NEWS.md
test-module-deps-methods.R (using igraph::cluster_optimal()) is fragile across igraph versions and GLPK link configurations. Despite existing platform-specific skips, individual Linux configurations on the CRAN check farm still triggered the assertion. The test now unconditionally skip_on_cran(), while retaining the existing platform skips for local/CI runs.randomLandscapes sample module called SpaDES.tools::neutralLandscapeMap() via a path that required NLMR whenever the installed SpaDES.tools was the CRAN version (2.1.1, which lacks the built-in gaussian generator). CRAN’s check machines do not install NLMR (it is not on a mainstream repository, and Additional_repositories is not used to install Suggests during routine checks), so every test that ran spades() with this module errored with “Package ‘NLMR’ not available”.randomLandscapes’s makeNLM() helper now degrades gracefully with no hard dependency: (1) SpaDES.tools (>= 2.1.2) -> built-in gaussian generator; (2) older SpaDES.tools with NLMR installed -> NLMR’s nlm_mpd (unchanged behaviour for users who have NLMR); (3) otherwise -> a zero-dependency terra fallback (smoothed i.i.d. normal noise), so the module never errors.NLMR fully removed as a declared dependency: dropped from Suggests, Additional_repositories, and the Description field. It is now used only opportunistically by the randomLandscapes sample module when the user happens to have it installed. Closes #334..robustDigest() for simList no longer contributes the @inputs and module-scoped @outputs data.frames to the cache digest. The rationale: if an object affects the event, it is already digested directly via the module’s expected inputs; whether it arrived through simInit(inputs = ...) should not change the cache key. The visible effect is that cached events written by SpaDES.core < 3.0.4.9020 will not be found by ≥ 3.0.4.9020 — the digest changed, so the next call to spades() recomputes (and re-caches) those events. Cloud caches keyed on the old digest are similarly invisible to the new code. No data is lost; the cache simply rebuilds.restartSpades() now defaults to numEvents = 1L (previously Inf). Callers that relied on the old default to replay every saved event must pass numEvents = Inf explicitly.reproducible ≥ 3.0.0. See the reproducible NEWS for migration notes.?SpaDES.core). Restructured into 14 sections, simpler language, every user-facing export is now linked, and the inlined options table is replaced with a pointer to [spadesOptions()] (which is the single source of truth). New sections cover code checking, persistence/recovery, memory monitoring, and conditional events.options(spades.codeCheckEngine = "v2")), built on xmlparsedata + xml2. Adds: parameter-use checks (Par$x, P(sim)$x, P(sim, module = "other")$x, params(sim)$mod$x, params(sim)[["m"]][["x"]]), broader sim accessor coverage (get/assign/exists/mget against envir(sim)), accurate source-position reporting (file:line:col), structured data.frame of findings (stashed on sim@.xData$.codeCheck), one suggestion per finding, and grouped cli table output. v1 (code-checking.R) remains the default and is selectable via options(spades.codeCheckEngine = "v1"). New standalone API codeCheckModule(path) runs the checks against a module directory without requiring simInit()..useCacheArgs: optional named list (keyed by event name) of extra arguments spliced into the per-event reproducible::Cache() call. Lets a developer pin a fixed cacheId so a pre-seeded cloud folder (useCloud = TRUE, cloudFolderID = ...) can short-circuit a deterministic event to a download. Falls through to existing defaults when absent. The newModule() template emits a commented-out opt-in example.saveSimList: resilient to individual file-backed objects whose backing files are inaccessible at save time; such objects are saved as NULL with a warning rather than aborting the entire save.loadSimList: mirror-image resilience on the load side via .unwrapResiliently() — file-backed objects that cannot be .unwrap()ped (e.g. backing files missing on this machine) are loaded as NULL with a warning instead of aborting the load.loadSimList: path-remap loops now skip non-character / NULL list elements (left behind by .wrapResiliently having nulled an object at save time), preventing dirname(fileHere) from aborting with “a character vector argument expected”.saveSimList: new lazy = TRUE option saves each user object individually into a <filename>_xData/ directory; loadSimList auto-detects this layout and loads objects lazily via delayedAssign, materialising each only on first access. During lazy load, .modObjs (per-module object copies held in the shell simList) is cleared before .unwrap() so that missing backing files do not cause a load failure; .modObjs is rebuilt by spades() on the next run.saveSimList(lazy = TRUE): restrict tools::makeLazyLoadDB to user objects (variables = userObjNames) so dot-prefixed internals (.mods, .modObjs, …) are not bundled into the lazy DB. Without this, makeLazyLoadDB’s envhook collapses each nested env’s bindings into a single serialized blob, and .mods alone can blow R’s 2 GB single-value lazyLoadDB limit (Error in lazyLoadDBinsertValue ... long vectors not supported yet: connections.c:6552).saveSimList: remove sim@.xData$._sim (circular reference) before saving to avoid redundant data in the saved file.archive::archive_extract) no longer flood the console during simInit/spades. Progress output is throttled to one line per getOption("spades.progressInterval", 2) seconds. Set options(spades.progressInterval = N) to