I am trying to simulate animal capture histories from camera trapping under different conditions of sigma and camera trap spacing. Ultimately I want to run it with a variety of trap spacing and sigma combinations. Below I have written example code to do one of these combinations. However, every time I run
the model output states that there was only one occasion (please see second code box for console output, here it states that "N occasions = 1", but should be 60). I have tried specifying the 
argument in both 
and 
functions. But that didn't help either. I am not sure what I am doing wrong... One of the things I noticed is the Warning message:Warning message:
In bias.D(buffer, temptrps, detectfn = output$detectfn, detectpar = dpar, :
bias.D() does not allow for variable effort (detector usage)
Is this what is causing it? What does it mean and can/should I bypass/ignore it?
Below is some reproducible code, the console output from
, and the session info for my machine. Any advice or guidance would be highly appreciated!
Simulate animal capture histories and fit model:
- Code: Select all
trap.test <- make.grid(spacing = 2000,
detector = "proximity",
nx = 10,
ny = 10)
usage(trap.test) <- matrix(sample(0:1,
100*60,
replace = T,
p = c(0.1, 0.9)),
nc = 60)
caphist.test <- sim.capthist(trap.test,
popn = list(D = 0.0001,
buffer = 15000),
detectfn = 'HN',
detectpar = list(lambda0 = 0.25,
sigma = 2000),
noccasions = 60,
nsessions = 1,
seed = 123)
fit.test <- secr.fit(caphist.test,
model = list(D~1, g0~1, sigma~1),
buffer = 15000,
trace = T,
detectfn = "HN",
ncores = 12)
fit.test
Console output from
:- Code: Select all
>
> fit.test <- secr.fit(caphist.test,
+ model = list(D~1, g0~1, sigma~1),
+ buffer = 15000,
+ trace = T,
+ detectfn = "HN",
+ ncores = 12)
Checking data
Preparing detection design matrices
Preparing density design matrix
Finding initial parameter values...
Initial values D = 6e-05, g0 = 0.22596, sigma = 2182.52908
Maximizing likelihood...
Eval Loglik D g0 sigma
1 -212.104 -9.7636 -1.2313 7.6882
2 -212.104 -9.7636 -1.2313 7.6882
...
...
...
88 -207.207 -9.3804 -1.3457 7.6396
89 -207.208 -9.3804 -1.3458 7.6404
Completed in 6.09 seconds at 14:00:49 26 May 2023
Warning message:
In bias.D(buffer, temptrps, detectfn = output$detectfn, detectpar = dpar, :
bias.D() does not allow for variable effort (detector usage)
>
>
> fit.test
secr.fit(capthist = caphist.test, model = list(D ~ 1, g0 ~ 1,
sigma ~ 1), buffer = 15000, detectfn = "HN", trace = T, ncores = 12)
secr 4.5.10, 14:00:43 26 May 2023
Detector type count
Detector number 100
Average spacing 2000 m
x-range 0 18000 m
y-range 0 18000 m
Usage range by occasion
1
min 48
max 60
N animals : 7
N detections : 318
N occasions : 1
Count model : Binomial, size from usage
Mask area : 211500 ha
Model : D~1 g0~1 sigma~1
Fixed (real) : none
Detection fn : halfnormal
Distribution : poisson
N parameters : 3
Log likelihood : -207.2064
AIC : 420.4128
AICc : 428.4128
Beta parameters (coefficients)
beta SE.beta lcl ucl
D -9.380410 0.37861257 -10.122477 -8.638343
g0 -1.345794 0.09217003 -1.526444 -1.165145
sigma 7.638823 0.03165316 7.576784 7.700862
Variance-covariance matrix of beta parameters
D g0 sigma
D 0.1433474767 0.0006908203 -0.0006864667
g0 0.0006908203 0.0084953153 -0.0016513867
sigma -0.0006864667 -0.0016513867 0.0010019223
Fitted (real) parameters evaluated at base levels of covariates
link estimate SE.estimate lcl ucl
D log 8.436064e-05 3.311956e-05 4.016652e-05 1.771803e-04
g0 logit 2.065588e-01 1.510595e-02 1.785145e-01 2.377338e-01
sigma log 2.077297e+03 6.576947e+01 1.952339e+03 2.210252e+03
>
>
:- Code: Select all
>
> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Africa/Johannesburg
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] secr_4.5.10
loaded via a namespace (and not attached):
[1] Matrix_1.5-4 dplyr_1.1.2 compiler_4.3.0
[4] tidyselect_1.2.0 Rcpp_1.0.10 RcppNumerical_0.5-0
[7] stringr_1.5.0 parallel_4.3.0 splines_4.3.0
[10] lattice_0.21-8 R6_2.5.1 generics_0.1.3
[13] classInt_0.4-9 sf_1.0-12 iterators_1.0.14
[16] doMC_1.3.8 MASS_7.3-58.4 tibble_3.2.1
[19] units_0.8-2 DBI_1.1.3 pillar_1.9.0
[22] rlang_1.1.1 utf8_1.2.3 sp_1.6-0
[25] stringi_1.7.12 terra_1.7-29 RcppParallel_5.1.7
[28] cli_3.6.1 magrittr_2.0.3 mgcv_1.8-42
[31] class_7.3-21 foreach_1.5.2 grid_4.3.0
[34] rstudioapi_0.14 lifecycle_1.0.3 nlme_3.1-162
[37] vctrs_0.6.2 KernSmooth_2.23-20 proxy_0.4-27
[40] glue_1.6.2 raster_3.6-20 codetools_0.2-19
[43] abind_1.4-5 fansi_1.0.4 e1071_1.7-13
[46] pkgconfig_2.0.3 tools_4.3.0
>
Thank you!