defineParameter: Define a parameter used in a module

In SpaDES.core: Core Utilities for Developing and Running Spatially Explicit Discrete Event Models

Define a parameter used in a module

Description

Used to specify a parameter's name, value, and set a default. The min and max arguments are ignored by simInit or spades; they are for human use only. To ensure that a user cannot set parameters outside of a range of values, the module developer should use assertions in their module code.

Usage

defineParameter(name, class, default, min, max, desc, ...)

Arguments

name	Character string giving the parameter name.
class	Character string giving the parameter class.
default	The default value to use when none is specified by the user. Non-standard evaluation is used for the expression.
min	With max, used to define a suitable range of values. Non-standard evaluation is used for the expression. These are not tested by simInit or spades. These are primarily for human use, i.e., to tell a module user what values the module expects.
max	With min, used to define a suitable range of values. Non-standard evaluation is used for the expression. These are not tested by simInit or spades. These are primarily for human use, i.e., to tell a module user what values the module expects.
desc	Text string providing a brief description of the parameter. If there are extra spaces or carriage returns, these will be stripped, allowing for multi-line character strings without using paste or multiple quotes.
...	A convenience that allows writing a long desc without having to use paste; any character strings after desc will be pasted together with desc.

Value

a data.frame

Note

Be sure to use the correct NA type: logical (NA), integer (NA_integer_), real (NA_real_), complex (NA_complex_), or character (NA_character_). See NA().

Author(s)

Alex Chubaty and Eliot McIntire

See Also

P(), params() for accessing these parameters in a module.

Examples

parameters = rbind(
  defineParameter("lambda", "numeric", 1.23, desc = "intrinsic rate of increase"),
  defineParameter("P", "numeric", 0.2, 0, 1, "probability of attack"),

  # multi-line desc without quotes on each line -- spaces and carriage returns are stripped
  defineParameter("rate", "numeric", 0.2, 0, 1,
                  "rate of arrival. This is in individuals
                  per day. This can be modified
                  by the user"),
  # multi-line desc with quotes on each line
  defineParameter("times", "numeric", 0.2, 0, 1,
                  desc = "The times during the year ",
                         "that events will occur ",
                         "with possibility of random arrival times")

)


# Create a new module, then access parameters using `P`
tmpdir <- file.path(tempdir(), "test")
checkPath(tmpdir, create = TRUE)

# creates a  new, "empty" module -- it has defaults for everything that is required
newModule("testModule", tmpdir, open = FALSE)

# Look at new module code -- see defineParameter
if (interactive()) file.edit(file.path(tmpdir, "testModule", "testModule.R"))

# initialize the simList
if (requireNamespace("ggplot2", quietly = TRUE)) {
  # Some things not necessary in this example, if not interactive (like plotting)
  opts <- if (interactive()) list() else
    options(spades.plot = NA, spades.useRequire = FALSE,
            spades.moduleCodeChecks = FALSE)
  mySim <- simInit(modules = "testModule",
                   paths = list(modulePath = tmpdir))

  # Access one of the parameters -- because this line is not inside a module
  #  function, we must specify the module name. If used within a module,
  #  we can omit the module name
  P(mySim, module = "testModule") # gets all params in a module
  P(mySim, ".useCache", "testModule") # just one param
  options(opts)
}
unlink(tmpdir, recursive = TRUE)

SpaDES.core documentation built on Nov. 10, 2023, 5:08 p.m.