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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

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

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

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

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

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.

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

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

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:

Code: Select all

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

Jared

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