L:4L)), ordered = TRUE),
"sigfox:lqi" = col_factor(
levels = c("Limit", "Average", "Good", "Excellent", "NA"), ordered = TRUE
),
"sigfox:operator" = col_factor(),
"sigfox:payload" = col_character(),
"sigfox:rssi" = col_double(),
"sigfox:sensor-data-raw" = col_character(), ## its in "hexadecimal format"
"sigfox:tx-interval" = col_double(), ### MB integer?
"sigfox:tx-interval-text" = col_character(),
"solar-cell-voltage" = col_double(),
"solar-voltage-percent" = col_double(),
"speed-accuracy" = col_double(),
"start-timestamp" = col_datetime(),
"study-id" = col_big_integer(),
"study-local-timestamp" = col_datetime(),
"study-name" = col_factor(),
"study-objective" = col_character(),
"study-permission" = col_factor(levels = c("collaborator", "data_manager", "na")),
"study-site" = col_character(),
"study-specific-measurement" = col_character(),
"study-summary" = col_character(),
"study-timezone" = col_factor(),
"study-type" = col_factor(),
"suspend-license-terms" = col_logical(),
"tag-backup-voltage" = col_double(),
# "tag-battery-voltage",# not documented in mb dictionary
"tag-beacon-frequency" = col_double(),
"tag-calibration" = col_character(),
"tag-comments" = col_character(),
"tag-failure-comments" = col_character(),
"tag-firmware" = col_factor(),
"tag-id" = col_big_integer(),
"tag-local-identifier" = col_factor(),
"tag-manufacturer-name" = col_factor(),
"tag-mass" = col_double(),
"tag-mass-total" = col_double(),
"tag-model" = col_factor(),
# "tag-processing-type" = col_character(), ## currently not used
"tag-production-date" = col_character(),
"tag-readout-method" = col_factor(
levels = c(
"ISS", "LPWAN", "multiple", "none", "other-wireless",
"phone-network", "satellite", "tag-retrieval",
"telemetry-network", "Wi-Fi/Bluetooth"
)
),
"tag-retrieval-date" = col_date(),
"tag-serial-no" = col_factor(),
"tag_serial_no" = col_factor(),
"tag-settings" = col_character(),
"tag-tech-spec" = col_character(),
"tag-voltage" = col_double(),
"taxon-canonical-name" = col_factor(),
"taxon_detail" = col_factor(),
"taxon-ids" = col_character(),
"tdr:depth" = col_double(),
"technosmart:activity" = col_factor(levels = c("active", "inactive")),
"technosmart:signal-quality" = col_double(),
"telemetry-detection-count" = col_integer(),
"telemetry-run-id" = col_integer(),
"temperature-max" = col_double(),
"temperature-min" = col_double(),
"there-are-data-which-i-cannot-see" = col_logical(),
"tilt-angle" = col_double(),
"tilt-x" = col_double(),
"tilt-y" = col_double(),
"tilt-z" = col_double(),
"timestamp" = col_datetime(),
"timestamp-end" = col_datetime(),
"timestamp-first-deployed-location" = col_datetime(),
"timestamp-last-deployed-location" = col_datetime(),
"timestamp-of-first-deployed-location" = col_datetime(),
"timestamp-of-last-deployed-location" = col_datetime(),
"timestamp-start" = col_datetime(),
"tinyfox:activity-percent-last-24h" = col_double(),
"tinyfox:error-happened" = col_logical(),
"tinyfox:last-error" = col_factor(levels = as.character(c(1L, 2L, 4L, 5L, 6L, 7L))),
"tinyfox:max-movement-index" = col_factor(levels = as.character(c(0L:3L)), ordered = TRUE),
"tinyfox:memory-full" = col_logical(),
"tinyfox:pressure-min-last-24h" = col_double(),
"tinyfox:software-version" = col_character(),
"tinyfox:sunny-index-start-voltage" = col_double(),
"tinyfox:sunny-index-voltage-increase" = col_double(),
"tinyfox:tag-activation" = col_logical(),
"tinyfox:temperature-max-last-24h" = col_double(),
"tinyfox:temperature-min-last-24h" = col_double(),
"tinyfox:total-vedba" = col_double(),
"tinyfox:total-vedba-count" = col_integer(),
"tinyfox:vedba-00h-ago" = col_double(),
"tinyfox:vedba-01h-ago" = col_double(),
"tinyfox:vedba-02h-ago" = col_double(),
"tinyfox:vedba-03h-ago" = col_double(),
"tinyfox:vedba-04h-ago" = col_double(),
"tinyfox:vedba-05h-ago" = col_double(),
"tinyfox:vedba-06h-ago" = col_double(),
"tinyfox:vedba-07h-ago" = col_double(),
"tinyfox:vedba-08h-ago" = col_double(),
"tinyfox:vedba-09h-ago" = col_double(),
"tinyfox:vedba-10h-ago" = col_double(),
"tinyfox:vedba-11h-ago" = col_double(),
"tinyfox:vedba-12h-ago" = col_double(),
"tinyfox:vedba-13h-ago" = col_double(),
"tinyfox:vedba-14h-ago" = col_double(),
"tinyfox:vedba-15h-ago" = col_double(),
"tinyfox:vedba-16h-ago" = col_double(),
"tinyfox:vedba-17h-ago" = col_double(),
"tinyfox:vedba-18h-ago" = col_double(),
"tinyfox:vedba-19h-ago" = col_double(),
"tinyfox:vedba-20h-ago" = col_double(),
"tinyfox:vedba-21h-ago" = col_double(),
"tinyfox:vedba-22h-ago" = col_double(),
"tinyfox:vedba-23h-ago" = col_double(),
"tinyfox:vedba-burst-sum" = col_double(),
"track-segment-id" = col_factor(),
"transmission-protocol" = col_factor(),
"transmission-timestamp" = col_datetime(),
"tsn" = col_integer(),
"twilight" = col_factor(),
"twilight-excluded" = col_logical(),
"twilight-inserted" = col_logical(),
"underwater-count" = col_integer(),
"underwater-time" = col_double(),
"update-ts" = col_datetime(),
"utm-easting" = col_double(),
"utm-northing" = col_double(),
"utm-zone" = col_factor(),
"vectronics-activity-mode" = col_factor(levels = as.character(1L:7L)),
"vedba" = col_double(),
"vertical-error-numerical" = col_double(),
"vertical-speed" = col_double(),
"visible" = col_logical(),
"voltage-resolution" = col_double(),
"waterbird-workshop:behaviour" = col_factor(levels = c("Nesting", "Roosting")),
"waterbird-workshop:deployment-special-event" = col_factor(
levels = c("BiologicallyIrrelevant", "Death", "ReleaseSite", "TagFailure")
),
"waterbird-workshop:migration-state" = col_factor(
levels = c(
"BreedingGrounds", "FallMigration", "MigrationOther",
"MigrationToMolt", "MoltSite", "SpringMigration",
"StopOver", "SummerNonBreedingAdult",
"SummerNonBreedingImmature", "WinterGrounds"
)
),
"wc-residual" = col_double(),
"weight" = col_double(),
"wet" = col_logical(),
"wet-count" = col_integer(),
"wildfi-acc-conversion-factor" = col_double(),
"wildfi-gyro-conversion-factor" = col_double(),
"wildfi-hall-burst" = col_character(),
"wildfi-last-error" = col_factor(),
"wildfi-mag-conversion-factor" = col_double(),
