traps with no detection / absence

Gilles Maurer

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Jul 31, 2025, 8:31:00 AM7/31/25

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Hi all,

I have the following message when running data2oscr :

some trap names in EDF not in TDF

I checked as follows :

> trap_ids_edf <- unique(lao_edf$trapID)
> trap_ids_tdf <- unique(lao_tdf$trapID)
> missing_trapIDs <- setdiff(trap_ids_edf, trap_ids_tdf)

character (empty)

Both are set as character

I do have 53 trapID in EDF and 2386 in TDF.

Where could be the problem ? Any clue ?
I am wondering if the issue may come from traps that never detect any individual ( absence only). Shall I discard them from the dataset ?

Thank you in advance for your help
Gilles

Gilles Maurer

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Jul 31, 2025, 9:42:49 AM7/31/25

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Sorry, I did not provide sufficient details

I have one session only.
Here are data2oscr arguments :
data <-
data2oscr(edf = edf,
tdf =list(tdf),
sess.col = 1,
id.col =2,
occ.col = 3,
trap.col = 4,
sex.col = 5,
sex.nacode = "U",
K = 7, # 7 occasions / only 1 session
ntraps = nrow(trap_operation), #number of capture traps per session
trapcov.names = c("habitat_class", "ob"),
tdf.sep = "/")

Apparently when running the function data2oscr, all trap names (53) that are in edf are not found in tdf
> class(edf)
[1] "data.frame"
> head(edf)
Session ID occasion trapID sex
1 1 18UG1 1 24845 U
2 1 18UG2 1 24845 M
3 1 18UG3 1 24845 U

> head(tdf)
# A tibble: 6 × 13
trapID X Y O.1 O.2 O.3 O.4 O.5 O.6 O.7 sep habitat_class ob
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <fct> <dbl>
1 20699 487482. 1969720. 0 0 0 0 0 0 1 / Trees 0.0259
2 20854 487576. 1969545. 0 0 0 0 0 0 1 / Trees 0.0234
3 21166 487775. 1969538. 0 0 0 0 0 0 1 / Trees 0.0238

thank you

Daniel Linden

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Jul 31, 2025, 9:43:54 AM7/31/25

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Hi Giles, you might need to send me your files so that I can try to replicate.

Chris Sutherland

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Jul 31, 2025, 9:44:51 AM7/31/25

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Can you try again, but convert the tdf to a data frame rather than a Ribble

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Gilles Maurer

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Aug 1, 2025, 7:04:14 PM8/1/25

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Indeed, my tdf was a tibble, I just found the answer in previous messages a minute ago. Sorry to bothered you

I am now on my way to the sSpace ;-) that is a bit tricky because of the presence of a lake (artificial reservoir with a tricky shape and varying levels of water ). Traps are indeed visited cells were feces have been collected and genotyped. While feces cannot be found in the water, they can be collected along the banks. And animals can cross the lake ...