ExpectedFirstCapture: Expected fraction of animals caught being first captures for...

In shanearichards/crrecruit: Infer recruitment from capture-recapture data

Description

A function that returns a vector containing the expected fraction of animals caught that were caught for the first time for each survey event. Model parameters are provided in the input vector. Survey information must be stored in specific-named global variables (see Details).

Usage

ExpectedFirstCapture(params)

Arguments

params

A vector containing six parameter values (see Details).

Details

The input params contains the following values:

1. [tbar] The day when recruitment peaks.

2. [sigma] The spread in recruitment (days). Approximately 95% of recruitments occur during days [tbar - 2*sigma, tbar + 2*sigma].

3. [alpha0] Baseline catch rate (per unit effort).

4. [alpha1] Age-dependence in catch rate.

5. [beta0] Base-line mortality rate (per day).

6. [beta1] Age-dependence in mortality rate.

Recruitment is described by a Guassian peak centred on day tbar with spread characterised by sigma. Per-capita catch rate is given by: alpha0*exp(alpha1*age), where age is the days since recruitment. Per-capita mortality rate is given by: beta0*exp(beta1*age).

Suppose the survey involves the capture of animals over J sampling events. The data must be stored and summarised by the following R-variables:

E

A double vector of size J quantifying the effort applied during each sampling event.

T

An integer vector of size J providing the day of each sampling event.

T.F

An integer indicating the first possible day of recruitment.

T.L

An integer (> T.F) indicating the last possible day of recruitment.

Value

A numeric vector of length J.

Author(s)

Shane A. Richards ([e-mail])

Examples

guess <- c(3.0, 3.0, 0.2, 0.0, 0.03, 0.1)
p.first <- ExpectedFirstCapture(guess)
plot(x = T, y = p.first, xlab = "Day", ylab = "Probability first time")

shanearichards/crrecruit documentation built on May 29, 2019, 8:07 p.m.