Using agouti output files in camtrapR

[Neofelis Nebulosa]

Hi friends,

One of my friends processed his camera trap images using the program agouti. Now he is having a difficulty figuring out what to do with the output files. And seems like the output files of agouti are compatible to be used for further analysis using camtrapR as writen in agouti's website. I was wondering if this is a simple way to create detection histories from agouti output files. Or if somebody in the group did this and wants to help?

[Jürgen Niedballa]

Hi,

Agouti output is in camtrap-dp format, not camtrapR format. camtrap-dp is a new standard for exchanging camera trapping data, but as far as I know not yet 100% finalized. I will provide support in camtrapR when the first iteration of the standard is completed.

Theoretically, one only needs to convert the output of Agouti to a record table and a camera trap table as used by camtrapR. Specifically, the "Deployments" table from the Agouti export corresponds to the camera trap table in camtrapR, and the "Observations" table from the Agouti output corresponds to the record table in camtrapR. The "Media" table should not be necessary. There are a lot of  information in the Agouti export (or rather, in the camtrap-dp format) that is useful but not essential for the detectionHistory function.

detectionHistory and other functions allow you to specify the names of the relevant input columns (e.g. arguments speciesCol, stationCol, etc.), so that may already provide enough flexibility to work directly with the Agouti output in camtrapR.

Feel free to share a sample of the output and I'll see if we can convert that to camtrapR input already.

Best regards,

Jürgen

Am Mo., 29. Aug. 2022 um 23:57 Uhr schrieb Neofelis Nebulosa <panthera...@gmail.com>:

Hi friends,

One of my friends processed his camera trap images using the program agouti. Now he is having a difficulty figuring out what to do with the output files. And seems like the output files of agouti are compatible to be used for further analysis using camtrapR as writen in agouti's website. I was wondering if this is a simple way to create detection histories from agouti output files. Or if somebody in the group did this and wants to help?

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[Jim Casaer]

hey everybody,

In the meantime, our open science lab for biodiversity  team has been and still is developing a R-package called camtraptor (https://inbo.github.io/camtraptor/)  that allows to easily read, explore and visualize the export format (camtrap-dp). It returns maps and basic data such as RAI, effort, ... More importantly in this context is that package also easily allows you to transform the export from camertrap platforms such as Agouti into the basic files required by camtrapR :-) One of the most important probably is the get_record_table() function in camtraptor, generating a record table allowing all further analysis (detection histories, ...) in camtrapR. So no extra datawrangling is required anymore when using this package. 

Though the package is still under development, please don't hesitate to use it !! and get back to us whenever questions or suggestions,

greetings

jim

Dr.ir. Jim Casaer

Senior Researcher

Research Group wildlife Management / OT  Faunabeheer en Exoten/ 

Research Institute for Nature and Forest / Instituut voor Natuur- en Bosonderzoek

Havenlaan 88 bus 73,

1000 Brussel

jim.c...@inbo.be

** 32 478 281 701 

www.inbo.be

orcid : 0000-0001-6788-5876

Op ma 29 aug. 2022 om 19:17 schreef Jürgen Niedballa <camt...@gmail.com>:

To view this discussion on the web, visit https://groups.google.com/d/msgid/camtrapr/CAKk9T33akPU%2BQsEdfMRmk4p8WE6L51LSer8NOzt6MQP3WTHLBw%40mail.gmail.com.

[Jürgen Niedballa]

Hi Jim,

thank you for informing, that sounds good. I haven't tried your package yet, but appreciate the effort and will give it a try.

A possibly unrelated question to you, the original poster privately shared the output of Agouti (observation and deployment csv files) and I found several issues with these. While I don't know if these may be artefacts from manual data processing after export from Agouti, I'd like to bring them to your attention. We can discuss this separately if more appropriate.

observations:

• timestamp format is not consistent (some are with time zone, others without)

deployments:

• some rows have identical setup and retrieval date and time (thus a deployment length of 0)
• there are multiple deployments at the same location & same camera. I suppose that is intended and means the camera malfunctioned or or sampling was interrupted. Does your package convert these to the ProblemX_from/to columns as used by camtrapR? (I am aware the ProblemX columns are not ideal from a data management point of view, but still)
  
• timestamp is not consistent (some are with time zone, others without; some of the entries with time zone are -06:00, others -07:00)

Best regards,

Jürgen