simMBmisscap: This function simulates a hair snare mark recapture...
In benaug/Mbmisscap: Mbmisscap

Description Usage Arguments Value

This function simulates a hair snare mark recapture experiment with hair sample subsampling and failed DNA identification.

1
2
3

simMBmisscap(N, p, occ, K, traptype, btype = "global", lambda_h,
  lambda_c = NULL, delta = NULL, kappa_h = NULL, kappa_t = NULL,
  cluster = FALSE, kappa_c = NULL, alpha = NULL)

`N`	an integer that is the true population size
`p`	a vector of size 2 containing the capture and recapture probabilities
`occ`	an integer that is the number of capture occasions to simulate
`K`	an integer that is the number of traps to simulate
`traptype`	a character string specifying the trap type. "single" allows individuals to be caught in at most 1 trap per occasion and "multi" allows individuals to be caught in multiple traps per occasion.
`btype`	a character string specifying the type of behavioral response to capture. Current options are "global" for a global trap response and "trap" for a trap-specific response. "trap" currently only works with traptype=multi.
`lambda_h`	a positive value specifying the parameter for the zero-truncated Poisson hair deposition process (S_ijk\|W_ijk=1)
`lambda_c`	a positive value specifying the parameter for the zero-truncated Poisson cluster deposition process if cluster=TRUE
`delta`	a numeric value between 0 and 1 specifying the probability a hair sample will be retained in the subsample. This is used if subsampling is done by pooling samples on each occasion and taking a simple random sample.
`kappa_h`	an integer specifying the number of hair samples to retain per occasion-trap if cluster=FALSE or per occasion-trap-cluster if cluster=TRUE. Used in sub-hair and sub-cluster methods
`kappa_t`	an integer specifying the number of traps per occasion at which to retain kappa_h hair samples. If no value is specified no trap-level subsampling occurs. Only works when cluster=FALSE. Used in the sub-trap method.
`cluster`	a logical indicating whether or not to simulate from the cluster model (multiple hair clusters per individual-occasion-trap).
`kappa_c`	an integer specifying the number of clusters per trap-occasion at which to retain kappa_h hair samples. Only works when cluster=TRUE. Sub-cluster method.
`alpha`	a numeric value between 0 and 1 specifying the probability that a hair sample produces an individual identification when genotyped.