simMhmisscap: This function simulates a hair snare mark recapture...

Description Usage Arguments Value

Description

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

Usage

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simMhmisscap(N, p, occ, K, traptype, lambda_h, lambda_c = NULL,
  delta = NULL, kappa_h = NULL, kappa_t = NULL, cluster = FALSE,
  kappa_c = NULL, alpha = NULL, hettype = "logitnormal")

Arguments

N

an integer that is the true population size

p

a vector of size 2 containing the capture and recapture probabilities...fix this

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.

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 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 param hettype a character string specifying the type of individual heterogeneity. Either "logitnormal" or "finitemixture".

Value

a list with the simulated quantities and statistics (expand description later)


benaug/Mbmisscap documentation built on May 12, 2019, 10:56 a.m.