"wildfi-prox-id-burst" = col_character(),
"wildfi-prox-rssi-burst" = col_character(),
"wildfi-record-type" = col_factor(),
"zero-crossings-amplitude" = col_double(),
"zero-crossings-steps" = col_integer(),
NULL
) # add null so it is easy to sort the list (all have comma at end)
movebank_column_types <- movebank_column_types[!unlist(lapply(movebank_column_types, is.null))]
movebank_colon_names <- list(
"lotek_" = "^lot:", "ornitela_" = "^orn:", "^heartrate:", "^mag:", "gsm" = "^gsm:gsm",
"gsm_mcc" = "^gsm:mcc",
"^bar:", "^gls:", "_" = ":"
)
to_download_names <- function(x) {
for (i in seq_along(movebank_colon_names)) {
x <- gsub(
movebank_colon_names[[i]],
names(movebank_colon_names)[[i]], x
)
}
x <- gsub("-", "_", x, fixed = TRUE)
return(x)
}
mb_column_units_underscore <- mb_column_units
names(mb_column_units_underscore) <-
to_download_names(names(mb_column_units_underscore))
mb_column_types_underscore <- movebank_column_types
names(mb_column_types_underscore) <-
to_download_names(names(mb_column_types_underscore))
toadd <- mb_column_types_underscore[grep(
"^animal_",
names(mb_column_types_underscore)
)]
names(toadd) <- sub("^animal_", "", names(toadd))
mb_column_types_underscore <- c(mb_column_types_underscore, toadd)
rm(toadd)
movebank_valid_entity_types <- c(
"study", "individual", "tag", "sensor", "tag_type", "taxon",
"deployment", "event", "event_reduced", "study_attribute"
)
movebank_minimal_columns <-
c(
"location-long",
"location-lat",
"timestamp",
"individual-local-identifier"
)
movebank_track_attributes <- c(
"individual-taxon-canonical-name",
"study-name",
"death-comments", "study-id"
) # comments don't seem to be attributes for sensors
movebank_track_attributes <- c(
movebank_track_attributes,
gsub("-", "_",
movebank_track_attributes,
fixed = TRUE
),
"individual_local_identifier"
) # individual local identifier here because in CSV its used as id column
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move2 documentation built on April 4, 2025, 12:24 a.m.
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Defines functions to_download_names
#' @importFrom vroom col_date col_datetime col_double col_factor col_integer col_character col_logical col_big_integer
NULL
# dput(movebank_retrieve("entity_type"='tag_type') ) # nolint: commented_code_linter
movebank_tag_type_table <- structure(list(description = c(
NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Localize tracking devices based on approximated distance to nearby GSM cell towers, WiFi or other network connectors.",
"Localize devices using a global navigation satellite system",
"Data derived from other sensor data", "Time-Depth Recording",
"Location Estimate by ATLAS system"
), external_id = c(
"bird-ring",
"gps", "radio-transmitter", "argos-doppler-shift", "natural-mark",
"acceleration", "solar-geolocator", "accessory-measurements",
"solar-geolocator-raw", "barometer", "magnetometer", "orientation",
"solar-geolocator-twilight", "acoustic-telemetry", "gyroscope",
"heart-rate", "sigfox-geolocation", "proximity", "geolocation-api",
"gnss", "derived", "tdr", "atlas-geolocation"
), id = structure(c(
1.96144061398975e-321,
3.22624866734334e-321, 3.32506179651159e-321, 4.09076473443635e-319,
1.16880220518501e-317, 1.16880269925066e-317, 1.92011745743723e-317,
3.87493413331319e-317, 4.59550368042471e-317, 3.8408856487366e-316,
3.84088619220881e-316, 4.04676003659103e-315, 4.51624043736367e-315,
6.1243104547751e-315, 6.41135836580693e-315, 1.09001844591634e-314,
1.13629901961024e-314, 1.30684843265253e-314, 1.52677095314155e-314,
1.52677095610594e-314, 1.52677095660001e-314, 2.10706387617373e-314,
2.14568681278764e-314
), class = "integer64"), is_location_sensor = c(
TRUE,
TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE,
FALSE, FALSE, TRUE, FALSE, FALSE, TRUE, FALSE, TRUE, TRUE, FALSE,
FALSE, TRUE
), name = structure(1:23, levels = c(
"Bird Ring",
"GPS", "Radio Transmitter", "Argos Doppler Shift", "Natural Mark",
"Acceleration", "Solar Geolocator", "Accessory Measurements",
"Solar Geolocator Raw", "Barometer", "Magnetometer", "Orientation",
"Solar Geolocator Twilight", "Acoustic Telemetry", "Gyroscope",
"Heart Rate", "Sigfox Geolocation", "Proximity", "Geolocation API",
"GNSS", "Derived", "TDR", "ATLAS Geolocation"
), class = "factor")), row.names = c(
NA,
-23L
), spec = structure(list(cols = list(description = structure(list(), class = c(
"collector_character",
"collector"
)), external_id = structure(list(), class = c(
"collector_character",
"collector"
)), id = structure(list(), class = c(
"collector_big_integer",
"collector"
)), is_location_sensor = structure(list(), class = c(
"collector_logical",
"collector"
)), name = structure(list(
levels = NULL, ordered = FALSE,
include_na = FALSE
), class = c("collector_factor", "collector"))), default = structure(list(), class = c(
"collector_guess",
"collector"
)), delim = ","), class = "col_spec"), class = c(
"spec_tbl_df",
"tbl_df", "tbl", "data.frame"
))
movebank_spatial_column_pairs <- list(
lora_gateway_location = c("lora_gateway_longitude", "lora_gateway_latitude"),
argos_location_1 = c("argos_lon1", "argos_lat1"),
argos_location_2 = c("argos_lon2", "argos_lat2"),
birth_location = c("birth_longitude", "birth_latitude"),
animal_birth_hatch_location = c("animal_birth_hatch_longitude", "animal_birth_hatch_latitude"),
animal_mortality_location = c("animal_mortality_longitude", "animal_mortality_latitude"),
mortality_location = c("mortality_longitude", "mortality_latitude"),
capture_location = c("capture_longitude", "capture_latitude"),
location_median = c("long_median", "lat_median"),
location_upper = c("long_upper", "lat_upper"),
location_lower = c("long_lower", "lat_lower"),
main_location = c("main_location_long", "main_location_lat"),
deploy_on_location = c("deploy_on_longitude", "deploy_on_latitude"),
deploy_off_location = c("deploy_off_longitude", "deploy_off_latitude"),
receiver_location = c("receiver_longitude", "receiver_latitude")
)
# Columns from movebank with these names are automatically converted to the correct units
mb_column_units <- c(
