Build the nested params list that SpaDES.core::simInit() consumes from
the user-supplied params argument to setupProject().
setupParams(
name,
params,
paths,
modules,
times,
options,
overwrite = FALSE,
envir = parent.frame(),
callingEnv = sys.frame(-2),
verbose = getOption("Require.verbose", 1L),
dots,
defaultDots,
...
)Optional. If supplied, the name of the project. If not supplied, an
attempt will be made to extract the name from the paths[["projectPath"]].
If this is a GitHub project, then it should indicate the full Github
repository and branch name, e.g., "PredictiveEcology/WBI_forecasts@ChubatyPubNum12"
Optional. Similar to options, however, this named list will be
returned, i.e., there are no side effects.
See setup.
a list with named elements, specifically, modulePath, projectPath,
packagePath and all others that are in SpaDES.core::setPaths()
(i.e., inputPath, outputPath, scratchPath, cachePath, rasterTmpDir).
Each of these has a sensible default, which will be overridden but any user
supplied values.
See setup.
a character vector of modules to pass to getModule. These
should be one of: simple name (e.g., fireSense) which will be searched for locally
in the paths[["modulePath"]]; or a GitHub repo with branch (GitHubAccount/Repo@branch e.g.,
"PredictiveEcology/Biomass_core@development"); or a character vector that identifies
one or more module folders (local or GitHub) (not the module .R script).
If the entire project is a git repository,
then it will not try to re-get these modules; instead it will rely on the user
managing their git status outside of this function.
For convenience, these can also be 2 other url formats:
the raw.githubusercontent.com url that points to the main module file or the folder e.g.,
"https://raw.githubusercontent.com/PredictiveEcology/Biomass_core/refs/heads/main/Biomass_core.R"
The github.com url used for cloning a git repository, with optional "@branch" specified:
"https://github.com/PredictiveEcology/Biomass_speciesParameters.git@development"
See setup.
Optional. This will be returned if supplied; if supplied, the values
can be used in e.g., params, e.g., params = list(mod = list(startTime = times$start)).
See help for SpaDES.core::simInit.
Optional. Either a named list to be passed to options
or a character vector indicating one or more file(s) to source,
in the order provided. These will be parsed locally (not
the .GlobalEnv), so they will not create globally accessible objects. NOTE:
options is run 2x within setupProject, once before setupPaths and once
after setupPackages. This occurs because many packages use options for their
behaviour (need them set before e.g., Require::require is run; but many packages
also change options at startup. See details.
See setup.
Logical vector or character vector, however, only getModule will respond
to a vector of values. If length-one TRUE, then all files that were previously downloaded
will be overwritten throughout the sequence of setupProject – including those downloaded via sideEffects.
If a length > 1 logical or character vector, these will be passed to getModule: only the named
modules will be overwritten or the logical vector of the modules.
NOTE: if length > 1, no other file specified anywhere in setupProject will be
overwritten except a module matching the vector names() (because
only setupModules is currently responsive to a vector). To have fine grained control,
a user can just manually delete a file, then rerun.
The environment where setupProject is called from. Defaults to
parent.frame() which should be fine in most cases and user shouldn't need
to set this
The environment from which the function was called. Defaults to sys.frame(-2)
which represents the case where the inner setup* functions are called inside
setupProject, which was called by a user.
Numeric or logical indicating how verbose should the function
be. If -1 or -2, then as little verbosity as possible. If 0 or FALSE,
then minimal outputs; if 1 or TRUE, more outputs; 2 even more. NOTE: in
Require function, when verbose >= 2, also returns details as if
returnDetails = TRUE (for backwards compatibility).
Any other named objects passed as a list a user might want for other elements.
A named list of any arbitrary R objects.
These can be supplied to give default values to objects that
are otherwise passed in with the ..., i.e., not specifically named for these
setup* functions. If named objects are supplied as top-level arguments, then
the defaultDots will be overridden. This can be particularly useful if the
arguments passed to ... do not always exist, but rely on external e.g., batch
processing to optionally fill them. See examples.
further named arguments that acts like objects, but a different
way to specify them. These can be anything. The general use case
is to create the objects that are would be passed to
SpaDES.core::simInit, or SpaDES.core::simInitAndSpades,
(e.g. studyAreaName or objects) or additional objects to be passed to the simulation
(in older versions of SpaDES.core, these were passed as a named list
to the objects argument). Order matters. These are sequentially evaluated,
and also any arguments that are specified before the named arguments
e.g., name, paths, will be evaluated prior to any of the named arguments,
i.e., "at the start" of the setupProject.
If placed after the first named argument, then they will be evaluated at the
end of the setupProject, so can access all the packages, objects, etc.
setupParams prepares a named list of named lists, suitable to be passed to
the params argument of simInit.
setupProject() for the high-level wrapper, setup_family for an overview.