SpaDES
simulationsAs part of a reproducible work
flow, caching of various function calls are a critical component. Down
the road, it is likely that an entire work flow from raw data to
publication, decision support, report writing, presentation building
etc., could be built and be reproducible anywhere, on demand. The
reproducible::Cache
function is built to work with any R
function. However, it becomes very powerful in a SpaDES
context because we can build large, powerful applications that are
transparent and tied to the raw data that may be many
conceptual steps upstream in the workflow. To do this, we have built
several customizations within the SpaDES
package. Important
to this is dealing correctly with the simList
, which is an
object that has slot that is an environment. But more important are the
various tools that can be used at higher levels, i.e., not just
for “standard” functions.
SpaDES
Some of the details of the simList
-specific features of
this Cache
function include:
The function converts all elements that have an environment as
part of their attributes into a format that has no unique environment
attribute, using format
if a function, and
as.list
in the case of the simList
environment.
When used within SpaDES
modules, Cache
(capital C) does not require that the argument cachePath
be
specified. If called from inside a SpaDES module, Cache
will use the cachePath
argument from a call to
cachePath(sim)
, taking the sim
from the call
stack. Similarly, if no cachePath
argument is specified,
then it will use getOption("spades.cachePath")
, which will,
by default, be a temporary location with no persistence between R
sessions! To persist between sessions, use
SpaDES::setPaths()
every session.
In a SpaDES
context, there are several levels of caching
that can be used as part of a reproducible workflow. Each level can be
used to a modeller’s advantage; and, all can be – and are often – used
concurrently.
spades
levelAnd entire call to spades
can be cached. This will have
the effect of eliminating any stochasticity in the model as the output
will simply be the cached version of the simList
. This is
likely most useful in situations where reproducibility is more important
than “new” stochasticity (e.g., building decision support
systems, apps, final version of a manuscript).
library(terra)
library(reproducible)
library(SpaDES.core)
mySim <- simInit(
times = list(start = 0.0, end = 3.0),
params = list(
.globals = list(stackName = "landscape", burnStats = "testStats"),
randomLandscapes = list(.plotInitialTime = NA),
fireSpread = list(.plotInitialTime = NA)
),
modules = list("randomLandscapes", "fireSpread"),
paths = list(modulePath = getSampleModules(tempdir()))
)
This functionality can be achieved within a spades
call.
# compare caching ... run once to create cache
system.time({
outSim <- spades(Copy(mySim), cache = TRUE, notOlderThan = Sys.time())
})
## Nov12 06:30:11 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
## Nov12 06:30:11 chckpn:init total elpsd: 0.077 secs | 0 checkpoint init 0
## Nov12 06:30:11 save :init total elpsd: 0.079 secs | 0 save init 0
## Nov12 06:30:11 prgrss:init total elpsd: 0.081 secs | 0 progress init 0
## Nov12 06:30:11 load :init total elpsd: 0.083 secs | 0 load init 0
## Nov12 06:30:11 rndmLn:init total elpsd: 0.085 secs | 0 randomLandscapes init
## Nov12 06:30:11 rndmLn:init New objects created:
## Nov12 06:30:11 rndmLn:init <char>
## Nov12 06:30:11 rndmLn:init 1: landscape
## Nov12 06:30:11 frSprd:init total elpsd: 0.18 secs | 0 fireSpread init 1
## Nov12 06:30:11 frSprd:init fireSpread
## Nov12 06:30:11 frSprd:init New objects created:
## Nov12 06:30:11 frSprd:init <char>
## Nov12 06:30:11 frSprd:init 1: testStats
## Nov12 06:30:11 frSprd:burn total elpsd: 0.21 secs | 1 fireSpread burn 5
## Nov12 06:30:11 frSprd:stats total elpsd: 0.24 secs | 1 fireSpread stats 5
## Nov12 06:30:11 frSprd:stats fireSpread
## Nov12 06:30:11 frSprd:burn total elpsd: 0.25 secs | 2 fireSpread burn 5
## Nov12 06:30:11 frSprd:stats total elpsd: 0.27 secs | 2 fireSpread stats 5
## Nov12 06:30:11 frSprd:stats fireSpread
## Nov12 06:30:11 frSprd:burn total elpsd: 0.28 secs | 3 fireSpread burn 5
## Nov12 06:30:11 frSprd:stats total elpsd: 0.31 secs | 3 fireSpread stats 5
## Nov12 06:30:11 frSprd:stats fireSpread
## simList saved in
## SpaDES.core:::savedSimEnv()$.sim
## It will be deleted at next spades() call.
## Saving large object (fn: spades, cacheId: ea26492956f47fe9) to
## Cache: 10.3 Mb
## Done!
## Saved! Cache file: ea26492956f47fe9.rds; fn: spades
## user system elapsed
## 1.974 0.048 2.026
Note that if there were any visualizations (here we turned them off
with .plotInitialTime = NA
above) they will happen the
first time through, but not the cached times.