"acceleration-sampling-frequency-per-axis" = "Hz",
"accelerations" = "m/s^2",
"acceleration-x" = "m/s^2",
"acceleration-y" = "m/s^2",
"acceleration-z" = "m/s^2",
"activity-count" = "count",
"angular-velocity-x" = "arc_degree/s",
"angular-velocity-y" = "arc_degree/s",
"angular-velocity-z" = "arc_degree/s",
"animal-mass" = "g",
"argos:altitude" = "m",
"argos:best-level" = "dB",
"argos:calcul-freq" = "MHz",
"argos:error-radius" = "m",
"argos:gdop" = "m/Hz",
"argos:orientation" = "arc_degree",
"argos:pass-duration" = "s",
"argos:semi-major" = "m",
"argos:semi-minor" = "m",
"atlas:varx" = "m^2",
"atlas:varxy" = "m^2",
"atlas:vary" = "m^2",
"bar:barometric-depth" = "m",
"bar:barometric-height" = "m",
"bar:barometric-pressure" = "mbar",
"barometric-depth" = "m",
"barometric-height" = "m",
"barometric-pressure" = "mbar",
# "bas:compensated-latitude" = , # decimal degrees, WGS84 reference system
"bas:mid-value-secs" = "s",
# "bas:stationary-latitude" = , # decimal degrees, WGS84 reference system
# "bas:transition-1" = , # units GMT
# "bas:transition-2" = , # units GMT
"battery-charge-percent" = "%",
"battery-charging-current" = "mA",
"battery-charging-voltage" = "mV",
"beacon:frequency" = "MHz",
"capture-handling-time" = "s",
"compass-heading" = "degree_north",
"cpu-temperature" = "degree_C",
"ctt:solar-current-since-last-fix" = "mA",
"deltatime" = "s",
# "deploy-off-latitude" = , # decimal degrees, WGS84 reference system
# "deploy-off-longitude" = , # decimal degrees, WGS84 reference system
# "deploy-on-latitude" = , # decimal degrees, WGS84 reference system
# "deploy-on-longitude" = , # decimal degrees, WGS84 reference system
"depth" = "m",
"dive-duration" = "s",
"ecg:sampling-frequency" = "Hz",
"eobs:acceleration-sampling-frequency-per-axis" = "Hz",
"eobs:battery-voltage" = "mV",
"eobs:fix-battery-voltage" = "mV",
"eobs:horizontal-accuracy-estimate" = "m",
"eobs:speed-accuracy-estimate" = "m/s",
"eobs:temperature" = "degree_C",
"eobs:used-time-to-get-fix" = "s",
"error-count" = "count",
"external-temperature" = "degree_C",
"geolocation-station-count" = "count",
"geolocator-sun-elevation-angle" = "arc_degree",
"gmatrix:gps-fix-interval" = "s",
"gnss:dop" = "1",
"gnss:hdop" = "1",
"gnss:maximum-signal-strength" = "dBm",
"gnss:message-count" = "count",
"gnss:pdop" = "1",
"gnss:satellite-count" = "count",
"gnss:time-to-fix" = "s",
"gnss:vdop" = "1",
"gps:activity-count" = "count",
"gps:dop" = "1",
"gps:gdop" = "1",
"gps:hdop" = "1",
"gps:maximum-signal-strength" = "dBm",
"gps:message-count" = "count",
"gps:pdop" = "1",
"gps:satellite-count" = "count",
"gps:speed-accuracy-estimate" = "m/s",
"gps:tdop" = "1",
"gps-time-to-fix" = "s",
"gps:vdop" = "1",
"ground-speed" = "m/s",
# "gsm:gsm-signal-strength" = "ASU", # arbitrary strength units
"gt:sys-week" = "count",
"gt:tx-count" = "count",
"gyroscope-sampling-frequency-per-axis" = "Hz",
"heading" = "degree_north",
"heartrate:ecg-sampling-frequency" = "Hz",
"heartrate:heart-rate" = "1/min", # Units: beats per minute
"heartrate:rr-interval" = "s",
"heartrate:voltage-resolution" = "mV",
"height-above-ellipsoid" = "m",
"height-above-ground-level" = "m",
"height-above-mean-sea-level" = "m",
"height-above-msl" = "m",
"icarus:solar-cell-current" = "mA",
"individual-count" = "count",
"internal-temperature" = "degree_C",
# "lat-lower" = , # decimal degrees, WGS84 reference system
# "lat-upper" = , # decimal degrees, WGS84 reference system
"location-error-3d" = "m",
"location-error-numerical" = "m",
"location-error-percentile" = "%",
# "long-lower" = , # decimal degrees, WGS84 reference system
# "long-upper" = , # decimal degrees, WGS84 reference system
"lora:rssi" = "dBm",
"lora:snr" = "dB",
"lora:uplink-count" = "count",
"lotek:deltatime" = "s",
"lotek-eres" = "1",
"mag:magnetic-field-sampling-frequency-per-axis" = "Hz",
"magnetic-field-sampling-frequency-per-axis" = "Hz",
"magnetic-field-x" = "microtesla",
"magnetic-field-y" = "microtesla",
"magnetic-field-z" = "microtesla",
"mw:activity-count" = "count",
"number-of-deployed-locations" = "count",
"number-of-deployments" = "count",
"number-of-events" = "count",
"number-of-individuals" = "count",
"number-of-tags" = "count",
"odba" = "standard_free_fall",
"opencollar:cold-retry" = "count",
"opencollar:hot-retry" = "count",
"opencollar:msg" = "count",
"opencollar:uptime" = "weeks",
"orientation-quaternions-sampling-frequency" = "Hz",
"pitch" = "arc_degree",
"quaternions-sampling-frequency" = "Hz",
"relative-humidity" = "%",
"roll" = "arc_degree",
"rr-interval" = "s",
"sampling-frequency" = "Hz",
"sequence-number" = "count",
"sigfox:computed-location-radius" = "m",
"sigfox:tx-interval" = "min",
"solar-cell-voltage" = "mV",
"solar-voltage-percent" = "%",
"speed-accuracy" = "m/s",
"tag-backup-voltage" = "mV",
"tag-beacon-frequency" = "MHz",
"tag-mass" = "g",
"tag-mass-total" = "g",
"tag-voltage" = "mV",
"tdr:depth" = "m",
# "technosmart:signal-quality" = ,
# MB figure out how to express the carrier to noise density ratio:
# https://en.wikipedia.org/wiki/Carrier-to-noise_ratio#Carrier-to-noise_density_ratio
# Units: dB-Hz (decibel-Hz?)(Wikipedia: dB(Hz) – bandwidth relative to one hertz. E.g., 20 dB‑Hz corresponds to a
# bandwidth of 100 Hz)
"temperature-max" = "degree_C",
"temperature-min" = "degree_C",
"tilt-angle" = "arc_degree", # Units: degrees
"tilt-x" = "standard_free_fall",
"tilt-y" = "standard_free_fall",
"tilt-z" = "standard_free_fall",
"tinyfox:activity-percent-last-24h" = "%",
"tinyfox:pressure-min-last-24h" = "mbar",
"tinyfox:sunny-index-start-voltage" = "mV",
"tinyfox:sunny-index-voltage-increase" = "mV",
"tinyfox:temperature-max-last-24h" = "degree_C",
"tinyfox:temperature-min-last-24h" = "degree_C",
"tinyfox:total-vedba-count" = "count",
"tinyfox:total-vedba" = "m/s^2",
"tinyfox:vedba-00h-ago" = "m/s^2",
"tinyfox:vedba-01h-ago" = "m/s^2",
"tinyfox:vedba-02h-ago" = "m/s^2",
"tinyfox:vedba-03h-ago" = "m/s^2",
"tinyfox:vedba-04h-ago" = "m/s^2",
"tinyfox:vedba-05h-ago" = "m/s^2",
"tinyfox:vedba-06h-ago" = "m/s^2",
