Karpfen108
commented
5 months ago I came across the same issue. It seems like several columns have changed. Below is my code and explanation that got me to run the detectionSummary.
Maybe this helps someone in the future.
upload IMOS data
data_raw <- read.csv("animal.csv")
Upload receiver metadata
receiver_raw <- read.csv("receiver.csv")
Upload tag metadata
tag_raw <-read.csv("tag.csv")
Rename the tag_id column in the data
Use the transmitter_id column in the IMOS data and tag metadata to create a new tag_id column (that is non existent before) in the tag metadata
tag_raw$tag_id <- data_raw$tag_id[match(tag_raw$transmitter_id, data_raw$transmitter_id)]
Filter out all the tag ids that are NA. If the tag doesn't exist it will put NA into the tag_id which will lead to a problem in the detSum function
tag_raw <- tag_raw[!is.na(tag_raw$tag_id), ]
Copy the measurement column into the tag_raw (For some reason the data is not provided with the tag_raw data but is required in this package)
tag_raw <- tag_raw %>% left_join((data_raw %>% distinct(tag_id, .keep_all = TRUE))[, c("tag_id", "measurement")], by = "tag_id")
Rename raw data columns to fit the VTrack functions
data_raw <- data_raw %>% rename(detection_timestamp = detection_datetime) data_raw <- data_raw %>% rename(longitude = receiver_deployment_longitude) data_raw <- data_raw %>% rename(latitude = receiver_deployment_latitude) data_raw <- data_raw %>% rename(sensor_value = transmitter_sensor_raw_value) data_raw <- data_raw %>% rename(sensor_unit = transmitter_sensor_unit)
Rename receiver columns to fit the VTrack functions
receiver_raw <- receiver_raw %>% rename(deploymentdatetime_timestamp = receiver_deployment_datetime) receiver_raw <- receiver_raw %>% rename(recoverydatetime_timestamp = receiver_recovery_datetime) receiver_raw <- receiver_raw %>% rename(station_latitude = receiver_deployment_latitude) receiver_raw <- receiver_raw %>% rename(station_longitude = receiver_deployment_longitude) receiver_raw <- receiver_raw %>% rename(status = receiver_status)
Rename tag columns to fit the VTrack functions
tag_raw <- tag_raw %>% rename(ReleaseDate = transmitter_deployment_datetime) tag_raw <- tag_raw %>% rename(common_name = species_common_name) tag_raw <- tag_raw %>% rename(scientific_name = species_scientific_name) tag_raw <- tag_raw %>% rename(sex = animal_sex) tag_raw <- tag_raw %>% rename(tag_project_name = tagging_project_name) tag_raw <- tag_raw %>% rename(release_id = transmitter_deployment_id) # not working yet. not sure which other column this could be)
tag_raw <- tag_raw %>% rename(release_latitude = transmitter_deployment_latitude) tag_raw <- tag_raw %>% rename(release_longitude = transmitter_deployment_longitude) tag_raw <- tag_raw %>% rename(tag_expected_life_time_days = transmitter_estimated_battery_life) tag_raw <- tag_raw %>% rename(tag_status = transmitter_status)
ATTdata <- setupData(Tag.Detections = data_raw, Tag.Metadata = tag_raw, Station.Information = receiver_raw, source = "IMOS")
Cheers,
Getting errors in setupData + others where the expected columns are not in the data downloaded from IMOS.
A few examples:, in the detection data setupData is looking for
detection_timestampwhen the column is nameddetection_datetime.For Station data, package expects:
deploymentdatetime_timestampandrecoverydatetime_timestamp; and instead receives:receiver_deployment_datetimeandreceiver_recovery_datetime.For Transmitter data, package expects:
ReleaseDatebut receivestransmitter_deployment_datetime.detectionSummary is looking for a column named
Tag.IDbut all I have I the ATT object areTransmittercolumns. Suspect further changes will come to light the more functions I use!The obvious reason for this, I imagine, is that the IMOS export format has changed in the last couple of years. Can probably fix manually but wanted to bring to your attention. :)