change the interval.suppliedElsewhere now treats both types of NULL as equal: list(a = 1)a were seen as different; now they are the sameR/module-malformed.R). A small registry of detectors (.CC_MALFORMED_CHECKS) catches common authoring mistakes and emits a clear, actionable error message instead of R’s cryptic parse-error or the deep failures that used to surface only inside defineModule(). Initial detectors: trailing comma in defineModule(sim, list(...)), missing comma between metadata rows inside rbind()/bindrows(), unquoted parameter name in defineParameter(), and unquoted objectName in expectsInput()/createsOutput(). New exported function checkModuleMetadata() runs the checks on a module file on disk (no simInit() needed). Adding a new check is one entry in the registry — no surgery elsewhere. Closes #325.randomLandscapes (inst/sampleModules/randomLandscapes) now calls SpaDES.tools::neutralLandscapeMap() in a version-adaptive way: with SpaDES.tools (>= 2.1.2) it uses the new built-in type = "gaussian" generator (dependency-free) and the per-layer smooth argument to control autocorrelation length; with the current CRAN SpaDES.tools (2.1.1) it falls back to the nlm_mpd generator, which requires NLMR. NLMR is not in the module’s reqdPkgs; the SpaDES.tools requirement is relaxed to >= 2.1.1. Step toward closing #334.NLMR is no longer a hard dependency, but it is not fully removed. It remains a Suggested package, available from the additional repository https://predictiveecology.r-universe.dev (declared via Additional_repositories, with installation instructions in the DESCRIPTION Description field). It is needed only when neutral-landscape generation runs against SpaDES.tools < 2.1.2; it can be dropped entirely once SpaDES.tools 2.1.2 reaches CRAN. The Remotes entry for NLMR was removed (no longer needed). Partial progress on #334.SpaDES.taols → SpaDES.tools (in i-introduction and ii-modules); wrong option name spades.modulesPath → spades.modulePath (three places); broken sentence about the simList’s environment; stale raster::Extent reference in the module-metadata table → terra::SpatExtent (with Extent kept for back-compat); stale sim$myFunction() call style — modules now use namespaced calls; wrong event name "save" in a plot scheduleEvent() example → "plot"; stale getOption("spades.cachePath") → reproducible.cachePath; stale SpaDES::setPaths() → SpaDES.core::setPaths(); Ubuntu 18.04 in v-automated-testing → 24.04. Modernized SpatialPoints* / Raster* mentions to SpatVector / sf / SpatRaster (older sp/raster classes still work). The Advanced vignette is rewritten and gains a section documenting the static code checker.Plots: refactor for stability, robustness, and expanded coverage.
<dataObjName>_time<simTime>.<ext> (e.g. myStack_time1.tif) rather than a tempfile()-based suffix, so repeated runs at the same sim time produce the same filename — making outputs deterministic and easier to diff/version.png, pdf, tiff, …) fails inside fn(data, ...), the device is still closed, a warning is emitted, and the offending file is recorded in a local failedFiles set so it is skipped when appending to sim@outputs. Previously, failures could leave an outputs row pointing at a missing file.useCache argument: TRUE (or a character vector of types) enables reproducible::Cache()-style memoization of the file-producing branch; the cached needNewPlot flag controls whether the plot is regenerated. Only relevant for non-screen types.data may now be a ggplot object directly (in addition to a quote()d expression or a raw value); detection moved to a single is(data, "gg") check, so passing Plots(data = myGgplot, ...) works.filenamesForSave / funsUsed (keyed by type), and a single isBaseFormat flag selects the base-R vs ggplot2::ggsave path — replacing two parallel, partly-overlapping code paths.tests/testthat/test-Plots.R) grow from 5 to 8 test_that blocks (PASS 37 → 51): base-R plotting function (hist) saving png + raw qs2, terra::SpatRaster saving tif raw, terra::SpatVector saving qs2 raw, named ... args without data =, and ggplot passed directly as data.restartSpades now has default numEvents = 1L instead of Inf
options(spades.dotInputObjects = FALSE), then it will not do .inputObjects even if options(spades.allowInitDuringSimInit = TRUE); previously, this was not respected.reproducible dependency version to 3.0.0;spades.recoveryMode (previously zero — the only exercise was gated behind if (interactive()) in test-mod.R and never ran in CI). Three new test_that() blocks cover the default 1-event recovery, the 2-event case (spades.recoveryMode = 2L, asserting length(.recoverableObjs) == 2L, most-recent-first ordering, and full rewind+replay via restartSpades(numEvents = 2L)), and the off case (spades.recoveryMode = FALSE leaves .recoverableObjs NULL while the sim is still stashed by saveSimOnExit).restartSpades(): drop unreachable “Cannot replay N events as requested” message — numMods is pre-clipped via min(length(.recoverableObjs), numEvents), so the gating condition could never be true. Silent clipping is the documented contract when numEvents exceeds available state.if (interactive()) guards that produced silent coverage gaps or “empty test” skips, and widen the known igraph cluster_optimal() community-count fragility skip to Linux (previously Windows-only).simList’s mod object: The mod object was previously placed in sim@.xData[[moduleName]]$.objects; even though it had parent.env that was emptyenv(), because it was attached to the environment sim@.xData[[moduleName]], this meant that the objects in mod