Data Preparation Protocols

The EUROWILDCAT database stores data from a large number of partners that use different formats and sensors. Before data provided by EUROWILDCAT partners can be ingested into the database, they must be harmonized. This is the main task of data curators. On this page you will find the guidelines to prepare your data sets in a format that is consistent with the EUROWILDCAT data model. If you provide data in this format, the data upload process will be faster and, more importantly, less error prone. While harmonizing the different data sets, data curators also perform accurate quality checks to be sure that only reliable data will be used during later analyses.

Below, you have the list of information that partners should provide, with a short description. In some cases, the information is categorized. This means that you have to use the most appropriate value in a defined list rather than a general description (e.g. reasons of death). These are provided in the templates. Additional information that are not coded or included in the existing fields can be reported in the generic "notes" fields.

The instructions in this page are grouped by data sets: animals, GPS, VHF, captures, contacts, and population. Note that not all the fields are compulsory and not all the data sets must be provided. Before you process your data, please discuss with the data curators any uncertainties.

Data generated by sensors (i.e. GPS, VHF and activity) must include, if possible, the original data sets, with errors/outliers that should be flagged and not removed.

In order to facilitate data preparation, if this is convenient for you, you can use a set of TEMPLATES (Excel spreadsheets) that can be filled with the relevant information. HERE, you find identical templates condensed in only one Excel spreadsheet.

If you have any problems you can always contact the data curators for technical support (eurowildcat.datacurator@gmail.com).

We encourage feedback, especially regarding data you believe would be beneficial to the network! Currently we are developing ideas for the "Population" concept (e.g. hunting regime, prey presence/abundance, interspecific competition ....) where input would be welcomed!

CONTENTS

  • Animals
  • GPS
  • VHF
  • Captures
  • Contacts
  • Population

ANIMALS

All the tracking information stored in the database are related to specific individuals. The list of monitored animals with their characteristics is the first piece of information that is processed and ingested into the database as no data can be imported if it is not referenced to an individual listed in the database. The information must be structured in a single table (see template) filled in the following columns:

  • identifier of the animal (code, number and/or name)
  • sex
  • year of birth (if the first contact with the animal is when it is an adult, the year of birth can be set 2 years before the contact and in the next field you must indicate FALSE)
  • year birth exact (TRUE/FALSE, if the year of birth is known with certainty or not)
  • reintroduction (yes/no)
  • study area (if you have multiple study areas)
  • number of captures (not compulsory)
  • date and time mortality (if the animals already died and the date is known, provide the date and time when the animal died; if you only know the date when the carcass was found [which is a piece of information that goes into the contacts table, see below] you can provide an estimation of the date of death and specify in the notes that the date is not precise)
  • mortality code (cause of death of the animal, see below for the list of codes):
    • 0 - alive
    • 1 - natural starvation
    • 2 - natural diseases
    • 3 - natural unknown
    • 4 - car accident
    • 5 - accident
    • 6 - hunted
    • 7 - unknown how the animal died
    • 8 - death caused by the capture
    • 9 - giving birth
    • 10 - unknown - inferred from sensor retrieval
    • 11 - drowning
    • 12 - not provided
    • 13 - intraspecific - adult / subadult
    • 14 - intraspecific - adult / adult
    • 15 - intraspecific - infanticide
    • 16 - intraspecific - unknown
    • 17 - interspecific - wolf
    • 18 - interspecific - dog
    • 19 - interspecific - canid
    • 20 - interspecific - bear
    • 21 - interspecific - lynx
    • 22 - interspecific - unknown
    • 23 - poaching - suspected
    • 24 - poaching - shot
    • 25 - poaching - poison
    • 26 - poaching - snare
    • 27 - poaching - other
  • notes (you can include any relevant information or additional detail on the animal that is not included in the above list).

Please, see template of the table structure. You are invited to use this template to format your data.

