mmmSim: Simulate Tag Recovery Data

In luke-a-rogers/mmmTMB: Fit Markov Movement Models (MMM) via Template Model Builder

Description

Simulate Tag Recovery Data

Usage

mmmSim(data, parameters = NULL, settings = mmmSet())

Arguments

data	list() Input data. See details.
parameters	list() Parameters to be treated as data. See details.
settings	list() Values that help define the simulation model. See mmmSet().

Details

The list() argument data must contain:

• x An integer matrix of tag release counts formatted as described in mmmTags().

• y An integer matrix of tag recovery counts formatted as described in mmmTags().

• z A square binary index matrix that indicates allowed direct movement between areas (from rows to columns) from one time step to the next. Ones off the diagonal indicate allowed direct movement. Zeros off the diagonal represent disallowed direct movement. Numbers on the diagonal are ignored because self-movement is always allowed. See mmmIndex().

• h The (positive) scalar instantaneous tag loss rate.

• u The scalar proportion of tags lost during release.

The list argument data may optionally contain:

• l A matrix of tag reporting rates (proportions). Defaults to one if omitted (full reporting). See mmmRates().

• w A matrix of fishing mortality rate weights. Useful when the tag time step is finer than the fishing rate step. Defaults to one (equal fishing rates across tag time steps within a fishing rate time step). See mmmWeights().

• f A matrix of fishing mortality rates. Must be included in data or parameters. See mmmRates().

• m The scalar instantaneous natural mortality rate. Must be included in data or parameters.

The list() argument parameters must contain:

• p An array of movement parameters. See create_movement_parameters().

The list argument parameters may optionally contain:

• f A matrix of fishing mortality rates. Must be included in data or parameters. See mmmRates().

• m The scalar instantaneous natural mortality rate. Must be included in data or parameters.

Value

An object of class mmmSim.

Examples

# Data
sim_x <- create_release_matrix()
sim_z <- mmmIndex(3, pattern = 1)
sim_f <- as.matrix(0.04)
sim_m <- 0.1
sim_h <- 0.02
sim_u <- 0.1
# Parameters
v <- c(0.9, 0.1, 0.0, 0.1, 0.8, 0.3, 0.0, 0.1, 0.7)
sim_r <- array(v, dim = c(3,3,1,1))
sim_p <-create_movement_parameters(sim_r, sim_z)
# Simulation
data <- list(
  x = sim_x,
  z = sim_z,
  f = sim_f,
  m = sim_m,
  h = sim_h,
  u = sim_u)
parameters <- list(p = sim_p)
s1 <- mmmSim(data, parameters)

luke-a-rogers/mmmTMB documentation built on Jan. 16, 2021, 3:53 p.m.