## Object to retrieve (fn: spades, ea26492956f47fe9.rds) ...
## Loaded! Cached result from previous spades call
## from module
## user system elapsed
## 0.851 0.000 0.853
## [1] "Names: 2 string mismatches"
## [2] "Length mismatch: comparison on first 3 components"
## [3] "Component 2: Modes: numeric, NULL"
## [4] "Component 2: Lengths: 4, 0"
## [5] "Component 2: target is numeric, current is NULL"
## [6] "Component 3: target is NULL, current is PackedSpatRaster"
If the parameter .useCache
in the module’s metadata is
set to TRUE
, then every event in the module will
be cached. That means that every time that module is called from within
a spades()
call, Cache
will be called. Only
the objects inside the simList
that correspond to the
inputObjects
or the outputObjects
from the
module metadata will be assessed for caching. For general use,
module-level caching would be mostly useful for modules that have no
stochasticity, such as data-preparation modules, GIS modules etc.
In this example, we will use the cache on the
randomLandscapes
module. This means that each subsequent
call to spades will result in identical outputs from the
randomLandscapes
module (only!). This would be useful when
only one random landscape is needed simply for trying something out, or
putting into production code (e.g., publication, decision
support, etc.).
# Module-level
params(mySim)$randomLandscapes$.useCache <- TRUE
system.time({
randomSim <- spades(Copy(mySim), .plotInitialTime = NA,
notOlderThan = Sys.time(), debug = TRUE)
})
## Nov12 06:30:15 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
## Nov12 06:30:15 chckpn:init eventTime moduleName eventType eventPriority
## Nov12 06:30:15 chckpn:init 0 checkpoint init 0
## Nov12 06:30:15 save :init 0 save init 0
## Nov12 06:30:15 prgrss:init 0 progress init 0
## Nov12 06:30:15 load :init 0 load init 0
## Nov12 06:30:15 rndmLn:init 0 randomLandscapes init 1
## Nov12 06:30:15 rndmLn:init Saving large object (fn: doEvent.randomLandscapes, cacheId:
## Nov12 06:30:15 rndmLn:init 7a1e1fac75a91549) to Cache: 10.2 Mb
## Done!
##
## Nov12 06:30:16 rndmLn:init Saved! Cache file: 7a1e1fac75a91549.rds; fn: doEvent.randomLandscapes
## Nov12 06:30:16 rndmLn:init New objects created:
## Nov12 06:30:16 rndmLn:init <char>
## Nov12 06:30:16 rndmLn:init 1: landscape
## Nov12 06:30:16 frSprd:init 0 fireSpread init 1
## Nov12 06:30:16 frSprd:init fireSpread
## Nov12 06:30:16 frSprd:init New objects created:
## Nov12 06:30:16 frSprd:init <char>
## Nov12 06:30:16 frSprd:init 1: testStats
## Nov12 06:30:16 frSprd:burn 1 fireSpread burn 5
## Nov12 06:30:16 frSprd:stats 1 fireSpread stats 5
## Nov12 06:30:16 frSprd:stats fireSpread
## Nov12 06:30:16 frSprd:burn 2 fireSpread burn 5
## Nov12 06:30:16 frSprd:stats 2 fireSpread stats 5
## Nov12 06:30:16 frSprd:stats fireSpread
## Nov12 06:30:16 frSprd:burn 3 fireSpread burn 5
## Nov12 06:30:16 frSprd:stats 3 fireSpread stats 5
## Nov12 06:30:16 frSprd:stats fireSpread
## simList saved in
## SpaDES.core:::savedSimEnv()$.sim
## It will be deleted at next spades() call.
## user system elapsed
## 1.431 0.008 1.441
# faster the second time
system.time({
randomSimCached <- spades(Copy(mySim), .plotInitialTime = NA, debug = TRUE)
})