would become part of the environment where the functions were defined. This created a memory leak, resulting in inflated caches when events for that module were cached. It is now in sim@.xData$.modObjs, which appears to no longer suffer from the memory leak. This change in location required many changes throughout all exported reproducible functions that had simList methods, e.g., .robustDigest, etc.simList objects, i.e., when simInit is called within a module;spades() debug logging;debug as verbose when caching (#322);.robustDigest.simList, Plots, allowInitDuringSimInit, .prepareOutput, defineParameter;moduleVersion when there are many pathssimList during event caching; missing ability to pass explicit classOptions for paramsreproducible::Cache and its many exported methods;cacheChaining: a new experimental feature that will reduce time spent on digesting objects when there is an unbroken sequence of cached events. Event level caching will assess whether the most recent event was Cached. If it was, then the current cache will skip digesting and use only the functions (and parameters) and the previous event’s cacheId to assess whether the sim can recover the current event from the cache repository. Turned on via options(spades.cacheChaining = TRUE)
reproducible package, specifically the Cache function;clearCacheEventsOnly is a convenience wrapper that will remove all event-level cached objects in the cache repository;dotObjs and dotMod which create a canonical pointer in the simList to these two parts of module-specific objects or functions, respectively;.inputObjects;Plots can now have a quote(data) argument, allowing the whole call to be Cached more easily;doCallSafe that can be used for doCallSafe(simInitAndSpades, out), and it does not suffer from the slow downs of do.call;.depsEdgeList gains a new argument, outputObjects, which will return “hanging” outputs as _OUTPUTS_, analogous to the hanging inputs as _INPUTS_. This is needed to address a new case of suppliedElsewhere where the object is contained within an objectSynonym, and has not yet been made, but is only listed as an outputObject in a module;evalPostEvent and options(spades.evalPostEvent), where a user can pass quoted code that will be evaluated at the end of each event and .inputObject call;outputs would create false positives (i.e., a change, when there wasn’t one); this meant that caching would only be successful after the 2nd time running the event, if another module had put objects in the outputs list, especially by using Plots.Plots() where plots were discarded if no filename was specified;spades.reqdPkgsDontLoad, a character vector. If anything is specified, then it will not be loaded with require or library, but it will be installed, if needed, and if spades.useRequire = TRUE, which is the default. Default for this new option is “box”, which is one of potentially many in the R universe that throws an error if it is loaded.globals(sim) in Sample modulesrestartSpades();newModule, new events argument bugs that caused unwanted objects to be put in the module. Fixed..wrap.simList did not anticipate objects with pointers in the metadata, so recovery from Cache failed if there was, e.g., a SpatExtent object in the metadata. Fixed.simList objects, when loading e.g., lists of lists;options("spades.allowSequentialCaching" = TRUE). When a series of events of events in sequence are cached, setting this option will treat them as a single Cache, so it may be much faster. Experimental and should be used with caution.colnames in completed<- and all.equal.simList (#272);simList objects when multiple paths were used (e.g., length(modulePath) > 1);newModule();saveSimList(..., inputs = FALSE, outputs = FALSE, cache = FALSE, files = FALSE));savedSimEnv()$.sim – savedSimEnv() is now exported for easier discovery – an internal package environment is used, unless the user specifies options(reproducible.memoisePersist = TRUE), which will use the global environment to store the .sim object;crayon (superseded) to cli for message colours;reproducible, loadSimList() is incompatible with simList objects saved with earlier versions of SpaDES.core.figurePath() to get the directory of a module’s output figures, which is now uses a separate subdirectory per module (i.e., file.path(outputPath(sim), "figures", <moduleName>)); Plots() defaults to using this path, and module developers are encouraged to update their module code to use figurePath(sim) where Plots() is not being used.simList no longer triggers on changes to .useCache parameter, when it doesn’t pertain to the event or module in question.bind_rows from dplyr within expectsInput or createsOutput. Now, if a module uses bind_rows and doesn’t have dplyr installed, SpaDES.core will intercept and use SpaDES.core::bindrows.saveSimList() better handles relative paths and symbolic links (#263)saveSimList() does an improved job at handling file-backed objects (previously, tests were passing because object was still there; now object is deleted, simList reloaded, and file-backed objects put back into place)reproducible changes to .wrap
reproducible changes to Cache messaging, specifically, remove cases where function was a userTag for an outer function call. Now these will display as otherFunction, so that individual functions can be more easily isolated.simInit and spades that allows for nested calls to simInit and/or spades
simInit is now reportedelapsedTime now displays the largest time unit, which may not be secs
