These provide top-level, powerful settings for a comprehensive
SpaDES workflow. To see defaults, run spadesOptions().
See Details below.
spadesOptions()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.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
reparse 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.inputPath | Default is a temporary directory (typically /tmp/RtmpXXX/SpaDES/inputs) | The default local directory in which to look for simulation inputs. |
spades.debug | TRUE | The default debugging value debug argument in spades() |
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 sim) into a future. In some
cases, this will speed up simulations, by running some events in parallel.
Still VERY experimental. Use cautiously. |
spades.lowMemory | FALSE | If true, some functions will use more memory efficient (but slower) algorithms. |
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 |
moduleDocument | NULL | When a module is an R package e.g., via convertToPackage,
it will not, by default, rebuild documentation during simInit. If
the user would like this to happen on every call to simInit,
set this option to TRUE |
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.recoveryMode | 1L | If this a numeric > 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
> 1 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.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. |