GPS

There are three sets of information related to GPS data that must be provided, these are: 1) the GPS sensors ("collars") with their main characteristics (see below), 2) the time interval of the GPS sensors deployment, and 3) the list of locations, including records without coordinates and erroneous locations (that should be marked as such). Locations outside the deployment period can be omitted, but double-check that the start and end date/time are correct to avoid loss of valid data. If you can, send the data set as it is received from the sensors. If possible, provide a single file for all GPS sensors data, but one file per sensor is also acceptable.

See template (please refer to both pages of the same .xlsx file: "sensor" and "deployment") for the content of the first 2 tables. You are invited to use this template to format your data.

Below follows specific information to the three data sets that should be provided.

1) GPS COLLARS

Information to be included:

  • identifier of the collar
  • vendor
  • model

2) DEPLOYMENT OF GPS SENSOR ON ANIMALS

Include each deployment of a GPS sensor on an animal and provide the start and end time of deployment. As a definition for deployment of the sensor, we mean when the sensor is physically attached to the animal , the animal is alive and the sensors is recording some kind of information.

NOTE THAT:

  • MULTIPLE sensors may have been deployed to ONE animal.
  • ONE sensor may have been deployed to MULTIPLE animals. 
  • ONE sensor may have been deployed MULTIPLE times to the same animal. e.g. only battery was changed.
  • You have to include one record for each new association animal/sensor.
  • Each sensor and animal should be identified with its unique code. If you use the same collar on different animals, keep the same collar id. Same thing for animals monitored with more than one collar (an animal must always be identified with the same code). If you used different codes, please inform the data curator.
  • Also include a deployment record if an animal died during capture and was supposed to be deployed with a sensor (even if it died before getting the sensor deployed).
  • Start and end time of deployment should be set carefully. This interval is used mainly to exclude fixes outside of deployment. The start time corresponds to the moment the collar is deployed to the animal. The end time is when at least one of the three conditions stops to be valid (sensor attached, animal alive, sensor recording or transmitting information).  Provide these dates WITH time and in UTC time zone or specify the time zone.
  • Each deployment should have a corresponding capture event (see capture table).
  • Any other data included in your original file can be included, just please add a file with a short description of all acronyms used.

With this in mind, the information to be included in the table (template, please refer to the page "deployment" of the .xlsx file) is:

  • identifier of the collar
  • identifier of the animal
  • start of the deployment (date and time - utc)
  • end of the deployment (date and time - utc; NULL if the collar is still deployed)
  • end deployment code (see table below for the end of deployment codes)
    • 1 - Drop off
    • 2 - Run out GPS battery
    • 3 - Malfunctioning.
      Sensor had a problem and stopped working
    • 4 - Death (in this case specify the cause of death, see specific list of options)
    • 5 - Failure to transmit
    • 6 - Not used for monitoring.
      Sensor has been deployed but the animal has never been monitored (e.g., animal moved out of range, project finished earlier than expected).
    • 7 - Recapture with removal of the sensor
    • 8 - Generic sensor failure (unknown if malfunctioning or run out of battery).
      Sensor had a problem and stopped working but it is not clear whether it is because of a malfunctioning or because of the battery.
    • 9 - Store-on-board sensor not recovered
    • 10 - Unknown.
      Information on end of deployment has been provided, but it is not known why the monitoring finished.
    • 11 - No data retrieved - unknown reason.
      Information on end of deployment has been provided, but it is not known why the monitoring finished and there is no data.
    • 12 - No longer monitored.
      No longer monitored means that they stopped following the animal. Is different from not used for monitoring in the sense that there can be fixes.
    • 13 - Not provided
    • 14 - Deployment still active
  • notes (here you can include any relevant information or additional detail on the deployment that is not included in the above list).

3) GPS DATA

This is the core of the database. The minimum set of information is:

  • identifier of the collar
  • identifier of the animal
  • acquisition time (date and time - utc)
  • longitude (can be null)
  • latitude (can be null)

Other useful (but not compulsory) data are:

  • altitude measured by GPS
  • temperature measured by GPS
  • number of satellites (“nav” and “validated” fields if available; otherwise “n_sats” or similar)
  • dop

The suggested format is .csv, but you can discuss how to provide this data set with the data curators.