"tinyfox:vedba-07h-ago" = "m/s^2",
"tinyfox:vedba-08h-ago" = "m/s^2",
"tinyfox:vedba-09h-ago" = "m/s^2",
"tinyfox:vedba-10h-ago" = "m/s^2",
"tinyfox:vedba-11h-ago" = "m/s^2",
"tinyfox:vedba-12h-ago" = "m/s^2",
"tinyfox:vedba-13h-ago" = "m/s^2",
"tinyfox:vedba-14h-ago" = "m/s^2",
"tinyfox:vedba-15h-ago" = "m/s^2",
"tinyfox:vedba-16h-ago" = "m/s^2",
"tinyfox:vedba-17h-ago" = "m/s^2",
"tinyfox:vedba-18h-ago" = "m/s^2",
"tinyfox:vedba-19h-ago" = "m/s^2",
"tinyfox:vedba-20h-ago" = "m/s^2",
"tinyfox:vedba-21h-ago" = "m/s^2",
"tinyfox:vedba-22h-ago" = "m/s^2",
"tinyfox:vedba-23h-ago" = "m/s^2",
"tinyfox:vedba-burst-sum" = "m/s^2",
"underwater-count" = "count",
"underwater-time" = "s",
"utm-easting" = "m", # Units: meters, WGS84 reference system
"utm-northing" = "m", # Units: meters, WGS84 reference system
"vedba" = "standard_free_fall",
"vertical-error-numerical" = "m",
"vertical-speed" = "m/s",
"voltage-resolution" = "mV",
"wc-residual" = "1",
"weight" = "g",
"wet-count" = "count",
"zero-crossings-steps" = "count",
NULL
)
movebank_column_types <- list(
"<html>" = col_character(),
"acceleration-axes" = col_character(),
"acceleration-raw-x" = col_double(),
"acceleration-raw-y" = col_double(),
"acceleration-raw-z" = col_double(),
"acceleration-sampling-frequency-per-axis" = col_double(),
"accelerations" = col_character(),
"accelerations-raw" = col_character(),
"acceleration-x" = col_double(),
"acceleration-y" = col_double(),
"acceleration-z" = col_double(),
"acknowledgements" = col_character(),
"activity-count" = col_integer(),
"activity-x" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000334/
"activity-y" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000335/
"activity-z" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000336/
"algorithm-marked-outlier" = col_logical(),
"alt-index-id" = col_character(),
"alt-project-id" = col_factor(),
# "ambiguous-detection", # not documented in mb dictionary
"angular-velocities-raw" = col_character(),
"angular-velocity-x" = col_double(),
"angular-velocity-y" = col_double(),
"angular-velocity-z" = col_double(),
"animal-birth-hatch-latitude" = col_double(),
"animal-birth-hatch-longitude" = col_double(),
"animal-comments" = col_character(),
"animal-death-comments" = col_character(),
"animal-earliest-date-born" = col_datetime(),
"animal-exact-date-of-birth" = col_datetime(),
"animal-group-id" = col_factor(),
"animal-id" = col_factor(),
"animal-latest-date-born" = col_datetime(),
"animal-life-stage" = col_factor(),
"animal-marker-id" = col_factor(),
"animal-mass" = col_double(),
"animal-mates" = col_factor(),
"animal-mortality-date" = col_date(),
"animal-mortality-latitude" = col_double(),
"animal-mortality-longitude" = col_double(),
"animal-mortality-type" = col_factor(
levels = c(
"bycatch", "capture", "electrocution", "harvest", "disease",
"natural-death", "other", "parasites", "poison", "predation",
"starvation", "unknown", "vehicle-collision"
)
),
"animal-nickname" = col_factor(),
"animal-offspring" = col_factor(),
"animal-parents" = col_factor(),
"animal-reproductive-condition" = col_factor(),
"animal-ring-id" = col_factor(),
"animal-sex" = col_factor(levels = c("m", "f", "u")),
"animal-siblings" = col_factor(),
"animal-taxon" = col_factor(),
"animal_taxon_detail" = col_factor(),
"argos:altitude" = col_double(),
"argos:best-level" = col_double(),
"argos:calcul-freq" = col_double(),
"argos:error-radius" = col_double(),
"argos:gdop" = col_double(),
"argos:iq" = col_factor(
levels = c(apply(expand.grid(0:6, 0:8), 1, paste0, collapse = ""), 0:8, "99")
), # MB argos:iq 99 is not in the documentation but does occur in study 1420256397
"argos:lat1" = col_double(),
"argos:lat2" = col_double(),
"argos:lc" = col_factor(levels = c("G", 3:0, "A", "B", "Z"), ordered = TRUE),
"argos:location-algorithm" = col_factor(levels = c("least-squares", "Kalman")),
"argos:lon1" = col_double(),
"argos:lon2" = col_double(),
"argos:nb-mes-120" = col_integer(),
"argos:nb-mes" = col_integer(),
# "argos:nb-mes-identical", # not documented in mb dictionary
"argos:nopc" = col_factor(ordered = TRUE, levels = as.character(c(0:4, 9))), # MB argos:nopc 9 is not in the documentation but does occur in study 1420256397
"argos:orientation" = col_double(),
"argos:pass-duration" = col_double(),
"argos:sat-id" = col_factor(),
"argos:semi-major" = col_double(),
"argos:semi-minor" = col_double(),
"argos:sensor-1" = col_integer(),
"argos:sensor-2" = col_integer(),
"argos:sensor-3" = col_integer(),
"argos:sensor-4" = col_integer(),
"argos:transmission-timestamp" = col_datetime(),
"argos:valid-location-algorithm" = col_factor(levels = as.character(1L:2L)),
"argos:valid-location-manual" = col_factor(levels = as.character(1L:2L)),
"atlas:varx" = col_double(),
"atlas:varxy" = col_double(),
"atlas:vary" = col_double(),
"attachment-body-part" = col_factor(),
"attachment-comments" = col_character(),
"attachment-type" = col_factor(
levels = c(
"backpack-harness", "collar", "ear-tag", "fin mount", "glue",
"harness", "implant", "leg-band", "leg-loop-harness", "none",
"other", "subcutaneous-anchor", "suction-cup", "sutures", "tape"
)
),
"awt:alarms-battery" = col_logical(),
"awt:alarms-cbit" = col_logical(),
"awt:alarms-coverage" = col_logical(),
"awt:alarms-geofence" = col_logical(),
"awt:alarms-memory" = col_logical(),
"awt:alarms-movement" = col_logical(),
"awt:alarms-tamperfoil" = col_logical(),
"awt:alarms-track-mode" = col_logical(),
"awt:log-interval" = col_factor(
levels = c(
"every 10 minutes", "every 30 minutes", "every 1 hour",
"every 2 hours", "every 3 hours", "every 4 hours",
"every 5 hours", "every 6 hours", "every 8 hours",
"every 12 hours", "every 24 hours", "every 48 hours", "off"
), ordered = TRUE
),
"bar:barometric-depth" = col_double(),
"bar:barometric-height" = col_double(),
"bar:barometric-pressure" = col_double(),
"barometric-depth" = col_double(),
"barometric-height" = col_double(),
"barometric-pressure" = col_double(),
"bas:compensated-latitude" = col_double(),
"bas:confidence" = col_factor(), # MB only integer values allowed?
