single_release: Single tag release estimate of population size

In paulburch/tagr: Tagging models for the estimation of abundance and demographic parameters

Description

Estimate population size from single release tag data

Usage

single_release(tags, catch, recaps, mean_wt = 0, prior_recaps = 0, method,
  unit, type, tag_mort = 0, reporting = 1, nat_mort = 0,
  chronic_shed = 0, chronic_mort = 0)

Arguments

tags	number of marked animals released (note these must be whole numbers for the bootstrap to work)
catch	vector of the number or weight of animals captured and checked for tags by haul on the second survey
recaps	vector of number of marked animals recaptured by haul
mean_wt	mean weight of a single fish (optional argument for Chapman weight method)
prior_recaps	vector of subsequent recaptures (first year this represents within season recaptures)
method	method
unit	measurement unit (numbers, kg, tonnes)
type	do we assume fishing occurs over a short period (Ricker type 1) or is extended over the year and competes with natural mortality and tag sheddding (Ricker type 2)
tag_mort	initial tag-induced mortality
reporting	vector of tag reporting rate
nat_mort	vector of natural mortality (instantaneous)
chronic_shed	vector of chronic (ongoing) tag shedding
chronic_mort	vector of chronic (ongoing) tag-induced mortality

Details

For a Type 1 fishery the adjusted releases are calculate as follows

1) Initial tag-induced mortality is applied

2) Within season recaptures divided by the tag reporting rate are removed

3) Natural mortality and chronic tag loss and tag-induced mortality is applied.

For a fishery that operates throughout the year (Ricker Type 2) fishing and natural mortality competed to deplete the tagged population. The adjusted releases are calculated as follows

1) Initial tag-induced mortality is applied

2) Half of the within season recaptures divided by the tag reporting rate are removed

3) Half of the natural mortality and chronic tag loss and tag-induced mortality is applied

4) The remaining within season recaptures divided by the tag reporting rate are removed

5) The remaining natural mortality and chronic tag loss and tag-induced mortality is applied.

Examples

## Chapman estimates of population numbers
single_release(tags=100, catch=200, recaps=5, method="Chapman",
               type=1, unit="numbers")
single_release(tags=100, catch=200, recaps=5, method="Chapman", 
               type=1, unit="numbers", tag_mort=0.1)
single_release(tags=100, catch=200, recaps=5, method="Chapman", type=1,
               unit="numbers", tag_mort=0.1, reporting=0.8) 

## Chapman estimate of the population size of carp in a lake
## Load the carphauls data
attach(carphauls)
fit <- single_release(tags = 803, catch = carphauls$catch,
                     recaps = carphauls$tagged,
                     prior_recaps = c(108, 181, 82),
                     method = "Chapman", unit = "numbers",
                     type = 2, tag_mort = 0.3, nat_mort = 0.04,
                     chronic_mort = 0.17)
summary(fit)

## Not run: 
#######################################
# estimate uncertainty with a bootstrap
#######################################

boot_fit <- bootstrap(fit, 1000)
summary(boot_fit)

## End(Not run)

paulburch/tagr documentation built on May 24, 2019, 8:26 p.m.