simdataClosedSCR | R Documentation |
This function generates encounter histories from spatially-explicit capture-mark-recapture data consisting of multiple non-invasive marks.
simdataClosedSCR(
N = 30,
ntraps = 9,
noccas = 5,
pbeta = 0.25,
tau = 0,
sigma2_scr = 0.75,
lambda = 0.75,
delta_1 = 0.4,
delta_2 = 0.4,
alpha = 0.5,
data.type = "never",
detection = "half-normal",
spatialInputs = NULL,
buffer = 3 * sqrt(sigma2_scr),
ncells = 1024,
scalemax = 10,
plot = TRUE
)
N |
True population size or abundance. |
ntraps |
The number of traps. If |
noccas |
Scaler indicating the number of sampling occasions per trap. |
pbeta |
Complementary loglog-scale intercept term for detection probability (p). Must be a scaler or vector of length |
tau |
Additive complementary loglog-scale behavioral effect term for recapture probability (c). |
sigma2_scr |
Complementary loglog-scale term for effect of distance in the “half-normal” detection function. Ignored unless |
lambda |
Complementary loglog-scale term for effect of distance in the “exponential” detection function. Ignored unless |
delta_1 |
Conditional probability of type 1 encounter, given detection. |
delta_2 |
Conditional probability of type 2 encounter, given detection. |
alpha |
Conditional probability of simultaneous type 1 and type 2 detection, given both types encountered. Only applies when |
data.type |
Specifies the encounter history data type. All data types include non-detections (type 0 encounter), type 1 encounter (e.g., left-side), and type 2 encounters (e.g., right-side). When both type 1 and type 2 encounters occur for the same individual within a sampling occasion, these can either be "non-simultaneous" (type 3 encounter) or "simultaneous" (type 4 encounter). Three data types are currently permitted:
|
detection |
Model for detection probability as a function of distance from activity centers. Must be " |
spatialInputs |
A list of length 3 composed of objects named
If |
buffer |
A scaler indicating the buffer around the bounding box of |
ncells |
The number of grid cells in the study area when |
scalemax |
Upper bound for grid cell centroid x- and y-coordinates. Default is |
plot |
Logical indicating whether to plot the simulated trap coordinates, study area, and activity centers using |
Please be very careful when specifying your own spatialInputs
; multimarkClosedSCR
and markClosedSCR
do little to verify that these make sense during model fitting.
A list containing the following:
Enc.Mat |
Matrix containing the observed encounter histories with rows corresponding to individuals and ( |
trueEnc.Mat |
Matrix containing the true (latent) encounter histories with rows corresponding to individuals and ( |
spatialInputs |
List of length 2 with objects named
|
centers |
|
Brett T. McClintock
Bonner, S. J., and Holmberg J. 2013. Mark-recapture with multiple, non-invasive marks. Biometrics 69: 766-775.
McClintock, B. T., Conn, P. B., Alonso, R. S., and Crooks, K. R. 2013. Integrated modeling of bilateral photo-identification data in mark-recapture analyses. Ecology 94: 1464-1471.
Royle, J.A., Karanth, K.U., Gopalaswamy, A.M. and Kumar, N.S. 2009. Bayesian inference in camera trapping studies for a class of spatial capture-recapture models. Ecology 90: 3233-3244.
processdataSCR
, multimarkClosedSCR
, markClosedSCR
#simulate data for data.type="sometimes" using defaults
data<-simdataClosedSCR(data.type="sometimes")
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