Errors inputting capture and trap files

[anna...@hotmail.com]

Hello all,

I'm trying to calculate the density of black rat populations on two islands (Gooseberry and Hooka) over 1 trapping session (4 days/occasions). I'm getting two different error codes when I try and read.capthist, and although the first error has been mentioned in a previous post I'm not sure how to solve it from the advice on that post.

Error 1:

> GRat <- read.capthist("Gooseberry Capt.txt", "Gooseberry Trap.txt", detector = "single")
Error in if (min(nfld) < 3) stop("requires 3 fields (detectorID, x, y)") : 
  missing value where TRUE/FALSE needed
In addition: Warning message:
In read.capthist("Gooseberry Capt.txt", "Gooseberry Trap.txt", detector = "single") :
  NAs introduced by coercion

Error 2:

> HRat <- read.capthist("Hooka Capt.txt", "Hooka Trap.txt", detector = "single")
Error in read.traps(file = "Hooka Trap.txt", detector = "single", covnames = NULL,  : 
  'usage' fields suggest varying number of occasions
In addition: Warning message:
In read.capthist("Hooka Capt.txt", "Hooka Trap.txt", detector = "single") :
  NAs introduced by coercion

Am I missing a particular term in the read.capthist function for when you have a different number of usages for each trap? I have read through the secr-varyingeffort.pdf, but was not sure how it applied to when the usage was within the capture input file. 

If anyone could help that would be much appreciated! I've attached the trap and capture files as well, as it seems to be a problem with the files in the first error and possibly a problem with the code in the second error?

Cheers,

Annabel

[Murray Efford]

Hi Annabel
If your files have header information it needs to be hidden from 'secr'. This one is really simple to fix: either prefix the header lines with a comment character (#) or include skip = 1 in the call to read.capthist (this argument is passed on to read.table

library(secr)
GRat <- read.capthist("Gooseberry Capt.txt", "Gooseberry Trap.txt", detector = "single", skip = 1)
# No errors found :-)
HRat <- read.capthist("Hooka Capt.txt", "Hooka Trap.txt", detector = "single", skip = 1)
# No errors found :-)

Murray

[anna...@hotmail.com]

Hi Murray,

Thanks for that - it worked!

In the summary output I noticed one of the rows is the number of losses, and although I did loose some animals, I didn't put it in the input data or code. How do you do that?

Cheers,

Annabel

[Murray Efford]

See the section 'Capture data format' in secr-datainput.pdf. It won't make much difference.
Murray

[Barkatullah Khan]

Hi Murray ! I am having the same " NAs introduced by coercion" error while reading the inputs (Transects detector) . 

i have tried your earlier response in this thread. " prefix the header lines with a comment character (#) or include skip = 1 in the call to read.capthist (this argument is passed on to read.table"

Still its the same.  I am doing the Snow leopard scats data. Inputs attached. Please look into my files. Very much appreciated that will be. 

I am doing this 

> captfile <- paste0('capt.txt')

> trapfile <- paste0('trap.txt')

> CH <- read.capthist (captfile, trapfile, detector = 'transect', trapcovnames= NULL, binary.usage = FALSE, fmt = "XY")

No errors found :-)

Warning message:

In verify.capthist(temp) : NAs introduced by coercion

> 

[Murray Efford]

' NAs introduced by coercion' here is a spurious warning from the verify.capthist function. It can be ignored.

One transect seems to be incomplete (only one point). Is it sensible to do capture-recapture analysis on 4 animals?

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[Barkatullah Khan]

Thanks Murray for the feedback. Indeed its a very small data, i was trying learning with the inputs and exploring how the outputs works. More data is to come both from genetics and cam traps.

Regarding error , there is a bit more, sorry i was sharing incomplete error. I thought this NA error is the main cause.  Here is what i am getting in full. 

> CH <- read.capthist (captfile, trapfile, detector = 'transect', trapcovnames= NULL, binary.usage = FALSE, fmt = "XY")

No errors found :-)

Warning message:

In verify.capthist(temp) : NAs introduced by coercion

> initialsigma <- RPSV(CH, CC = TRUE)

> fit <- secr.fit (CH, buffer = 2 * initialsigma)

Checking data 

Error in if (tmp$x[1] == tmp$x[2]) data.frame(x = rep(tmp$x[1], n), y = seq(tmp$y[1],  : 

  missing value where TRUE/FALSE needed

In addition: Warning message:

In verify.capthist(capthist, report = 1) : NAs introduced by coercion

Is it because of the one incomplete transect you highlighted???  Thanks again for the kind response 

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