"bas:fix-type" = col_factor(levels = c("noon", "midnight")),
"bas:mid-value-secs" = col_double(),
"bas:stationary-latitude" = col_double(),
"bas:transition-1" = col_double(),
"bas:transition-2" = col_double(),
"battery-charge-percent" = col_integer(), # integer in study
"battery-charging-current" = col_double(),
"battery-charging-voltage" = col_logical(),
"beacon:frequency" = col_double(),
"behavior-according-to" = col_character(),
"behavioural-classification" = col_factor(),
"breed-stage" = col_character(),
"canonical-name" = col_factor(),
"capture-handling-time" = col_double(),
"capture-latitude" = col_double(),
"capture-longitude" = col_double(),
"capture-method" = col_character(),
"capture-timestamp" = col_datetime(),
"citation" = col_character(),
"comments" = col_character(),
"compass-heading" = col_double(),
"conductivity" = col_double(),
"contact-person" = col_character(),
"contact-person-id" = col_factor(),
"contact-person-name" = col_factor(),
"cpu-temperature" = col_double(),
"ctt:solar-current-since-last-fix" = col_integer(),
"data-decoding-software" = col_factor(),
"data-processing-software" = col_factor(),
"dba-comments" = col_character(),
"death-comments" = col_character(),
"deltatime" = col_integer(),
"deployment-comments" = col_character(),
"deployment-end-comments" = col_character(),
"deployment-end-type" = col_factor(
levels = c(
"captured", "dead", "dead/fall-off",
"equipment-failure", "fall-off", "other", "released",
"removal", "transmission-end", "unknown"
)
),
"deployment-id" = col_big_integer(), # deployment id now can be a given name defined by de user and, in its absence a large integer created by movebank
"deployment-image" = col_character(),
"deploy-off-date" = col_datetime(),
"deploy-off-latitude" = col_double(),
"deploy-off-longitude" = col_double(),
"deploy-off-measurements" = col_character(),
"deploy-off-person" = col_character(),
"deploy-off-sampling" = col_character(),
"deploy-off-timestamp" = col_datetime(),
"deploy-on-date" = col_datetime(),
"deploy-on-latitude" = col_double(),
"deploy-on-longitude" = col_double(),
"deploy-on-measurements" = col_character(),
"deploy-on-person" = col_character(),
"deploy-on-sampling" = col_character(),
"deploy-on-timestamp" = col_datetime(),
"depth" = col_double(),
"dive-duration" = col_integer(),
"druid:alert" = col_factor(levels = 1),
"druid:data-source" = col_factor(
levels = c("[1]", "[2]", "[4]", "[8]", "[10]", "[100]", "[101]")
),
"duty-cycle" = col_character(),
"earliest-date-born" = col_datetime(), # seems to be undocumented api name
"ecg:raw" = col_double(),
"ecg:sampling-frequency" = col_double(),
"ecgs:raw" = col_character(),
"end-timestamp" = col_datetime(),
"eobs:acceleration-axes" = col_factor(),
"eobs:acceleration-sampling-frequency-per-axis" = col_double(),
"eobs:accelerations-raw" = col_character(),
"eobs:activity" = col_integer(),
"eobs:activity-samples" = col_integer(),
"eobs:battery-voltage" = col_integer(),
"eobs:fix-battery-voltage" = col_integer(),
"eobs:horizontal-accuracy-estimate" = col_double(),
"eobs:key-bin-checksum" = col_big_integer(),
"eobs:speed-accuracy-estimate" = col_double(),
"eobs:start-timestamp" = col_datetime(),
"eobs:status" = col_factor(ordered = TRUE, levels = LETTERS[1L:4L]),
"eobs:temperature" = col_integer(),
"eobs:type-of-fix" = col_factor(), # MB galapagos albatrosses have a type of fix 0 for eobs:type-of-fix I expect either 2 or 3 : http://vocab.nerc.ac.uk/collection/MVB/current/MVB000100/
"eobs:used-time-to-get-fix" = col_integer(),
"error-count" = col_integer(),
"event-group-id" = col_factor(),
"event-id" = col_big_integer(),
"exact-date-of-birth" = col_datetime(), # seems to be undocumented api name
"external-temperature" = col_double(),
"flt:switch" = col_factor(
levels = c(as.character(c(0L, 6L, 48L, 49L, 64L, 69L, 72L, 77L, 112L))), ordered = TRUE
), # MB check if ordered
"format-type" = col_character(),
"geolocation-station-count" = col_integer(),
"geolocator-calibration" = col_character(),
"geolocator-fix-type" = col_factor(),
"geolocator-light-threshold" = col_double(),
"geolocator-rise" = col_logical(),
"geolocator-sensor-comments" = col_character(),
"geolocator-sun-elevation-angle" = col_double(),
"geolocator-twilight3" = col_datetime(),
"georeference-protocol" = col_factor(),
"gls:light-level" = col_double(),
"gls:twilight" = col_integer(),
"gmatrix:alert" = col_integer(),
"gmatrix:alert-message" = col_factor(),
"gmatrix:device-type" = col_factor(),
"gmatrix:event" = col_factor(levels = as.character(c(16L, 48L, 49L, 50L, 51L, 52L, 80L))),
"gmatrix:firmware-version" = col_factor(),
"gmatrix:gps-event" = col_factor(levels = as.character(c(0L:5L))),
"gmatrix:gps-event-text" = col_factor(
levels = c("Unknown location", "Alert", "Panic", "Timed", "Fall", "Heartbeat")
),
"gmatrix:gps-fix-interval" = col_integer(),
"gmatrix:gps-fix-interval-text" = col_factor(),
"gmatrix:hardware-version" = col_factor(),
"gmatrix:is-moving" = col_factor(levels = c("A1", "0")),
"gmatrix:is-moving-text" = col_factor(levels = c("MOVING", "STATIC")),
"gmatrix:last-location" = col_factor(levels = c("null", "0", "1")),
"gmatrix:last-location-text" = col_factor(
levels = c("not available", "new location", "last known location")
),
"gmatrix:mode" = col_factor(levels = as.character(c(0:6))),
"gmatrix:mode-text" = col_factor(
levels = c(
