How to start analysing Agouti data with camtrapR

[Raphaelle Abn]

Hi,

I am working on data exported from agouti (data from different camera traps and different sites, from different years). 

I have my csv file with all the data and species names, hours, dates, locations...

I don't know how to start with camtrapR to analyse that and make comparisons of species richness between sites. 

How should I organize the data? 

I would really appreciate to have some advices or recommendations of easy CamtrapR guides for beginners :)

[Juergen Niedballa]

Hello,

can you please share the data structure of the agouti export? Then I can provide some guidance.

Generally I'd expect something analogous to the camera trap table and record table from camtrapR, and then it is mostly a matter of telling camtrapR which columns to use for what (since the default column names used by camtrapR most likely won't match the Agouti export).

I think Agouti can export to camtrapDP format. That would likely be the easiest option.

Anyways, please provide some more detail.

Thank you

[Raphaelle Abn]

Hello, 

Thank you for the answer. Finally I managed to start analyses. The data format was camtrapDP with a .json file, and 3 .csv media, observations and deployments files all exported from Agouti. 

I used camtraptor on R studio to open the .json file and managed to create a record table from this file with all independent observations from the cameras (I chose 30min as a limit to have independent observations of the same species). 

Now I am working on species accumulation curves using the package iNEXT to plot species accumulation with camera days. I have some issues to organize the data as I have 7 sites, each site has a different amount of cameras and each camera has a different deployment time (accumulated camera days). I started to make accumulation curves for each camera. For example, for the site 1, I have 9 cameras. I generated 9 accumulation curves, but I would like to have like a mean curve for all these 9 cameras. 

I tried to organize my data as a matrix of incidence frequencies : the first number is the total number of camera days for each camera, the second number is the incidence frequency of species 1, then species 2 etc. (data format for https://chao.shinyapps.io/iNEXTOnline/)

#Site 1

CAM1 145 4 3 2 2 2 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

CAM2 145 2 38 9 17 4 0 5 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

CAM3 146 0 24 10 0 3 0 0 8 2 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0

CAM4 147 1 9 16 8 15 0 2 8 1 5 1 3 14 1 1 1 0 0 0 0 0 0 0 0

CAM5 148 1 18 12 3 2 0 1 12 1 2 2 0 2 1 0 0 1 0 0 0 0 0 0 0

CAM6 149 2 6 29 13 2 0 1 24 0 2 0 3 0 0 0 0 3 2 1 0 0 0 0 0

CAM7 149 0 7 4 3 13 0 29 5 0 26 0 0 24 0 0 0 17 2 0 2 0 0 0 0

CAM8 198 6 105 62 22 0 1 0 40 2 2 1 4 3 6 0 1 6 1 0 0 1 1 1 0

CAM9 150 3 49 45 21 8 0 19 12 8 4 2 4 7 1 0 3 1 1 0 6 0 2 0 1

If I want to make only one mean curve combining all the cameras of the site, I made the sum of all camera days (of the 9 cameras). Then I generated the incidence frequency of each species combining all cameras of the site. Thus, I had the following data line : 

ALLCAM 1377 19 52 354 58 10 8 3 7 1 205 64 1 5 125 67 1 10 146 1 2 1 1 15 15 41 0 0 0 0

I was thinking that I can do this "mean" data for the 7 sites, so I could plot the species accumulation curves for each site. Does it make sense to make means like that ? I am not sure of that. I would appreciate some advices if you know what would be the best for this kind of data!

Raphaelle

[Juergen Niedballa]

Hello,

as mentioned in the other thread this is beyond the scope of camtrapR and this group. I'd welcome if others can provide input, but I currently don't have capacities for tasks that don't immediately concern the functionalities of camtrapR. I'm sorry I can't help with this.

If you find a solution please feel free to share for other users to explore though.

Best regards