In modCall... is removed.options that are either RequireOptions(), spadesOptions() or reproducibleOptions() can now be set during the simInit by passing them as arguments, e.g., simInit(useMemoise = FALSE). See ?simInit, specifically the ... parameter description. This is not passed as an argument named options: these are just options. For convenience, user can omit the package prefix, e.g., useMemoise for reproducible.useMemoise
reproducible updates to exported methodsdmin to go with the other d* SpaDES times.coltab<- from terra changed how it deals with multi-layer SpatRasters. Two sample modules have been modified to set colours on these multi-layer SpatRasters
asc raster-type files using inputs did not work; fixed.simInit parameter checkingCacheing of events and modules. Now, for example, a change to the parameter .useCache = c("init") to .useCache = c("init", ".inputObjects") will not trigger a rerun of the init event. Also, .inputObjects is no longer evaluated for Cacheing of doEvent
Error in if (is.na(sim@params[[m]][[x]])) fixed.asc spatial map files were incorrectly loaded by terra package: fixed.getSampleModules() and getMapPath() ) now used throughout examples, vignettes, and tests to avoid writing files in package installation directories.options(spades.futureEvents = TRUE) has been reworked and now works under a wider array of conditions.Copy, .wrap, wrap and unwrap all have fairly robust methods for simList class. The generics are in reproducible or terra
sampleModules to use Plots and .plot parameter.registerOutputs can be used by a developer to add saved files to the outputs(sim) data.frame.simInit or spades calls will now not duplicate time prefixparams and .globals were previously not expected to change during Cached events. Thus returned cached values were always the same as input as params and .globals. They are now assessed and returned as part of the Cache, as expected.Require and reproducible, including renaming cacheRepo to cachePath in some inherited functions.SpaDES.tools::neutralLandscapeMap instead of NLMR package directlyterra and sf instead of raster, sp, rgeos, and rgdal as defaults. Attempts have been made to maintain backwards compatibility in all cases.moduleMetadata now handles multiple module pathsmemoryUse
options("spades.allowInitDuringSimInit" = TRUE), a user will have init events of one ore more modules run during the simInit call, but only if they have no upstream dependencies, i.e., their expectsInputs cannot be supplied by another module’s createsOutputs. simInit will determine which modules have no upstream dependencies and only these will be selected for running only their init events. This can be useful e.g., if there is a module that createsOutputs for a studyArea..plots arg in spades can be set to NA to turn of all plotting. This can also be set with option(spades.plots = NA),moduleMetadata no longer runs .inputObjects. In addition to being unnecessary and slow, it was also failing with reproducible (==1.2.16) because it was trying to run Cache, which had a bug for this case. Now, moduleMetadata no longer runs the .inputObjects internally, so this bug is no longer relevant.spades.loadReqdPkgs, so a user can turn off loading of packages, and spades.dotInputObjects, so a user can omit running of the .inputObjects function in modules during simInit. These are updated in spadesOptions.runScheduleEventsOnly will extract only the scheduleEvents call; needed for options(spades.futureEvents = TRUE)
spades.saveFileExtensions which allows users to use the outputs(sim) mechanism for saving, for file extensions that are not already supported by .saveFileExtensions()
reproducible v2.0.5 or higher;quickPlot v1.0.2 or higher;googledrive from Suggests.Plots when not specifying fn, but usePlot = FALSE
\dontrun or \donttest were stale; these have been updatedsaveFiles bugfix: multiple objects names can now be passed to .saveOutputs module parameters.remoteFileSize(), updateList(). These will be removed by mid-2023."\b" in the message, and it will occur on same line as previous messagePlots now appends the filename any file saved during Plots to the outputs slot of the sim, i.e., it will show up in outputs(sim)
logPath is now a function that points to a sub-folder of file.path(outputPath(sim), "log")
defineEvent is a new function that allows a different way of specifying events than the doEvent function. This is not yet being used in the module templates, so does not appear with newModule.spades can now run correctly, with “incomplete” modules that don’t have metadata or even a module file. Now, a “module” will work with simInit and spades if a doEvent.XXX exists somewhere e.g., in the .GlobalEnv. spades will find it through inheritance and no longer complain if specific structures are absent. This may make it easier to learn how to use SpaDES as it mimics a more normal user experience where functions are all in the .GlobalEnv.spades.DTthreads to limit the number of threads used by data.table (default 1). Users can override this default if needed; modules can setDTthreads() as needed, but should restore the original value on.exit.saveSimList() and loadSimList() accept .qs or .rds filesspades and simInit now force UTF-8 encoding; this is reset on.exit. If a module needs a different character encoding, then it can be set within the module code..studyAreaName parameter added to default module metadata when using newModule.spades.scratchPath, to be used for e.g., temporary raster files and temporary SpaDES recovery mode objects.rasterTmpDir has changed to be a subdirectory of scratchPath. rasterPath will be deprecated in a future release.
