assessMh: This function asseses some frequentist properties when...

Description Usage Arguments Value

Description

This function asseses some frequentist properties when naively fitting Mb to capture histories that are missing data.

Usage

1
2
3
assessMh(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", sims = 100, cores = 1)

Arguments

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.

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

hettype

...

sims

the number of simulated data sets to generate and fit Mb to

cores

the number of cores to do the simulation on. A typical for loop is used if cores=1 and the foreach package is used if cores>1

Value

a list with the simulation results (expand later)


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