VHF

VHF data are very similar to GPS in their submission. There are three sets of information related to VHF data that must be provided; 1) the VHF sensors (collars) with their main characteristics (see below), 2) the time interval of VHF sensors deployment, and 3) the list of locations (VHF data).

See template (please refer to both pages of the same .xlsx file: "sensor" and "deployment") for the content of the first 2 tables. You are invited to use this template to format your data.

1) VHF SENSORS

Information to be included:

  • identifier of the collar
  • vendor
  • model

2) DEPLOYMENT OF COLLARS ON ANIMALS

Include each deployment of a VHF sensor to an animal and provide the start and end time of deployment.

NOTE THAT:

  • MULTIPLE sensors may have been deployed to ONE animal.
  • ONE sensor may have been deployed to MULTIPLE animals.
  • ONE sensor may have been deployed MULTIPLE times to the same animal. e.g. only battery was changed.
  • Each sensor and animal should be identified with its unique code.
  • Also include a deployment record if an animal died during capture and was supposed to be deployed with a sensor.
  • The start time corresponds to the moment the collar is deployed to the animal. The end time is when one of the three conditions stop to be valid (sensor attached, animal alive, sensor recording or transmitting information). Provide these dates WITH time in UTC time zone or specify the time zone.
  • Each deployment should have a corresponding capture event (see capture table).

With this in mind, below follows the information to be included:

  • identifier of the collar
  • identifier of the animal
  • start of the deployment (date and utc time)
  • end of the deployment (date and utc time; NULL if the collar is still deployed)
  • end deployment code (see table below for the end of deployment codes)
    • 1 - Drop off
    • 2 - Run out GPS battery
    • 3 - Malfunctioning
      Sensor had a problem and stopped working.
    • 4 - Death (in this case specify the cause of death, see specific list of options)
    • 5 - Failure to transmit
    • 6 - Not used for monitoring.
      Sensor has been deployed but the animal has never been monitored (e.g., animal moved out of range, project finished earlier than expected).
    • 7 - Recapture with removal of the sensor
    • 8 - Generic sensor failure (unknown if malfunctioning or run out of battery).
      Sensor had a problem and stopped working but it is not clear whether it is because of a malfunctioning or because of the battery.
    • 9 - Store-on-board sensor not recovered
    • 10 - Unknown
      Information on end of deployment has been provided, but it is not known why the monitoring finished
    • 11 - No data retrieved - unknown reason
      Information on end of deployment has been provided, but it is not known why the monitoring finished and there is no data.
    • 12 - No longer monitored
      No longer monitored means that they stopped following the animal. Is different from not used for monitoring in the sense that there can be fixes.
    • 13 - Not provided
    • 14 - Deployment still active
  • identifier of associated GPS collar (if any)
  • notes

3) VHF DATA

Information to be included:

  • identifier of the collar
  • identifier of the animal
  • acquisition time (date and utc time)
  • coordinates
  • coordinates reference system (including EPSG code, if known)
  • if available locations type (valid locs, observation, findings, outliers)

CAPTURES

In this file we collect information about captures. Only captures of animals that are monitored with a tracking sensor or that were captured to be monitored (e.g. animals that were captured to be collared but that died during the capture) must be included in the dataset. Please include all captures for each specific animal, including those captures before deployment of sensors (e.g. when the animal was too young to deploy a collar, but was deployed with a sensor in the next years), during deployment (e.g. recapture when the animal already has a sensor) and after deployment (e.g. animal has no sensor anymore but was recaptured).