terraTmpDir set as a subdirectory of scratchPath.stop.README.md instead of README.txt in new modules.RandomFields dependency, as that package is no longer maintained;NLMR to Suggests to provide random landscape generation capabilities previously provided by RandomFields.memoryUse was not correctly handling timezones; if the system call to get time stamps was in a different timezone compared to the internal SpaDES event queue, then the memory stamps were not correctly associated with the correct events.data.table objects using loadSimList()
.inputObjects to correctly capture objects that were assigned to mod$xxx.simList objects where changes to functions appeared to be undetected, and so a Cache call would return a stale module with function code from the Cached simList, which was incorrect.options(spades.scratchPath) (see above).objSize could have infinite recursion problem if there are simList objects inside simList objects. Fixed with new reproducible::objSize, which uses lobstr::obj_size.Plots
saveFiles related to data.table assignment and use in outputs(sim)
paramCheckOtherMods to deal with call parametersSpaDES modules can now be R packages. The simplest way to convert a module to a package is using the new function convertToPackage. Benefits of doing this are so that a SpaDES module can benefit from the infrastructure of an R package (e.g., devtools::document, devtools::check, setting up Continuous Integration systems etc.). Any documentation written using #' i.e., roxygen2 will be copied immediately above the function where it was sitting.newModule now correctly places the SpaDES.core package dependency in the reqdPkgs element of the metadata, instead of # SpaDES.core. It will put the full GitHub reference if SpaDES.core was installed directly from GitHub.qs package: either qsave or qread converts data.table objects to list objects. loadSimList has a work around internally to convert these objects back to data.table, if the metadata indicate that the objects should be data.table objects.paramCheckOtherMods. Can be used within a module to assert that a parameter has the same value as the same parameter in other modules. This is therefore a check of a parameter that might be considered a .global and passed within simInit(..., params = list(.globals = list(someParam = "someValue"))), but the user did not do that.spades messaging when e.g., debug = 1 can correctly accommodate nested spades calls, i.e., a SpaDES module calling spades internally.newModule now puts SpaDES.core dependency in the correct reqdPkgs instead of # SpaDES.core metadata element.plots instead of .plotInitialTime, Plots will check whether .plotInitialTime is actually set in the module metadata first. Only if it is there, will it evaluate its value. Currently, modules get default values for .plotInitialTime even if the module developer did not include it in the module metadata.debug arg of spades is set to an event type that is also in the core modules (e.g., save, load), such as “init”Cache-ing of a simList, when quick is a character vector, errored. Now fixed.moduleMetadata incorrectly dropped defineModuleListItems under certain signatures.moduleCoverage has been rewritten to estimate code coverage of a module using covr package.P now has a replacement method. So, to update a parameter within a module (where it is namespaced, i.e., don’t have to specify the module name): P(sim, "paramName") <- 1. If using this outside a module, then module (3rd argument) will have to be specified.P argument order changed to accommodate the fact that namespacing is used to detect module name: the user does not need to supply module, so it should not be second. This is for the normal P method and the new replace method above: it is now P(sim, param, module); there are attempts to capture errors (i.e., parameter supplied that matches a module, but not a parameter; vice versa) and give a warning for user to change code. This may have little downstream effect as all known cases use the P(sim)$paramName, which will still work fine, instead of P(sim, "paramName").Plots does a better job with RasterStack objects plotted to screen without ggplot2
.isFALSE: use base::isFALSE nowPlots can now omit the data argument; just use the named arguments in …defineParameter now allows multi-line desc or multiple strings; paste is no longer needed for long desc
moduleCodeFiles a new function that identifies all the code files in a collection of modules.globals functionality is modified. If a user specifies a .globals in the parameters object (passed into simInit), then all identical parameters in all modules will be overridden with these .global valuesdefineParameter, expectsInput and createsOuptut can all now have multi-line desc, without needing to use paste or paste0. Extraneous spaces and carriage returns will all be stripped. This can either be using a single multi-line quote or via multiple lines, each with its own "".simList is no longer “locked” with lockBinding. It is already hidden in sim$.mods, and since sim$.mods can be modified, this was a weak caution against user modification. Further, for moduleCoverage, the module environment needed to be unlocked, which is not allowed by CRAN..inputObjects was cached (via setting useCache = '.inputObjects' parameter), it was “too sensitive”. Changes to any module’s parameters, not just the current module, would cause rerun of .inputObjects. Now it correctly identifies parameter changes only in the current module. THIS WILL CAUSE some existing caches to trigger a rerun once; after this, it will be less sensitiverestartSpades did not correctly deal with objects that did not yet exist prior to the event. Fixed with: 24b9cd12973aa81a9a4923a02225e095fa28f77a.restartSpades was losing the previous completed events list. This has been fixed; it is now kept after restartSpades
data only (e.g. quickPlot::Plot-like behaviour)simInitAndSpades now has .plots arg to match spades
Plots function that will produce zero to 4 types of items that are relevant for plotting: 1) Visual on screen, 2) The plot object saved to disk, 3) The raw data that went into the plot and 4) The plot as one or more image files, e.g., .png or .pdf via ggsave
