This function generates encounter histories from simulated open population capture-mark-recapture data consisting of multiple non-invasive marks.
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"
)A list containing the following:
A matrix containing the observed encounter histories with rows corresponding to individuals and columns corresponding to sampling occasions.
A matrix containing the true (latent) encounter histories with rows corresponding to individuals and columns corresponding to sampling occasions.
Number of individuals.
Number of sampling occasions. floor(N/noccas) individuals are first encountered on each occasion.
Logit- or probit-scale intercept term(s) for capture probability (p). Must be a scaler or vector of length noccas.
Logit- or probit-scale individual heterogeneity variance term for capture probability (p).
Logit- or probit-scale intercept term(s) for survival probability (\(\phi\)). Must be a scaler or vector of length noccas.
Logit- or probit-scale individual heterogeneity variance term for survival probability (\(\phi\)).
Conditional probability of type 1 encounter, given detection.
Conditional probability of type 2 encounter, given detection.
Conditional probability of simultaneous type 1 and type 2 detection, given both types encountered. Only applies when data.type="sometimes".
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:
data.type="never" indicates both type 1 and type 2 encounters are never observed for the same individual within a sampling occasion, and observed encounter histories therefore include only type 1 or type 2 encounters (e.g., only left- and right-sided photographs were collected). Observed encounter histories can consist of non-detections (0), type 1 encounters (1), and type 2 encounters (2). See bobcat. Latent encounter histories consist of non-detections (0), type 1 encounters (1), type 2 encounters (2), and type 3 encounters (3).
data.type="sometimes" indicates both type 1 and type 2 encounters are sometimes observed (e.g., both-sided photographs are sometimes obtained, but not necessarily for all individuals). Observed encounter histories can consist of non-detections (0), type 1 encounters (1), type 2 encounters (2), type 3 encounters (3), and type 4 encounters (4). Type 3 encounters can only be observed when an individual has at least one type 4 encounter. Latent encounter histories consist of non-detections (0), type 1 encounters (1), type 2 encounters (2), type 3 encounters (3), and type 4 encounters (4).
data.type="always" indicates both type 1 and type 2 encounters are always observed, but some encounter histories may still include only type 1 or type 2 encounters. Observed encounter histories can consist of non-detections (0), type 1 encounters (1), type 2 encounters (2), and type 4 encounters (4). Latent encounter histories consist of non-detections (0), type 1 encounters (1), type 2 encounters (2), and type 4 encounters (4).
Link function for detection probability. Must be "logit" or "probit". Note that multimarkCJS is currently implemented for the probit link only.
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.
processdata, multimarkCJS
#simulate data for data.type="sometimes" using defaults
data<-simdataCJS(data.type="sometimes")
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