"reserved", "help me", "press it", "track it",
"guard it", "monitor it", "don't lose it"
)
),
"gmatrix:packet-type" = col_factor(), # MB check with Sarah if can be integer
"gnss:dop" = col_double(),
"gnss:fix-type" = col_factor(ordered = TRUE, levels = 1L:3L),
"gnss:fix-type-raw" = col_factor(),
"gnss:hdop" = col_double(),
"gnss:maximum-signal-strength" = col_double(),
"gnss:message-count" = col_integer(),
"gnss:pdop" = col_double(),
"gnss:satellite-count" = col_integer(),
"gnss:time-to-fix" = col_double(),
"gnss:vdop" = col_double(),
"go_public_date" = col_datetime(),
"gps:activity-count" = col_integer(),
"gps:dop" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000115/
"gps:fix-type" = col_factor(
levels = as.character(0:3), ordered = TRUE
), # MB 0 not in vocabulary for fix type but in study 619097045
"gps:fix-type-raw" = col_factor(),
"gps:gdop" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000360/
"gps:hdop" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000118/
"gps:maximum-signal-strength" = col_double(),
"gps:message-count" = col_integer(),
"gps:pdop" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000284/
"gps:satellite-count" = col_integer(),
"gps:speed-accuracy-estimate" = col_double(),
"gps:tdop" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000361/
"gps-time-to-fix" = col_double(),
"gps:twilight" = col_factor(),
"gps:vdop" = col_double(), # http://vocab.nerc.ac.uk/collection/MVB/current/MVB000122/
"grants-used" = col_character(),
"ground-speed" = col_double(),
"gsat:charge-mode" = col_factor(
levels = c("Discharge", "ChargeSlow", "ChargeMedium", "ChargeHigh"), ordered = TRUE
),
"gsat:low-power-mode" = col_logical(),
"gsat:orientation" = col_factor(
levels = c("XPositive", "XNegative", "YPositive", "YNegative", "ZPositive", "Znegative")
),
"gsm:gsm-signal-strength" = col_integer(),
"gsm:mcc-mnc" = col_integer(),
# "gt:activity-count", # not documented in mb dictionary
"gt:sys-week" = col_integer(),
"gt:tx-count" = col_integer(),
"guaternions-raw" = col_character(),
"gundi-urn" = col_character(),
"gyroscope-axes" = col_factor(),
"gyroscope-sampling-frequency-per-axis" = col_double(),
"habitat-according-to" = col_character(),
"habitat" = col_factor(),
"heading" = col_double(),
"heartrate:ecg-raw" = col_integer(),
"heartrate:ecg-sampling-frequency" = col_double(),
"heartrate:ecgs-raw" = col_character(),
"heartrate:heart-rate" = col_double(),
"heartrate:rr-interval" = col_double(),
"heartrate:voltage-resolution" = col_double(),
"height-above-ellipsoid" = col_double(),
"height-above-ground-level" = col_double(),
"height-above-mean-sea-level" = col_double(),
"height-above-msl" = col_double(),
"height-raw" = col_character(),
"i-am-collaborator" = col_logical(),
"i-am-owner" = col_logical(),
"i-can-see-data" = col_logical(),
"icarus:solar-cell-current" = col_double(),
"id" = col_big_integer(),
"i-have-download-access" = col_logical(),
"import-marked-outlier" = col_logical(),
"individual-count" = col_integer(),
"individual-id" = col_big_integer(),
"individual-local-identifier" = col_factor(),
"individual-taxon-canonical-name" = col_factor(),
"internal-temperature" = col_double(),
"is-location-sensor" = col_logical(),
"is-test" = col_logical(),
"latest-date-born" = col_datetime(), # seems to be undocumented api name
"lat-lower" = col_double(),
"lat-median" = col_double(),
"lat-sd" = col_double(),
"lat-upper" = col_double(),
"license-terms" = col_character(),
"license-type" = col_factor(levels = c("CC_BY", "CC_BY_NC", "CC_0", "CUSTOM")),
"light-level" = col_double(),
"local-identifier" = col_factor(), # needed because api does not append tag_ / individual_ when downloading the specific info
"locality-according-to" = col_character(),
"locality" = col_factor(),
"location-accuracy-comments" = col_character(), # deployment property
"location-error-3d" = col_double(),
"location-error-numerical" = col_double(),
"location-error-percentile" = col_double(),
"location-error-text" = col_character(),
"location-lat" = col_double(),
"location-long" = col_double(),
"long-lower" = col_double(),
"long-median" = col_double(),
"long-sd" = col_double(),
"long-upper" = col_double(),
"lora:data-rate" = col_double(),
"lora:gateway-id" = col_factor(),
"lora:gateway-latitude" = col_double(),
"lora:gateway-longitude" = col_double(),
"lora:payload" = col_character(),
"lora:port" = col_integer(),
"lora:rssi" = col_double(),
"lora:snr" = col_integer(),
"lora:spreading-factor" = col_double(),
"lora:uplink-count" = col_integer(),
"lot:crc-status" = col_factor(levels = c("G", "E", "F")),
"lot:crc-status-text" = col_factor(levels = c("OK", "Fail", "OK(corrected)")), # might be outdated
"lotek:deltatime" = col_integer(),
"lotek-eres" = col_double(),
# "lotek-fix-status", # not documented in mb dictionary
"mag:magnetic-field-axes" = col_factor(),
"mag:magnetic-field-raw-x" = col_double(),
"mag:magnetic-field-raw-y" = col_double(),
"mag:magnetic-field-raw-z" = col_double(),
"mag:magnetic-field-sampling-frequency-per-axis" = col_double(),
"mag:magnetic-fields-raw" = col_character(),
"magnetic-field-sampling-frequency-per-axis" = col_double(),
"magnetic-field-x" = col_double(),
"magnetic-field-y" = col_double(),
"magnetic-field-z" = col_double(),
"main-location-lat" = col_double(),
"main-location-long" = col_double(),
"manipulation-comments" = col_character(),