spades now accepts an events argument, which will limit the events that are run to those specified in the argument. This seems to be most useful for the init case, e.g., spades(sim, events = "init"). See ?spades.simInit now is prefixed with Sys.time() and "simInit”spades is simplified to take up fewer characters: INFO:: has been removedsimInit now checks for minimum # SpaDES.core of SpaDES.core needed in a module and stops if it fails, giving instructions how to upgrade.spatialExtent, as they are not used by the spades algorithmsanyPlotting to test whether plotting of one form or another should occurspades call is now more informative, including module name (by default shortened – can be changed with options("spades.messagingNumCharsModule")))defineParameter can now accept a vector of “class”, so a parameter can be more than one class. Presumably this should generally not be used, but a good reason could be, say, c("numeric", "function"), where the use can pass either a numeric or a function that would calculate that numeric.simFile to generate file names for use with e.g., saveSimList
zipSimList is now exportedspades will now attempt to load reqdPkgs, which is already done in simInit. In cases where simInit was not run, e.g., Cache(simInitAndSpades, ..., events = "init"), then modules will not have access to packages. For cases where simInit was called, then this should add very little overhead.saveSimList will now convert file-backed Raster* class objects to memory if fileBackend = 0. Previously, it left them as is (on disk if on disk, in memory if in memory).time(sim) in the case where it is equal to or after end(sim). Previously, this would not run any events if time(sim) >= end(sim) && events(sim)[[1]] < time(sim)..seed parameter for modules (#163)defineParameter was throwing is.na(default) warning when a parameter was not an atomic.spades.useRequire = FALSE (#141)sim; user informed with a warning
try() with communities() to skip tests on systems without igraph GLPK support.RandomFields being unavailable.spades.futureEvents option. If set to TRUE, spades will run module events in a “future” (see future package), if they do not produce outputs for other modules.use_gha() and corresponding vignette; #74)newProject creates Rstudio .Rproj file if invoked in RstudiopaddedFloatToChar to reproducible; but re-exported here, so still usable..seed which is a named list where names are the events and the elements are the seed with which to run the event. During doEvent, SpaDES.core will now set.seed(P(sim)$.seed[[currentEvent]]) and reset to random number stream afterwards.desc argument in defineParameter, expectsInput, and createsOutput can now have extraneous spaces and End-of-Line characters. This means that they can now be written more easily with a single set of quotes, without needing paste. The accessor functions, moduleParams, moduleInputs, and moduleOutputs all will strip extraneous spaces and End-of-Line characters.writeEventInfo() and writeRNGInfo() to write info to file.Par is now an activeBinding (similar to mod) pointing to P(sim); this allows for tab autocomplete to function correctly.moduleParams(), moduleInputs(), moduleOutputs(). These are now used in default .Rmd template.memoryUse functionalitysim is now created at .pkgEnv$.sim at the start of spades call, rather than on.exit; failures due to “out of memory” were not completing the on.exit
newModule() sets useGitHub = TRUE by default).options('spades.recoveryMode' = 0) may further helpreproducible
simInit, e.g., simInit(times = list(start = "test")) now fails because times must be a list of 2 numeric objectsmessage instead of a mixture of message, cat and print. This allows for easier suppressing of messaging, e.g., via suppressMessages. This was requested in a downstream package, SpaDES.experiment that was submitted to CRAN but rejected due to the now former inability to suppress messages.restartR saves simulation objects using qs::qsave() which is faster and creates smaller file sizes.codetools, future, httr, logging, and tcltk
archivist
qs now used for improved object serialization to diskobjectSynonyms caused a breakage under some conditions related to recovering a module from Cache.print and cat statements to message to allow use of suppressMessages, as recommended by CRANlogging package, invoked by setting debug argument in spades function call to a list(...). ?spades describes detailsDEoptim, future.apply, Matrix, parallel, pryr, purrr, and rgenoud, which are no longer required. See “deprecated” info below.whisker to Imports to facilitate module file templating (#100)future is installed. See new vignette iv-advanced and ?memoryUse.restartR. Restarts R mid-stream to deal with apparent memory leaks in R. In our experience with large projects that have long time horizons, there appears to be a memory leak at a low level in R (identified here: https://github.com/r-lib/fastmap). This has prevented projects from running to completion. Without diagnosing the root cause of the memory inflation, we have noticed that interrupting a simulation, saving the simList, restarting R, resets the memory consumption back to levels near the start of a simulation. The new functionality allows a user who is hitting this memory leak issue to restart R as a work around. See ?restartR for instructions.newProject to initialize a SpaDES project with subdirectories cache/, inputs/, modules/, and outputs/, and setPaths() accordingly.newModule() now uses open = interactive() as default to prevent files being left open during tests.experiment(), experiment2(), and POM() have been moved to the SpaDES.experiment packageSpaDES.core. Too many dependency packages are not maintaining their backwards compatibility.backports to Imports for R-oldrel supportgoogledrive dependency (this functionality moved to reproducible)objSize.simList method with 2 new arguments from reproducible package.robustDigest method for simList class objects now does only includes parameters that are listed within the module metadata, if Cache or .robustDigest is called within a module. This means that changes to parameter values in “other” modules will not affect the Caching of “the current” module.outputObjectNames will extract just the object names of all outputObjects across modulesrestartSpades and its associated options(spades.recoveryMode = 1), the new default, which is still experimental. Its purpose is to be able to restart a simulation in the case of an error or interruption.mod is now an active binding to sim[[currentModule(sim)]]$.objects (move from sim[[currentModule(sim)]]) and its parent environment is emptyenv(). This should cause no changes to users who use mod$..., but it will cause a change if user was calling objects directly via sim[[currentModule(sim)]]$.... This change is to separate the function enclosing environments and object enclosing environments, which should be different.sim@completed is now an environment instead of a list. Of the three event queues, this one can become the largest. The list would get increasingly slow as the number of completed events increased. There should be no user visible changes when using completed(sim)
igraph
RandomFields >= 3.3.4new vignette on caching SpaDES simulations moved from SpaDES package.
