Exclude "sync tag" when returning detections

[peterdesmet]

See list in #21. I would propose to exclude "sync tag" by default when returning occurrences, but maybe allow a flag to include those. @jreubens @PieterjanVerhelst are there other non animal detections in the database?

[PieterjanVerhelst]

Yes, the Built-in and Sentinel are non-animals as well.

[peterdesmet]

Ok, so for any relevant function, it would be useful something like a exclude_non_animals parameter, with default value TRUE. Better name suggestions welcome.

[PieterjanVerhelst]

Indeed and name is good for me.

[jreubens]

Ok to have an function to exclude non-animals.
as name I would go for 'reference_tags'
@PieterjanVerhelst OK?

[peterdesmet]

I'd opt for parameter, not separate functions. Maybe called include_reference_tags, default FALSE

[PieterjanVerhelst]

Reference tags are a good, general name for non-animal tags. Function name proposed by Peter is ok for me.

[stijnvanhoey]

For which functions is this relevant?

• get_projects() | Get project overview
• get_receivers() | Get receiver data
• get_deployments() | Get deployments data
• get_animals() | Get animals data
• get_transmitters() | Get transmitter metadata

@PieterjanVerhelst and @jreubens can you verify this?

[PieterjanVerhelst]

I think it is only relevant for the get_transmitters() function. Deployments reflect receiver activity and therefore not relevant for that function.

[jreubens]

get_animals as well.
BUT... we will link 'scientific_name' to aphia of worms soon. Thus this means that built-in, sentinel, ... can't be seen as 'animals' any longer. an new field will be needed. @bwydoogh en @jreubens wil work on this

[stijnvanhoey]

Regarding issue #50 and the discussion above. Let's summarize the required implementation:

The aim is an additional argument include_reference_tags (default FALSE), so for example the implementation would be:

get_transmitters(con) #no reference tags included
get_transmitters(con, include_reference_tags = FALSE) #no reference tags included
get_transmitters(con, include_reference_tags = TRUE) #reference tags included

Still, I do not completely get how to exclude these? On what field name doe we have to filter or how can I extend the query? Moreover, we need a complete and proper list of values to identify non-animals.

What is the field to use for get_transmitters()?
What is the field to use for get_animals()?
What terms need to be excluded: built-in, Sentinel and Sync-tag? Or others as well?

[jreubens]

Referring to #50 you should use the field 'Acoustic_tag_type' to filter on. only the type "animal" is animal, all the other (built-in, sentinel, sync) are non-animal.

[stijnvanhoey]

@jreubens I can see the acoustic_tag_type when requesting the transmitter information (get_transmitters), but I do not get it for the animals.

How can I exclude them when requesting animals? Should I use the field scientific_name (and how to make the difference there)? As an animal can be linked to different tags, how should I be able to exclude based on the acoustic_tag_type, which is linked to tags... so, If any of the tags is an animal, it is an animal?!?

To conclude, this also make sense for the get_detections... Should I also use the scientific_name and exclude certain names?

[jreubens]

I'm not sure whether I understand your question correctly.

for get_transmitters() use the 'acoustic_tag_type' and exclude everything that is not 'animal'
for get_animals() the problem will be solved once we use the aphia_ID. Thus I would wait with this one.

[stijnvanhoey]

@jreubens for the get_animalsyou can add a separate issue now of later on when the ID is available.

This issue is particularly about the get_transmitters() and using the acoustic_tag_type and exclude as such everything that is not 'animal'... @damianooldoni any fit to take this in your schedule?

[damianooldoni]

Hi! Yes, @stijnvanhoey, I will.

[damianooldoni]

After reading the entire issue, I will proceed by introducing a new input parameter for function get_transmitter() called include_reference_tags which acts as a filter. I will follow the instructions as written by @stijnvanhoey above, i.e.

get_transmitters(con) #no reference tags included
get_transmitters(con, include_reference_tags = FALSE) #no reference tags included
get_transmitters(con, include_reference_tags = TRUE) #reference tags included

I will deploy it in a new branch called include_reference_tags_param.