Error message in R when trying to run SECR model

[Lachlan McRae]

Hi everyone,

I'm currently following the "A tutorial on fitting spatially explicit capture–recapture models in secr " document but I keep getting an error message when trying to estimate sigma.

This is where I get up to:

library(secr)

setwd("C:/Users/lmcra/OneDrive/Desktop/Career/Uni/Honours/Data/Combined")

PossumCH <- read.capthist("CHistory.txt", "TrapLocations.txt", detector = "multi")

summary(PossumCH)

par(mar = c(1,1,3,1)) 

plot (PossumCH, tracks = TRUE)

m <- unlist(moves(PossumCH))

par(mar = c(3.2,4,1,1), mgp = c(2.1,0.6,0))

hist(m, breaks = seq(-61/2, 500,61), xlab = "Movement m", main = "")

initialsigma <- RPSV(PossumCH, CC = TRUE)

cat("Quick and biased estimate of sigma =", initialsigma, "m\n")

Once I click enter on the "cat..." line I get an error message saying Quick and biased estimate of sigma = Error in cat("Quick and biased estimate of sigma =", initialsigma, "m\n") : argument 2 (type 'list') cannot be handled by 'cat'

Does anyone know how to get passed this error?

Cheers,

Lachlan McRae

[Russell J Gray]

I could be wrong, but I suspect the error may be due to the "\" in "m\n" rather than using "/" for "m/n". 

--

Russell J. Gray
Wildlife Ecology & Conservation Consultant

0934581341 |  rjgray...@gmail.com https://www.rjgrayecology.com/ 705 alligator ranch rd. New Smyrna Beach, FL, USA. 32168

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[Lachlan McRae]

Cheers for the suggestion Russel but unfortunately that didn't work. Any other suggestions?

Regards,

Lachie

[Russell J Gray]

Sorry, I didn't realize it was an argument value of the cat() function. 

So I ran a reprex and it worked for me without error:

library(secr)

dbar(captdata)

initialsigma <- RPSV(captdata, CC = TRUE)

cat("Quick and biased estimate of sigma =", initialsigma, "m\n")

So I suspect something is wrong with the initialsigma value on your end. It should be a single value after you ran the RPSV() function. However, the error suggests that the value you inputted is a list rather than a value. So make sure you're running an unlisted version of your capthist in the RPSV function. 

--

Russell J. Gray
Wildlife Ecology & Conservation Consultant

0934581341 |  rjgray...@gmail.com https://www.rjgrayecology.com/ 705 alligator ranch rd. New Smyrna Beach, FL, USA. 32168

[Murray Efford]

That was my guess, too. If PossumCH is multi-session then it should work with initialsigma <- RPSV(PossumCH, CC = TRUE)[[1]].

[Lachlan McRae]

That worked Murray! Cheers. I just needed to add "[[1]]" to the end.