simList environment now has emptyenv() as its parent.env. The biggest user-facing changes are:
envir(sim) (unusual, but may occur) won’t find objects in the .GlobalEnv;parent.env in which they are defined (little know fact identified here: http://adv-r.had.co.nz/memory.html#gc identified as a possible source of memory leaks).module’s function environment in the simList now has its parent asNamespace("SpaDES.core") instead of the envir(sim) (as mentioned above), i.e,. parent.env(sim[[currentModule(sim)]]) is asNamespace("SpaDES.core"). The main user-noticeable changes of this are that module functions will not accidentally find objects in the simList unless they are actually passed in explicitly as arguments.
New active binding, mod that works as a module-specific variable, similar to a private object, i.e., mod$a is a local object inside the module that persists across events. It is a pointer to sim[[currentModule(sim)]]$a
New function scheduleConditionalEvent, which allows an event to be scheduled based on a condition. Still experimental.
An experimental new function and feature, objectSynonyms, which will create active bindings of two names to a single object
User can now specify modulePath as a character vector, e.g., simInit(..., paths = list(modulePath = c(".", "test"))). This means that a user can organize the modules in different locations.
modulePath now has a new argument, module, where user can specify (a) specific module(s)’s path. Modifications were implemented to dataPath to utilize this new feature
simInit and spades now call setPaths(paths) or setPaths(sim$paths), unsetting them on.exit internally to make the paths used for functions e.g., reproducible::Cache to use the correct path
under-the-hood speed improvements for the DES (about 20% faster) – 38 microseconds per event under ideal conditions
improved default path settings in .inputObjects (#83)
following reproducible package updates, now uses data.table::setattr internally to avoid copying of objects (this may have very little/no effect on simList objects)
suppliedElsewhere has a new argument, returnWhere, a logical which will cause a logical of length 3 to be returned, indicating in which of the 3 other places the object may have been supplied, instead of length 1, still the default.
data.table v1.12.0 (#85, @mattdowle)Copy (error existed because function inheritance persisted even though the location of the function was moved)RandomFields to Suggests, as it is in the Suggests of SpaDES.tools and used in examples/tests.options("spades.saveSimOnExit" = TRUE). This will save the state of the simList to an object as SpaDES.core:::.pkgEnv$.sim, with a message, if there is a hard exist. There is virtually no computational cost to this, as the object is already in RAM.simList internals changed. It now inherits from environment. Amongst other things, this means that tab autocomplete in RStudio now works for objects in the simList. Also, we removed several associated methods, $, [[, ls, ls.str, objects, as the defaults for environments work correctly with the simList nowdebug arg in spades call can now take numeric, currently 1 or 2, giving a few pre-packaged informative messaging each eventelapsedTime which gives a summary of the clock time used by each module or eventinputObjects(sim) returns the inputObjects data.frame.citation replaces utils::citation with an S4 generic. If package arg is a character, it dispatches utils::citation; if a simList, it gives the citation for the module(s)downloadModule() now prints the module # SpaDES.core downloaded (#77).inputObjects() name conflict (internal .inputObjects renamed to ._inputObjectsDF; .outputObjects renamed to ._outputObjectsDF).inputObjects evaluated based on module load order (#72).robustDigest fix for simList objects – needed to omit ._startClockTime and .timestamp
spades.useRequire: a logical which causes simInit to load packages with Require or require. Lower case is generally faster, but will not handle the case of uninstalled packages, so should only be used once all packages are installed.spades.keepCompleted: a logical which causes spades() to keep (TRUE) or not keep a record of completed events. Keeping track of completed events when they are many (>1e5) gets slow enough that it may be worth turning it off.tests
all.equal.simList now removes all time dependent attributes, e.g., ._startClockTime and .timestamp
options("spades.keepCompleted" = FALSE)
Improvements to caching of functions with simList objects:
simList in the arguments would erroneously return cached copies of functions. These now are copied through from argument simList, rather than cached simList. This means that changes to the function definitions in a module will persist (e.g., debugging via browser() will work correctly)simList in arguments that return a simList will now do a post digest of the output. This will be compared with the predigest, and only those object which changed in the simList will be modified..inputObjects function was incorrect. Fixed.module metadata now in named lists inside depends(sim)
new debugging – if debug is not FALSE, then any error will trigger a browser() call inside the event function. User can continue (c) or quit (Q) as per normal. c will trigger a reparse and events will continue as scheduled.