"manipulation-status" = col_factor(),
"manipulation-type" = col_factor(
levels = c(
"confined", "domesticated", "manipulated-other",
"none", "reintroduction", "relocated"
)
), # MB see https://github.com/movebank/movebank-api-doc/issues/16 about manipulated-other
"manually-marked-outlier" = col_logical(),
"manually-marked-valid" = col_logical(),
"manufacturer-name" = col_factor(),
"migration-stage" = col_factor(),
"migration-stage-standard" = col_factor(
levels = c(
"altitudinal-migration", "breeding-grounds", "fall-migration",
"foraging-grounds", "foraging-migration", "irruptive-migration",
"latitudinal-migration", "migration-to-molt-site", "molt-site",
"natal-area", "nomadic-migration", "other-seasonal-migration",
"removal-migration", "reproductive-migration", "spawning-grounds",
"spring-migration", "stopover", "summer-non-breeding",
"vertical-migration-(aquatic)", "wintering-grounds"
)
),
"model" = col_factor(), # = tag_model
"modelled" = col_logical(),
"mortality-status" = col_factor(),
# "motus:batch-id", # not documented in mb dictionary
"mw:activity-count" = col_double(), # in study 108391885
"mw:show-in-kml" = col_logical(),
"mw:show-in-KML" = col_logical(),
"name" = col_factor(), # = study name
"nick-name" = col_factor(),
"number-of-deployed-locations" = col_integer(),
"number-of-deployments" = col_integer(),
"number-of-events" = col_integer(),
"number-of-individuals" = col_integer(),
"number-of-tags" = col_integer(),
"observer" = col_factor(),
"odba" = col_double(),
"opencollar:active-tracking" = col_logical(),
"opencollar:cold-retry" = col_integer(),
"opencollar:error-acc" = col_logical(),
"opencollar:error-bat" = col_logical(),
"opencollar:error-ble" = col_logical(),
"opencollar:error-flash" = col_logical(),
"opencollar:error-lr" = col_logical(),
"opencollar:error-lr-join" = col_logical(),
"opencollar:error-ublox" = col_logical(),
"opencollar:error-ublox-fix" = col_logical(),
"opencollar:hot-retry" = col_integer(),
"opencollar:locked" = col_logical(),
"opencollar:msg" = col_integer(),
"opencollar:payload-type" = col_factor(),
"opencollar:reset" = col_integer(),
"opencollar:uptime" = col_double(),
"opencollar:ver-fw-major" = col_factor(),
"opencollar:ver-fw-minor" = col_factor(),
"opencollar:ver-fw-type" = col_factor(),
"orientation:quaternion-raw-w" = col_double(),
"orientation:quaternion-raw-x" = col_double(),
"orientation:quaternion-raw-y" = col_double(),
"orientation:quaternion-raw-z" = col_double(),
"orientation-quaternions-raw" = col_character(),
"orientation-quaternions-sampling-frequency" = col_double(),
"orn:transmission-protocol" = col_factor(levels = c("GPRS", "SMS")),
"outlier-comments" = col_character(),
"pitch" = col_double(),
"principal-investigator-address" = col_character(),
"principal-investigator" = col_character(),
"principal-investigator-email" = col_character(),
"principal-investigator-name" = col_character(),
# "processing-type" = col_character(), # currently not used
"proofed" = col_logical(),
"provider-update-ts" = col_datetime(),
"prox-id" = col_factor(),
"prox-signal-strength" = col_double(),
"quaternion-raw-w" = col_double(),
"quaternion-raw-x" = col_double(),
"quaternion-raw-y" = col_double(),
"quaternion-raw-z" = col_double(),
"quaternions-sampling-frequency" = col_double(),
"raptor-workshop:behaviour" = col_factor(levels = c("Nesting", "Roosting")),
"raptor-workshop:deployment-special-event" = col_factor(
levels = c("BiologicallyIrrelecant", "Death", "ReleaseSite", "TagFailure")
),
"raptor-workshop:migration-state" = col_factor(
levels = c(
"BreedingGrounds", "FallMigration", "Migration", "NatalArea",
"NonBreedingGrounds", "SpringMigration", "StopOver", "SummerNonBreeding"
)
),
"receiver-deployment-id" = col_factor(),
"receiver-detector-id" = col_factor(),
"receiver-id" = col_factor(),
"receiver-latitude" = col_double(),
"receiver-longitude" = col_double(),
"relative-humidity" = col_double(),
"roll" = col_double(),
"rr-interval" = col_double(),
"sampling-frequency" = col_double(),
"savannah:alarm-type" = col_factor(),
"savannah:record-type" = col_factor(levels = c("P", "A")),
"scheduled-detachment-date" = col_date(),
"sensolus:fix-type" = col_character(),
"sensolus:location-source" = col_character(),
"sensor-type" = col_factor(levels = movebank_tag_type_table$`external_id`),
"sensor-type-id" = col_big_integer(),
"sensor-type-ids" = col_character(),
"sequence-number-burst" = col_character(),
"sequence-number" = col_integer(),
"serial_no" = col_factor(),
"sigfox:computed-location-radius" = col_double(),
"sigfox:computed-location-source" = col_factor(levels = as.character(c(1L, 2L, 6L))),
"sigfox:computed-location-status" = col_factor(levels = c("00", "01", "02", "20"), include_na = T),
"sigfox:country" = col_factor(),
"sigfox:device-type" = col_factor(),
"sigfox:duplicates" = col_character(),
"sigfox:format-character" = col_factor(levels = c(0:9, LETTERS[1L:6L]), ordered = TRUE),
"sigfox:link-quality" = col_factor(levels = as.character(c(0L:4L)), ordered = TRUE),
"sigfox:lqi" = col_factor(
levels = c("Limit", "Average", "Good", "Excellent", "NA"), ordered = TRUE
),
"sigfox:operator" = col_factor(),
"sigfox:payload" = col_character(),
"sigfox:rssi" = col_double(),
"sigfox:sensor-data-raw" = col_character(), ## its in "hexadecimal format"
"sigfox:tx-interval" = col_double(), ### MB integer?
