Built-in closures
The SimSurvey package makes frequent
use of “closures”, which are functions that contain data and return
functions (Wickham 2014), to control how
the simulations are structured. There are various closures built into
the package and the data supplied to these closures tend to be parameter
inputs and the closures return functions that require inputs such as
ages and/or years. This was done to avoid the repeated specifications of
key arguments, such as ages and years. Moreover, this approach provides
an option for advanced R users to inspect and modify the closures
implemented in the package to supply custom closures with alternate
equations. For instance, the sim_logistic closure was
created to control the shape of survey catchability and it requires
parameter inputs that control the shape of the logistic curve and it
returns a function that requires a vector of ages.
sim_logistic <- function(k = 2, x0 = 3, plot = FALSE) {
function(x = NULL) {
y <- 1 / (1 + exp(-k * (x - x0)))
if (plot) plot(x, y, type = "b")
y
}
}Such that when this closure is run, the object returned is a function.
ages <- 1:20
logistic_fun <- sim_logistic(k = 1, x0 = 5)
logistic_curve <- logistic_fun(ages)
plot(x = ages, y = logistic_curve, xlab = "Age", ylab = "Catchability", type = "l")
Notice that some simple plotting code has been included inside the
sim_logistic closure, as it is with the other closures
included with SimSurvey, such that when
plot = TRUE a plot is automatically generated. This is
useful for visual explorations of parameter settings.
When these closures are supplied to the core functions of
SimSurvey, the argument ends up being a
function and this function is used internally to control various aspects
of the simulation, such as the shape of survey catchability. The
internal inputs to these functions (e.g. ages and years) can therefore
be dynamic.
set.seed(438)
sim <- sim_abundance() %>%
sim_distribution() %>%
sim_survey(n_sims = 5, q = sim_logistic(k = 1, x0 = 5))Custom closures
Users are not restricted to the limited number of parametric
relationships captured inside the closures built into the
SimSurvey package. The code can be copied
and modified to impose different relationships. For instance, the
sim_logistic closure can be modified to make a
sim_gaussian closure for use in the sim_survey
function to impose dome-shaped survey catchability.
sim_gaussian <- function(a = 1, b = 10, c = 5, plot = FALSE) {
function(x = NULL) {
y <- a * exp(-((x - b) ^ 2) / (2 * c ^ 2))
if (plot) plot(x, y, type = "b")
y
}
}
gaussian_fun <- sim_gaussian(b = 15, c = 5)
gaussian_curve <- gaussian_fun(ages)
plot(x = ages, y = gaussian_curve, xlab = "Age", ylab = "Catchability", type = "l")
And this closure can be used in lieu of
sim_logistic.
set.seed(438)
sim <- sim_abundance() %>%
sim_distribution() %>%
sim_survey(n_sims = 5, q = sim_gaussian(b = 15, c = 5))