introduction of code checking for modules, currently turned on or off by an option spades.moduleCodeChecks, which is TRUE by default. Code checking includes various types:
codetools to check for various code problemsraster::level, raster::scale, quickPlot::Plot)checkCodeEnv on every function inside a modulesim$xxx occurrences in modules, comparing to outputObjects in metadata if used in assignment (i.e., left hand side of assign operator), or comparing to inputObjects if used on the right hand sideinputObjects have default values assigned in the .inputObjects functionoption spades.debug set to TRUE by default, instead of FALSE. This is better for new users.
moduleMetadata argument order changed, so sim is first, more consistent with all other simList accessors.
downloadData has changed dramatically, now it is a wrapper around reproducible::prepInputs which does more checking.
extractURL will extract the sourceURL from metadata, given an object name.
makeMemoiseable and unmakeMemoisable, new methods, each the inverse of the other, to deal with imperfect memoised returns under some cases of simList.
new option, spades.keepCompleted, TRUE by default, which can be useful for dramatically speeding up the DES when there are many (>10,000) events.
fileExt – use tools::file_ext insteaddata.table changes (@mattdowle, #64).start and end.newModule template modified slightly based on workshop feedback.setPaths now only sets the directories that are passed into it.all.equal.simList method strips a small number of attributes that are used internally that create false failures.uses reproducible::Require instead of SpaDES.core::loadPackages to load required packages. Currently, does not use SpaDES.core control for packages, but does use installing (from CRAN or GitHub), and loading (via require). This means a module can indicate a GitHub package, e.g,. achubaty/amc@development
environments in modules are now as follows:
sim@.envir$<moduleName>, and it is a is a child of sim@.envir. Functions can be found in this environment, but prefixing functions is not necessary, because modules functions are within this environment already.sim@.envir is a child of SpaDES.core
scoping from within a function that is defined in a module is thus:
sim@.envir$<moduleName> –> sim@.envir –> SpaDES.core –> all imported packages including base –> .GlobalEnv –> search()
speed improvements:
data.table objects. For small objects (e.g., the event queue) that have fewer than 200 objects, lists are faster. Accessors (e.g., events(sim), completed(sim)) of the event queues still show data.table objects, but these are made on the fly..parseModule and .parseModuePartial now put their parsed content into a temporary environment (sim@.envir$.parsedFiles$<Full Filename>) during the simInit, which gets re-used. Previously, files were parsed multiple times in a given simInit call. Several functions now have envir argument to pass this through (including module# SpaDES.core, packages, checkParams)parsing of modules is now more intelligent, allowing for modules to contain functions (the current norm) and but they can also create objects at the module level. These can use the sim object in their definition. These objects can, for example, be used to help define parameters, for example, e.g., startSimPlus1 <- start(sim) + 1 can be defined in the module and used in defineModule
remove grDevices from Imports as it was not used (#1)
remove chron and CircStats dependencies
remove functions dwrpnorm2 and move to package SpaDES.tools
remove unused function F() due to conflicts with F/FALSE.
improved download of module data: added new quickCheck argument
improved download of modules: use fuzzy matching
new option: spades.switchPkgNamespaces which allows the user to turn off the SpaDES feature that loads and unloads libraries specific to each module. While useful, it slows down computations, in some cases, by a lot.
bug fixes:
zipModule that omitted the checksum file from being included when data = FALSE (#3).inputObjects functions was evaluating outputObjects instead of inputObjects. Now corrected.If .inputObjects contains arguments other than just sim, these will be evaluated as function inputs by the Cache mechanism (via .useCache), therefore correctly assessing when those inputs changed, e.g., if they are files and the arg is wrapped in asPath, then any change to the underlying file will cause a re-cache. e.g., .inputObjects <- function(sim, importantFile = asPath(file.path(inputPath(sim), "theFile.rdata"))) { ... }
default debug option in spades() now uses the package option spades.debug and default is set to FALSE (#5)
various other speed improvements and bug fixes
convert P to a function, rather than S4 generic and method, for speed.
@importFrom only used functions from utils due to name conflicts with raster::stack and utils::stack
new function remoteFileSize to check the size of remote files
new namespaced function dataPath will return file.path(modulePath(sim), currentModule(sim), "data"), which will return a different path, depending on which module it is placed inside.
add crayon to Imports – now messages are more colour-coded;
bug fix in ‘inputs’ for the case of loading objects from the global environment, either from the same object to the same object, or from different global objects overwriting on the same simList object;
A new package, which takes all core DES functionality out of the SpaDES package:
?SpaDES.core for an overviewvarious speed improvements and bug fixes