"sigfox:tx-interval-text" = col_character(),
"solar-cell-voltage" = col_double(),
"solar-voltage-percent" = col_double(),
"speed-accuracy" = col_double(),
"start-timestamp" = col_datetime(),
"study-id" = col_big_integer(),
"study-local-timestamp" = col_datetime(),
"study-name" = col_factor(),
"study-objective" = col_character(),
"study-permission" = col_factor(levels = c("collaborator", "data_manager", "na")),
"study-site" = col_character(),
"study-specific-measurement" = col_character(),
"study-summary" = col_character(),
"study-timezone" = col_factor(),
"study-type" = col_factor(),
"suspend-license-terms" = col_logical(),
"tag-backup-voltage" = col_double(),
# "tag-battery-voltage",# not documented in mb dictionary
"tag-beacon-frequency" = col_double(),
"tag-calibration" = col_character(),
"tag-comments" = col_character(),
"tag-failure-comments" = col_character(),
"tag-firmware" = col_factor(),
"tag-id" = col_big_integer(),
"tag-local-identifier" = col_factor(),
"tag-manufacturer-name" = col_factor(),
"tag-mass" = col_double(),
"tag-mass-total" = col_double(),
"tag-model" = col_factor(),
# "tag-processing-type" = col_character(), ## currently not used
"tag-production-date" = col_character(),
"tag-readout-method" = col_factor(
levels = c(
"ISS", "LPWAN", "multiple", "none", "other-wireless",
"phone-network", "satellite", "tag-retrieval",
"telemetry-network", "Wi-Fi/Bluetooth"
)
),
"tag-retrieval-date" = col_date(),
"tag-serial-no" = col_factor(),
"tag_serial_no" = col_factor(),
"tag-settings" = col_character(),
"tag-tech-spec" = col_character(),
"tag-voltage" = col_double(),
"taxon-canonical-name" = col_factor(),
"taxon_detail" = col_factor(),
"taxon-ids" = col_character(),
"tdr:depth" = col_double(),
"technosmart:activity" = col_factor(levels = c("active", "inactive")),
"technosmart:signal-quality" = col_double(),
"telemetry-detection-count" = col_integer(),
"telemetry-run-id" = col_integer(),
"temperature-max" = col_double(),
"temperature-min" = col_double(),
"there-are-data-which-i-cannot-see" = col_logical(),
"tilt-angle" = col_double(),
"tilt-x" = col_double(),
"tilt-y" = col_double(),
"tilt-z" = col_double(),
"timestamp" = col_datetime(),
"timestamp-end" = col_datetime(),
"timestamp-first-deployed-location" = col_datetime(),
"timestamp-last-deployed-location" = col_datetime(),
"timestamp-of-first-deployed-location" = col_datetime(),
"timestamp-of-last-deployed-location" = col_datetime(),
"timestamp-start" = col_datetime(),
"tinyfox:activity-percent-last-24h" = col_double(),
"tinyfox:error-happened" = col_logical(),
"tinyfox:last-error" = col_factor(levels = as.character(c(1L, 2L, 4L, 5L, 6L, 7L))),
"tinyfox:max-movement-index" = col_factor(levels = as.character(c(0L:3L)), ordered = TRUE),
"tinyfox:memory-full" = col_logical(),
"tinyfox:pressure-min-last-24h" = col_double(),
"tinyfox:software-version" = col_character(),
"tinyfox:sunny-index-start-voltage" = col_double(),
"tinyfox:sunny-index-voltage-increase" = col_double(),
"tinyfox:tag-activation" = col_logical(),
"tinyfox:temperature-max-last-24h" = col_double(),
"tinyfox:temperature-min-last-24h" = col_double(),
"tinyfox:total-vedba" = col_double(),
"tinyfox:total-vedba-count" = col_integer(),
"tinyfox:vedba-00h-ago" = col_double(),
"tinyfox:vedba-01h-ago" = col_double(),
"tinyfox:vedba-02h-ago" = col_double(),
"tinyfox:vedba-03h-ago" = col_double(),
"tinyfox:vedba-04h-ago" = col_double(),
"tinyfox:vedba-05h-ago" = col_double(),
"tinyfox:vedba-06h-ago" = col_double(),
"tinyfox:vedba-07h-ago" = col_double(),
"tinyfox:vedba-08h-ago" = col_double(),
"tinyfox:vedba-09h-ago" = col_double(),
"tinyfox:vedba-10h-ago" = col_double(),
"tinyfox:vedba-11h-ago" = col_double(),
"tinyfox:vedba-12h-ago" = col_double(),
"tinyfox:vedba-13h-ago" = col_double(),
"tinyfox:vedba-14h-ago" = col_double(),
"tinyfox:vedba-15h-ago" = col_double(),
"tinyfox:vedba-16h-ago" = col_double(),
"tinyfox:vedba-17h-ago" = col_double(),
"tinyfox:vedba-18h-ago" = col_double(),
"tinyfox:vedba-19h-ago" = col_double(),
"tinyfox:vedba-20h-ago" = col_double(),
"tinyfox:vedba-21h-ago" = col_double(),
"tinyfox:vedba-22h-ago" = col_double(),
"tinyfox:vedba-23h-ago" = col_double(),
"tinyfox:vedba-burst-sum" = col_double(),
"track-segment-id" = col_factor(),
"transmission-protocol" = col_factor(),
"transmission-timestamp" = col_datetime(),
"tsn" = col_integer(),
"twilight" = col_factor(),
"twilight-excluded" = col_logical(),
"twilight-inserted" = col_logical(),
"underwater-count" = col_integer(),
"underwater-time" = col_double(),
"update-ts" = col_datetime(),
"utm-easting" = col_double(),
"utm-northing" = col_double(),
"utm-zone" = col_factor(),
"vectronics-activity-mode" = col_factor(levels = as.character(1L:7L)),
"vedba" = col_double(),
"vertical-error-numerical" = col_double(),
"vertical-speed" = col_double(),
"visible" = col_logical(),
"voltage-resolution" = col_double(),
"waterbird-workshop:behaviour" = col_factor(levels = c("Nesting", "Roosting")),
"waterbird-workshop:deployment-special-event" = col_factor(
levels = c("BiologicallyIrrelevant", "Death", "ReleaseSite", "TagFailure")
),
"waterbird-workshop:migration-state" = col_factor(
levels = c(
"BreedingGrounds", "FallMigration", "MigrationOther",
"MigrationToMolt", "MoltSite", "SpringMigration",
"StopOver", "SummerNonBreedingAdult",
"SummerNonBreedingImmature", "WinterGrounds"
)
),
"wc-residual" = col_double(),
"weight" = col_double(),
"wet" = col_logical(),
"wet-count" = col_integer(),
"wildfi-acc-conversion-factor" = col_double(),
"wildfi-gyro-conversion-factor" = col_double(),
"wildfi-hall-burst" = col_character(),
"wildfi-last-error" = col_factor(),
"wildfi-mag-conversion-factor" = col_double(),
"wildfi-prox-id-burst" = col_character(),
"wildfi-prox-rssi-burst" = col_character(),
"wildfi-record-type" = col_factor(),
"zero-crossings-amplitude" = col_double(),
"zero-crossings-steps" = col_integer(),
NULL
) # add null so it is easy to sort the list (all have comma at end)
movebank_column_types <- movebank_column_types[!unlist(lapply(movebank_column_types, is.null))]
movebank_colon_names <- list(
"lotek_" = "^lot:", "ornitela_" = "^orn:", "^heartrate:", "^mag:", "gsm" = "^gsm:gsm",
"gsm_mcc" = "^gsm:mcc",
"^bar:", "^gls:", "_" = ":"
)
to_download_names <- function(x) {
for (i in seq_along(movebank_colon_names)) {
x <- gsub(
movebank_colon_names[[i]],
names(movebank_colon_names)[[i]], x
)
}
x <- gsub("-", "_", x, fixed = TRUE)
return(x)
}
mb_column_units_underscore <- mb_column_units
names(mb_column_units_underscore) <-
to_download_names(names(mb_column_units_underscore))
mb_column_types_underscore <- movebank_column_types
names(mb_column_types_underscore) <-
to_download_names(names(mb_column_types_underscore))
toadd <- mb_column_types_underscore[grep(
"^animal_",
names(mb_column_types_underscore)
)]
names(toadd) <- sub("^animal_", "", names(toadd))
mb_column_types_underscore <- c(mb_column_types_underscore, toadd)
rm(toadd)
movebank_valid_entity_types <- c(
"study", "individual", "tag", "sensor", "tag_type", "taxon",
"deployment", "event", "event_reduced", "study_attribute"
)
movebank_minimal_columns <-
c(
"location-long",
"location-lat",
"timestamp",
"individual-local-identifier"
)
movebank_track_attributes <- c(
"individual-taxon-canonical-name",
"study-name",
"death-comments", "study-id"
) # comments don't seem to be attributes for sensors
movebank_track_attributes <- c(
movebank_track_attributes,
gsub("-", "_",
movebank_track_attributes,
fixed = TRUE
),
"individual_local_identifier"
) # individual local identifier here because in CSV its used as id column
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