These provide top-level, powerful settings for a comprehensive SpaDES workflow.
To see defaults, run spadesOptions().
See Details below.
spadesOptions()named list of the default package options.
Below are options that can be set with options("spades.xxx" = newValue),
where xxx is one of the values below, and newValue is a new value to
give the option. Sometimes these options can be placed in the user's .Rprofile
file so they persist between sessions.
The following options are likely of interest to most users
| OPTION | DEFAULT VALUE | DESCRIPTION |
spades.allowInitDuringSimInit | FALSE | New feature as of SpaDES.core > 1.1.1.9001; If set to TRUE,
simInit will evaluate the dependencies in the metadata objects and determine whether
there are modules whose init events can be run safely prior to
the .inputObjects of other modules, i.e., if a module's expectsInput
is not being supplied by any other module's createsOutput. |
spades.browserOnError | FALSE | If TRUE, the default, then any
error rerun the same event with debugonce called on it to allow editing
to be done. When that browser is continued (e.g., with 'c'), then it will save it
re-parse it into the simList and rerun the edited version.
This may allow a spades() call to be recovered on error,
though in many cases that may not be the correct behaviour.
For example, if the simList gets updated inside that event in an iterative
manner, then each run through the event will cause that iteration to occur.
When this option is TRUE, then the event will be run at least 3 times: the
first time makes the error, the second time has debugonce and the third time
is after the error is addressed. TRUE is likely somewhat slower. |
reproducible.cachePath | getOption('reproducible.cachePath') | The default local directory in which to cache simulation outputs.
Default is a temporary directory (typically /tmp/RtmpXXX/SpaDES/cache). |
spades.debug | TRUE | The default debugging value debug argument in spades() |
spades.dotInputObjects | TRUE | This is used in simInit; if set to TRUE then the .inputObjects
function will be run; if FALSE, then it will be skipped. |
spades.DTthreads | 1L | The default number of data.table threads to use.
See also ?data.table::setDTthreads. |
spades.futureEvents | FALSE | If set to TRUE, the event simulator will attempt to spawn events
whose outputs are not needed (by other events in the simList) into a future.
In some cases, this will speed up simulations, by running some events in parallel.
Still VERY experimental. Use cautiously. |
spades.logPath | Defaults to a subdirectory (logs/) of the simulation output directory. | The default local directory in which to look for simulation inputs. |
spades.inputPath | Default is a temporary directory (typically /tmp/RtmpXXX/SpaDES/inputs) | The default local directory in which to look for simulation inputs. |
spades.loadReqdPkgs | Default is TRUE meaning that any reqdPkgs will be loaded via Require
or require. If FALSE, no package loading will occur. This will mean that
modules must prefix every function call from a package with that package name
with double colon (::). | spades.lowMemory |
FALSE | If true, some functions will use more memory efficient (but slower) algorithms. | spades.memoryUseInterval |
FALSE | A numeric in seconds indicating how often sample the memory use. This will
be run in a separate "future" process so it can monitor the main process.
To access the resulting memory use table, use memoryUse(sim) after the simulation
has terminated. | spades.messagingNumCharsModule |
21 | The number of characters to use for the messaging preamble on each line of the messaging during spades calls. | spades.moduleCodeChecks |
list(suppressParamUnused = FALSE, suppressUndefined = TRUE, suppressPartialMatchArgs = FALSE, suppressNoLocalFun = TRUE, skipWith = TRUE) | Should the various code checks be run
during simInit. These are passed to codetools::checkUsage().
Default is given by the function, plus these: | spades.moduleDocument |
TRUE | When a module is an R package e.g., via convertToPackage,
it will, by default, rebuild documentation and reparse during simInit.
Since rebuilding documentation (from the roxygen2 tags) can be time consuming,
a user may wish to prevent this from happening each simInit call. If so,
set this option to FALSE | spades.modulePath |
file.path(tempdir(), "SpaDES", "modules")) | The default local directory where modules and data will be downloaded and stored. Default is a temporary directory | spades.moduleRepo |
"PredictiveEcology/SpaDES-modules" | The default GitHub repository to use when
downloading modules via downloadModule | spades.nCompleted |
1000L | The maximum number of completed events to
retain in the completed event queue. | spades.outputPath |
file.path(tempdir(), "SpaDES", "outputs") | The default local directory in which to save simulation outputs. | spades.plots |
The value of this will passed to .plots within every module; it will thus
override all module parameter values for .plots. This can, e.g., be used
to turn off all plotting. | The default is NULL, meaning accept the module-level parameter | spades.recoveryMode |
1L | If this is a numeric greater than 0 or TRUE, then the
discrete event simulator will take a snapshot of the objects in the simList
that might change (based on metadata outputObjects for that module), prior to
initiating every event. This will allow the
user to be able to recover in case of an error or manual interruption (e.g., Esc).
If this is numeric, a copy of that number of "most
recent events" will be maintained so that the user can recover and restart
more than one event in the past, i.e., redo some of the "completed" events.
Default is TRUE, i.e., it will keep the state of the simList
at the start of the current event. This can be recovered with restartSpades
and the differences can be seen in a hidden object in the stashed simList.
There is a message which describes how to find that. | spades.saveFileExtensions |
NULL | a data.frame with 3 columns, exts, fun, and package indicating which
file extension, and which function from which package will be used when
using the outputs mechanism for saving files during a spades call. e.g.,
options(spades.saveFileExtensions = data.frame(exts = "shp", fun = "st_write", package = "sf").
Then specify e.g.,
simInit(outputs = data.frame(objectName = "caribou", fun = "st_write", package = "sf")) | spades.scratchPath |
file.path(tempdir(), "SpaDES", "scratch")) | The default local directory where transient files from modules and data will written.
This includes temporary raster and terra files, as well as SpaDES recovery mode files.
Default is a temporary directory. | spades.sessionInfo |
TRUE) | Assigns the utils::sessionInfo() to the simList during simInit with
the name sim$._sessionInfo. This takes about 75 milliseconds, which may be
undesirable for some situations where speed is critical. If FALSE, then
this is not assigned to the simList. | spades.switchPkgNamespaces |
FALSE to keep computational
overhead down. | Should the search path be modified
to ensure a module's required packages are listed first?
If TRUE, there should be no name conflicts among package objects,
but it is much slower, especially if the events are themselves fast. | spades.testMemoryLeaks |
TRUE. | There is a very easy way to create a memory leak with R and SpaDES,
by adding formulas or functions to sim$ when the enclosing environment
of the formula or function contained a large object, most relevant here is
the sim object. SpaDES.core now tests for likely culprits for this
and suggests alternatives with a warning | spades.tolerance |
.Machine$double.eps^0.5. | The default tolerance value used for floating point number comparisons. | spades.useragent |
"https://github.com/PredictiveEcology/SpaDES". | : The default user agent to use for downloading modules from GitHub. | spades.useRequire |
!tolower(Sys.getenv("SPADES_USE_REQUIRE")) %in% "false" | : The default for that environment variable is unset, so this returns
TRUE. If this is TRUE, then during the simInit call, when packages are
identified as being required, these will be installed if missing, only if
spades.useRequire option is TRUE, otherwise, simInit will fail because
packages are not available. |