PrNotDetect: Probability animals will not be detected during the survey In shanearichards/crrecruit: Infer recruitment from capture-recapture data

Description

A function that returns the probability a randomly chosen animal will not be detected during the survey, given the survey design. Model parameters are provided in a vector. Survey information must be stored in specific-named global variables (see Details).

Usage

 `1` ```PrNotDetect(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.

A single value.

Author(s)

Shane A. Richards ([email protected])

Examples

 ```1 2``` ```guess <- c(3.0, 3.0, 0.2, 0.0, 0.03, 0.1) PrNotDetect(guess) ```

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