Known issues: https://github.com/PredictiveEcology/SpaDES.core/issues
"\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modules.RandomFields dependency, as that package is no
longer maintained;NLMR to Suggests to provide random landscape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 simLists inside simLists. Fixed with new
reproducible::objSize, which uses
lobstr::obj_size.PlotssaveFiles related to data.table
assignment and use in outputs(sim)SpaDES
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 version. 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 version
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
descmoduleCodeFiles 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
restartSpadesdata only (e.g. quickPlot::Plot-like
behaviour)simInitAndSpades now has .plots arg to
match spadesPlots function can be used like Plot, but
with types specified. The devices to save on disk will have
some different behaviours to the screen representation, since “wiping”
an individual plot on a device doesn’t exist for a file device.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 ggsavespades 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 version 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., saveSimListzipSimList 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
warningtry() 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)$.seed[[currentEvent]]) and reset to random
number stream afterwards.dplyr, lubridate,
R.utils, tools, backports and
rlang from dependenciestcltk to Suggestsdevtools, microbenchmark from
Suggestsall.equal(..., check.environment = FALSE) for
internal testingRCurl dependency (#120)sp because it’s linked in documentation
(#120)pkgDeps example for new version of
Requiredesc argument in defineParameter,
expectsInput, and createsOutput can now have
extraneous spaces and End-of-Line characters. This means that they can
now be written more easily with a single set of quotes, without needing
paste. The accessor functions, moduleParams,
moduleInputs, and moduleOutputs all will strip
extraneous spaces and End-of-Line characters.writeEventInfo()
and writeRNGInfo() to write info to file.stringi.. for
moduleParams etc. This is more accurate.Par is now an activeBinding (similar to
mod) pointing to P(sim); this allows for tab
autocomplete to function correctly.moduleParams(),
moduleInputs(), moduleOutputs(). These are now
used in default .Rmd template.memoryUse functionalitysim is now created at
.pkgEnv$.sim at the start of spades call,
rather than on.exit; failures due to “out of memory” were
not completing the on.exitnewModule() sets
useGitHub = TRUE by default).usethis to Suggests for use with GitHub
ActionsFilenames function coming from
reproducible packageoptions('spades.recoverMode') was creating temp folders
every event and not removing them; now it does.options('spades.recoveryMode' = 0) may further helpreproduciblesimInit,
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
tcltkarchivistqs now used for improved object serialization to
disk.objSizeInclEnviros and removed
objectSynonyms 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
detailsrestartR minor bug fixesDEoptim,
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)P, params, and
parameters, thanks to Louis-Etienne Robert.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)]]$.... This
change is to separate the function enclosing environments and object
enclosing environments, which should be different.sim@completed is now an environment instead of a list.
Of the three event queues, this one can become the largest. The
list would get increasingly slow as the number of completed
events increased. There should be no user visible changes when using
completed(sim)spades.debug is now set to 1
spades.recoveryMode is new and set to 1 (i.e., the current
event will be kept at its initial state)
simInit especially in some weird
cases of childModules.reqdPkgs not being loaded when only
listed in child modules. Fixed in
5cd79ac95bc8d190e954313f125928458b0108d2.igraphRandomFields >= 3.3.4archivist and devtools added to Suggests
because they are used in vignettesreproducible version 0.2.6new vignette on caching SpaDES simulations moved
from SpaDES package.
simList environment now has emptyenv()
as its parent.env. The biggest user-facing changes are:
envir(sim) (unusual, but may
occur) won’t find objects in the .GlobalEnv;parent.env in which they are defined (little know
fact identified here: http://adv-r.had.co.nz/memory.html#gc identified
as a possible source of memory leaks).module’s function environment in the simList now has its parent
asNamespace("SpaDES.core") instead of the
envir(sim) (as mentioned above), i.e,.
parent.env(sim[[currentModule(sim)]]) is
asNamespace("SpaDES.core"). The main user-noticeable
changes of this are that module functions will not accidentally find
objects in the simList unless they are actually passed in
explicitly as arguments.
New active binding, mod that works as a
module-specific variable, similar to a private object, i.e.,
mod$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 eventcitation 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 version
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 simLists – needed to omit
._startClockTime and .timestampsp from importsreproducible (>=0.2.2)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.testsall.equal.simList now removes all time dependent
attributes, e.g., ._startClockTime and
.timestampoptions("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.tools, pryr.rgeos, RCurl and
googledrive.uses reproducible::Require instead of
SpaDES.core::loadPackages to load required packages.
Currently, does not use version 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$<moduleName>, and it is a is
a child of sim@.envir. Functions can be found in this
environment, but prefixing functions is not necessary, because modules
functions are within this environment already.sim@.envir is a child of SpaDES.corescoping from within a function that is defined in a module is thus:
sim@.envir$<moduleName> –>
sim@.envir –> SpaDES.core –> all
imported packages including base –>
.GlobalEnv –> search()speed improvements:
data.table objects. For small objects (e.g., the
eventQueue) 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
moduleVersion, 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