Description Usage Arguments Value Author(s) References See Also Examples
This function generates encounter histories from simulated open population capturemarkrecapture data consisting of multiple noninvasive marks.
1 2 3  simdataCJS(N = 100, noccas = 5, pbeta = 0.25, sigma2_zp = 0,
phibeta = 1.6, sigma2_zphi = 0, delta_1 = 0.4, delta_2 = 0.4,
alpha = 0.5, data.type = "never", link = "probit")

N 
Number of individuals. 
noccas 
Number of sampling occasions. 
pbeta 
Logit or probitscale intercept term(s) for capture probability (p). Must be a scaler or vector of length 
sigma2_zp 
Logit or probitscale individual heterogeneity variance term for capture probability (p). 
phibeta 
Logit or probitscale intercept term(s) for survival probability (φ). Must be a scaler or vector of length 
sigma2_zphi 
Logit or probitscale individual heterogeneity variance term for survival probability (φ). 
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 nondetections (type 0 encounter), type 1 encounter (e.g., leftside), and type 2 encounters (e.g., rightside). When both type 1 and type 2 encounters occur for the same individual within a sampling occasion, these can either be "nonsimultaneous" (type 3 encounter) or "simultaneous" (type 4 encounter). Three data types are currently permitted:

link 
Link function for detection probability. Must be " 
A list containing the following:
Enc.Mat 
A matrix containing the observed encounter histories with rows corresponding to individuals and columns corresponding to sampling occasions. 
trueEnc.Mat 
A matrix containing the true (latent) encounter histories with rows corresponding to individuals and columns corresponding to sampling occasions. 
Brett T. McClintock
Bonner, S. J., and Holmberg J. 2013. Markrecapture with multiple, noninvasive marks. Biometrics 69: 766775.
McClintock, B. T., Conn, P. B., Alonso, R. S., and Crooks, K. R. 2013. Integrated modeling of bilateral photoidentification data in markrecapture analyses. Ecology 94: 14641471.
1 2  #simulate data for data.type="sometimes" using defaults
data<simdataCJS(data.type="sometimes")

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