SpaDES.core (version 2.0.5)

defineModule: Define a new module.

Description

Specify a new module's metadata as well as object and package dependencies. Packages are loaded during this call. Any or all of these can be missing, with missing values set to defaults

Usage

defineModule(sim, x)
# S4 method for simList,list
defineModule(sim, x)

Value

Updated simList object.

Arguments

sim

A simList object from which to extract element(s) or in which to replace element(s).

x

A list with a number of named elements, referred to as the metadata. See details.

Required metadata elements

name	Module name. Must match the filename (without the .R extension). This is currently not parsed by SpaDES; it is for human readers only.
description	Brief description of the module. This is currently not parsed by SpaDES; it is for human readers only.
keywords	Author-supplied keywords. This is currently not parsed by SpaDES; it is for human readers only.
childModules	If this contains any character vector, then it will be treated as a parent module. If this is a parent module, then only this list entry will be read. For normal, i.e., 'child modules', this should be character(0) or NA. If a character vector is provided, then these must be the names of the modules located in the same file path as this parent module that will be loaded during the simInit.
authors	Module author information (as a vector of person() objects. This is currently not parsed by SpaDES; it is for human readers only.
version	Module version number (will be coerced to numeric_version() if a character or numeric are supplied). The module developer should update manually this with each change that is made to the module. See https://semver.org/ for a widely accepted standard for version numbering.
spatialExtent	The spatial extent of the module supplied via terra::ext. This is currently unimplemented. Once implemented, this should define what spatial region this module is scientifically reasonable to be used in.
timeframe	Vector (length 2) of POSIXt dates specifying the temporal extent of the module. Currently unimplemented. Once implemented, this should define what time frame this module is scientifically reasonable to be used for.
timeunit	Time scale of the module (e.g., "day", "year"). If this is not specified, then .timeunitDefault() will be used. It indicates what '1' unit of time means for this module. SpaDES interprets this and if modules have different timeunit values then it will correctly schedule each module, using the smallest (currently the default) timeunit as the 'model' timeunit in the spades call.
citation	List of character strings specifying module citation information. Alternatively, a list of filenames of .bib or similar files. This is currently not parsed by SpaDES; it is for human readers only.
documentation	List of filenames referring to module documentation sources. This is currently not parsed by SpaDES; it is for human readers only.
loadOrder	Named list of length 0, 1, or 2, with names being after and before. Each element should be a character string/vector naming 1 or more modules that will be loaded after or before this module. after and before are used from the current module's perspective. So, list(after = c("Biomass_core")) means that this module must come after "Biomass_core". This should only be used when there are cyclic dependencies (2 or more modules have 1 or more objects that is in both inputObjects and outputObjects of both/all modules) between this module and other modules. In cases where the dependencies are not cyclic, SpaDES is able to resolve the order correctly.
reqdPkgs	List of R package names required by the module. These packages will be loaded when simInit is called. Require::Require() will be used internally to load if available, and install if not available. Because Require::Require() can also download from GitHub.com, these packages can specify package names stored on GitHub, e.g., "PredictiveEcology/SpaDES.core@development".
parameters	A data.frame specifying the parameters used in the module. Usually produced by rbind-ing the outputs of multiple defineParameter() calls. These parameters indicate the default values that will be used unless a module user overrides them with the params argument in the simInit() call. The minimum and maximum are currently used by the SpaDES.shiny::shine function and the POM function, and they should indicate the range of values that are reasonable scientifically.
inputObjects	A data.frame specifying the data objects expected as inputs to the module, with columns objectName (class character), objectClass (class character), sourceURL (class character), and other (currently spades does nothing with this column). This data.frame identifies the objects that are expected, but does not do any loading of that object into the simList. The sourceURL gives the developer the opportunity to identify the source of a data file that can be used with the model. This URL will be used if the user calls downloadData (or downloadModule(..., data = TRUE). If the raw data must be modified, the developer can use create a function called .inputObjects in their module. That function will be run during the simInit call. The developer should ensure that if the object is supplied by the module user as an argument in the simInit, then the .inputObjects should not be run, i.e., use an (is.null(sim$xxx))).
outputObjects	A data.frame specifying the data objects output by the module, with columns identical to those in inputObjects. Like inputObjects above, this only identifies the objects that this module will output into the simList. The module developer must create the necessary functions that will cause these objects to be put into the simList.

Author

Alex Chubaty

See Also

moduleDefaults(), defineEvent()

Examples

# \donttest{
  ## a default version of the defineModule is created with a call to newModule
  newModule("test", path = tempdir(), open = FALSE)

  ## view the resulting module file
  if (interactive()) file.edit(file.path(tempdir(), "test", "test.R"))
# }