Coding detector usage across sessions

[Tom.B]

Hi all,

I have a data set consisting of 12 sessions (59 occasions in total). For 11 of those 12 sessions, the detector array was identical (200 traps arranged in a 10x10 grid, with 2 traps at each point). However, for the first session I only used a subset of those traps (90 traps in a 10x9 grid, one trap per point).

I've tried coding this into the trap file like so...

A1A -45.0 -45.0 11111111111111111111111111111111111111111111111111111111111
A1B -45.0 -45.0 00001111111111111111111111111111111111111111111111111111111

But when I go to read.capthist I get the following error -

Session 1
Conflicting number of occasions in usage matrix
capthist : 4 occasions
usage(traps(capthist)) : 59 occasions

Evidently secr is assuming all occasions are part of the same session.

Is there a better way of approaching this? All I want to do is use a different trap layout for the first session.

I've considered just excluding the first session from the analysis, but session 2 has very low capture numbers which causes further issues with calculating start values.

Thanks,
Tom

[murray.efford]

Tom
Your diagnosis is correct. The missing fact is that 'secr' uses a distinct detector layout for each session. If you provide only one then it is copied across sessions in your capthist object. You are free to modify these individually as follows:

Code: Select all

## remove usage attribute from detectors in all sessions
for (i in 1:12)
    usage(traps(myCH[[i]])) <- NULL
## restrict detectors to first 90 for session 1
traps(myCH)[[1]] <- subset(traps(myCH)[[1]], 1:90)


Replace 1:90 with the indices of the traps you used in session 1. 'usage' is not needed if the same set of traps was used on each occasion within a session.

Murray

[Tom.B]

Thanks Murray, looks promising. Will give it a shot tomorrow.

[Tom.B]

OK, so using your code seems to work well-

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> cmmaleCH<-read.capthist("CMmale.txt", "10x10x2grid.txt", fmt="trapID", covnames=c("Age", "Rep"))
No errors found :-)
> usage(traps(cmmaleCH[[1]]))<-NULL
> traps(cmmaleCH)[[1]]<-subset(traps(cmmaleCH)[[1]],1:90)

> summary(cmmaleCH[[1]])
Object class      capthist
Detector type     multi
Detector number   90
Average spacing   10 m
x-range           -45 35 m
y-range           -45 45 m

etc



However, secr.fit is now unhappy with me specifying cmmaleCH as the capthist -

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> cmmaledetect0<-secr.fit(cmmaleCH, detectfn=0, trace=TRUE, buffer=100)
Error in secr.fit(cmmaleCH, detectfn = 0, trace = TRUE, buffer=100)  :
  requires 'capthist' object

It runs fine if I specify cmmaleCH[[1]] or another single session.

Any way around this?

Thanks again,
Tom

[murray.efford]

Try with the right parentheses on 'traps' moved right outside the ]]:

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traps(cmmaleCH[[1]]) <-subset(traps(cmmaleCH[[1]]),1:90)

(Remember I'm assuming that it's the first 90 traps you used in session 1)

Murray

[Tom.B]

Well don't I feel silly now

Thanks again Murray. I may have one further unrelated question for you, but will start a separate thread once I've checked a few things.

[jlaufenb]

Hi Murray,

I have a similar situation requiring session-specific trap arrays. I have 2 years of data with 8 occasions each from the same study area, but the trap array slightly changed between years. Overall, I have 144 trap sites where 126 of them were operated in year 1 and 129 of them were operated in year 2. So far, I have read in a traps file containing all 144 traps and used that with the capture data to create a capthist object. Given that I have specified years as sessions, I took the above suggestion and subsetted the traps element for each session of the capthist object. However, verify() returns the following warning:

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Session Y1
traps object incompatible with reported detections
traps(capthist) : 126 detectors
capthist : 144 detectors
Session Y2
traps object incompatible with reported detections
traps(capthist) : 129 detectors
capthist : 144 detectors

Since the original post here is a few year old, I thought I'd ask is there a better way to handle/format this type of data? Are spatially independent trap arrays treated as sessions handled differently?

Thanks
Jared

[murray.efford]

Hi Jared
Assuming you have 'proximity' detectors, the capthist component for each session is based on a 3-D array whose 3rd dimension has length equal to the number of traps. Hence the mismatch you have encountered when you work backwards from a pooled set of traps (capthist in each session still has the enlarged 3rd dimension). I think the solution is to input your capthist again, providing a vector of session-specific trapfile names to read.capthist, or using make.capthist. You may also need to specify a vector of session-specific 'occasions'.
Murray

[jlaufenb]

Hi Murray,

Thanks for the response. My solution was to create separate traps objects for each session using the read.traps() function and then read them into the make.capthist() function as a list for the traps argument. Below is some code to illustrate for others:

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trapsS1 <- read.csv("trapsY1.csv")
trapsS2 <- read.csv("trapsY2.csv")

trapsS1.secr <- read.traps(data = trapsS1, detector = "proximity")
trapsS2.secr <- read.traps(data = trapsS2, detector = "proximity")

caps.secr <- read.csv("mycaps.csv") # years treated as sessions

my.capthist <- make.capthist(captures=caps.secr, traps = list(trapsS1.secr,trapsS2.secr), fmt="trapID")


Note: The session-specific trap objects must be brought into the make.capthist() function as a list. Otherwise, you get the following error message:

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multi-session 'traps' list does not match 'captures'

Jared

[murray.efford]

It sounds like you have this sorted. I think this simpler code should work, too:

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my.capthist <- read.capthist(captfile = "mycaps.csv", trapfile = c("trapsY1.csv", "trapsY2.csv"))

although I'm not 100% sure about csv.
Murray