For each animal, we ask for general information such as; sensor deployed (if any), animal id, age at capture and capture info like capture date, coordinates and method, handling characteristics, standard measures and sampling. More specifically (see also template):

  • Animal id
  • Age class at capture - specify the age class at capture:
    Age classes (change date 1st of May)
    • 1 - Juvenile = 0 - 12 months
    • 2 - Subadult = 12 - 24 months
    • 3 - Adult > 24 months
  • First capture specify if it is the first capture of the animal or not.
  • Capture result (if none of the following describes the result of the capture, please provide a detailed description):
    • 1 - Sensor deployed (animal collared)
    • 2 - Sensor deployed but animal died just after the collaring
    • 3 - Sensor not deployed (not collared) because animal died during the capture
    • 4 - Sensor deployed in a previous capture
    • 5 - Sensor deployed in a next capture
    • 6 - No sensor deployed on the animal
    • 7 - Sensor removed from animal during recapture
  • gps/vhf/activity sensor (if the capture result code is 'sensor deployed', please provide the associated gps/vhf/activity sensors)
  • Coordinates Capture specify the coordinates (in lat/long) of the place of capture (also approximate, if not know with higher precision).
  • Coordinates Release specify the rough coordinates (in lat/long) of the place of release. In case of relocation this will be different from the coordinates of actual capture.
  • Capture method used:
    • 1 - Box trap - wood
    • 2 - Box trap - wire mesh
    • 3 - Net trap
    • 4 - Treed - with dog
    • 5 - Automatic immobilisation gun
    • 6 - Other
  • Capture date the date the animal was captured.
  • Capture time the time (UTC) the animal fell into the trap, box, net, etc.
  • Start handling the time (UTC) the animal is taken out from the box, trap, net etc. and is in direct contact with people.
  • End handling the time (UTC) when the animal handling ended (animals is no more in direct contact with people for marking and measurements or it is released or put back into a transportation box.
  • Release time: time (UTC) when the animal was released (animal taken out from the box, trap, net, etc or put back into a transportation box).
  • Release type code: how the animal has been released
    • 1 - soft release (use of a enclosure for habituation)
    • 2 - hard release
  • Relocated if the animal has been relocated after capture (e.g. for reintroduction)
  • Sedation if animals are sedated, indicate this clearly and indicate in separated fields what drug that was used, amount, and at what point in time. Also indicate the same information of a possible antidote that was given.
  • Heart rate at capture beats/min.
  • Heart rate measurement time at capture if several consecutive measurements throughout the capture/handling are taken.
  • Sampling specify if sampling of faeces, biopsy (tissue), blood and hair have been done (yes or no).
  • Body mass at capture in kg.
  • Rectal temperature at capture in °C.
  • Injury if injury at capture, with description.
  • Death description  if death at capture, provide a description.

See template for the table structure, ideally to be used as a form to enter your data.

CONTACT DATA

In this table we collect information  on contacts with animals. These can be both direct sightings of the animal – dead or alive – or indirect like the finding of the sensor after drop off, or others. A contact is an evidence of (the presence/activity of) the animal (excluding captures, that are already reported in the capture data set table) detected in a specific place at a specific time. This information is specially useful for survival analysis. If an animal is found dead, the time of recovery is the contact time, while the estimated death time is reported in the table animal, where and how the animal died is also specified. We collect contacts for all the radio-monitored animals. For each contact, we ask the following information (see alsotemplate):

  • Identifier of the animal (animal code, name)
  • Contact timestamp (date and time, UTC)
  • Contact mode code (type of contact, see table below)
    • 1 - Direct - recovery of the carcass
    • 2 - Indirect - recovery of the sensor/tag without evidence of death
    • 3 - Direct - Sightseeing
    • 4 - Direct - Camera trap
    • 5 - Indirect - footprints
    • 6 - Indirect - recovery of the sensor/tag with evidence of death
    • 7 - Generic evidence/contact that the animal is dead
    • 8 - Generic evidence/contact that the animal is alive
  • Coordinates (longitude & latitude - WGS84, location of the contact event)
  • Notes

See template of the table structure, ideally to be used as a form to enter your data.

POPULATION

...WORK IN PROGRESS...