llRecruit: Returns the log-likelihood of the recruitment model
In shanearichards/crrecruit: Infer recruitment from capture-recapture data

Description Usage Arguments Details Value Author(s) Examples

View source: R/RcppExports.R

A function that returns the log-likelihood of the model of recruitment, survival and catchability, given capture-recapture data. Model parameters are provided in the function's single argument, which is a vector. Capture-recapture data must be stored in specific-named global variables (see Details).

1	llRecruit(params)

params

A vector containing six parameter values (see Details).

The input params contains the following values:

[tbar] The day when recruitment peaks.
[sigma] The spread in recruitment (days). Approximately 95% of recruitments occur during days [tbar - 2*sigma, tbar + 2*sigma].
[alpha0] Baseline catch rate (per unit effort).
[alpha1] Age-dependence in catch rate.
[beta0] Base-line mortality rate (per day).
[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 I animals over J sampling events. The data must be stored and summarised by the following R-variables:

y: An integer matrix containing the capture data (I rows and J columns). Rows indicate the animal and columns indicate the sampling event.
f: An integer vector of size I identifying the sampling event when the animal was first caught. Values lie in the range [1,J].
l: An integer vector of size I identifying the sampling event when the animal was last caught. Values lie in the range [1,J]. All element satisfy l >= f.
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.

Note that the vectors f and l are determined by the matrix y but must be calculated by the user.

This function is usually used in conjunction with the optim function (see Examples).

A double.

Shane A. Richards (shane.richards@csiro.au)

guess <- c(3.0, 3.0, 0.2, 0.0, 0.03, 0.1) # dummy model parameters
ll <- llRecruit(guess) # calculate log-likelihood of the model

# find the maximum-likelihood parameter estimates
# box constraint method allows control over parameter estimates
#   age-dependent capture is turned off by restricting alpha1 (parameter 4)
# tracer flags are turned on to check for convergence
fit <- optim(par = guess, fn = llRecruit,
  lower = c(0, 1.0, 0.10, -0.001, 0.0025, 0.001),
  upper = c(6, 5.0, 0.35,  0.001, 0.1000, 0.190),
  method = "L-BFGS-B",
  control = list(fnscale = -1, trace = 1, maxit = 100, REPORT = 20))

fit$par # display maximum-likelihood parameter estimates