## Nov12 06:30:16 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
## Nov12 06:30:17 chckpn:init eventTime moduleName eventType eventPriority
## Nov12 06:30:17 chckpn:init 0 checkpoint init 0
## Nov12 06:30:17 save :init 0 save init 0
## Nov12 06:30:17 prgrss:init 0 progress init 0
## Nov12 06:30:17 load :init 0 load init 0
## Nov12 06:30:17 rndmLn:init 0 randomLandscapes init 1
## Nov12 06:30:17 rndmLn:init Object to retrieve (fn: doEvent.randomLandscapes,
## Nov12 06:30:17 rndmLn:init 7a1e1fac75a91549.rds) ...
## Nov12 06:30:17 rndmLn:init Loaded! Cached result from previous doEvent.randomLandscapes call
## Nov12 06:30:17 rndmLn:init for init event in randomLandscapes module
## Nov12 06:30:17 rndmLn:init randomLandscapes
## Nov12 06:30:17 rndmLn:init New objects created:
## Nov12 06:30:17 rndmLn:init <char>
## Nov12 06:30:17 rndmLn:init 1: landscape
## Nov12 06:30:17 frSprd:init 0 fireSpread init 1
## Nov12 06:30:17 frSprd:init fireSpread
## Nov12 06:30:17 frSprd:init New objects created:
## Nov12 06:30:17 frSprd:init <char>
## Nov12 06:30:17 frSprd:init 1: testStats
## Nov12 06:30:17 frSprd:burn 1 fireSpread burn 5
## Nov12 06:30:17 frSprd:stats 1 fireSpread stats 5
## Nov12 06:30:17 frSprd:stats fireSpread
## Nov12 06:30:17 frSprd:burn 2 fireSpread burn 5
## Nov12 06:30:17 frSprd:stats 2 fireSpread stats 5
## Nov12 06:30:17 frSprd:stats fireSpread
## Nov12 06:30:17 frSprd:burn 3 fireSpread burn 5
## Nov12 06:30:17 frSprd:stats 3 fireSpread stats 5
## Nov12 06:30:17 frSprd:stats fireSpread
## simList saved in
## SpaDES.core:::savedSimEnv()$.sim
## It will be deleted at next spades() call.
## user system elapsed
## 0.676 0.004 0.682
Test that only layers produced in randomLandscapes
are
identical, not fireSpread
.
layers <- list("DEM", "forestAge", "habitatQuality", "percentPine", "Fires")
same <- lapply(layers, function(l) {
identical(randomSim$landscape[[l]], randomSimCached$landscape[[l]])
})
names(same) <- layers
print(same) # Fires is not same because all non-init events in fireSpread are not cached
## $DEM
## [1] TRUE
##
## $forestAge
## [1] TRUE
##
## $habitatQuality
## [1] TRUE
##
## $percentPine
## [1] TRUE
##
## $Fires
## [1] FALSE
If the parameter .useCache
in the module’s metadata is
set to a character or character vector, then that or those
event(s), identified by their name, will be cached. That means that
every time the event is called from within a spades
call,
Cache
will be called. Only the objects inside the
simList
that correspond to the inputObjects
or
the outputObjects
as defined in the module metadata will be
assessed for caching inputs or outputs, respectively. The fact that all
and only the named inputObjects
and
outputObjects
are cached and returned may be inefficient
(i.e., it may cache more objects than are necessary) for
individual events.
Similar to module-level caching, event-level caching would be mostly
useful for events that have no stochasticity, such as data-preparation
events, GIS events etc. Here, we don’t change the module-level caching
for randomLandscapes
, but we add to it a cache for only the
“init” event for fireSpread
.
params(mySim)$fireSpread$.useCache <- "init"
system.time({
randomSim <- spades(Copy(mySim), .plotInitialTime = NA,
notOlderThan = Sys.time(), debug = TRUE)
})
## Nov12 06:30:18 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
## Nov12 06:30:18 chckpn:init eventTime moduleName eventType eventPriority
## Nov12 06:30:18 chckpn:init 0 checkpoint init 0
## Nov12 06:30:18 save :init 0 save init 0
## Nov12 06:30:18 prgrss:init 0 progress init 0
## Nov12 06:30:18 load :init 0 load init 0
## Nov12 06:30:18 rndmLn:init 0 randomLandscapes init 1
## Nov12 06:30:18 rndmLn:init Saving large object (fn: doEvent.randomLandscapes, cacheId:
## Nov12 06:30:18 rndmLn:init 7a1e1fac75a91549) to Cache: 10.2 Mb
## Done!
##
## Nov12 06:30:19 rndmLn:init Saved! Cache file: 7a1e1fac75a91549.rds; fn: doEvent.randomLandscapes
## Nov12 06:30:19 rndmLn:init New objects created:
## Nov12 06:30:19 rndmLn:init <char>
## Nov12 06:30:19 rndmLn:init 1: landscape
## Nov12 06:30:19 frSprd:init 0 fireSpread init 1
## Nov12 06:30:20 frSprd:init Saving large object (fn: doEvent.fireSpread, cacheId:
## Nov12 06:30:20 frSprd:init 26e10df22356beb4) to Cache: 10.3 Mb
## Done!
##
## Nov12 06:30:20 frSprd:init Saved! Cache file: 26e10df22356beb4.rds; fn: doEvent.fireSpread
## Nov12 06:30:20 frSprd:init New objects created:
## Nov12 06:30:20 frSprd:init <char>
## Nov12 06:30:20 frSprd:init 1: testStats
## Nov12 06:30:21 frSprd:burn 1 fireSpread burn 5
## Nov12 06:30:21 frSprd:stats 1 fireSpread stats 5
## Nov12 06:30:21 frSprd:stats fireSpread
## Nov12 06:30:21 frSprd:burn 2 fireSpread burn 5
## Nov12 06:30:21 frSprd:stats 2 fireSpread stats 5
## Nov12 06:30:21 frSprd:stats fireSpread
## Nov12 06:30:21 frSprd:burn 3 fireSpread burn 5
## Nov12 06:30:21 frSprd:stats 3 fireSpread stats 5
## Nov12 06:30:21 frSprd:stats fireSpread
## simList saved in
## SpaDES.core:::savedSimEnv()$.sim
## It will be deleted at next spades() call.
## user system elapsed
## 2.905 0.040 2.950
# faster the second time
system.time({
randomSimCached <- spades(Copy(mySim), .plotInitialTime = NA, debug = TRUE)
})
## Nov12 06:30:21 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
## Nov12 06:30:21 chckpn:init eventTime moduleName eventType eventPriority
## Nov12 06:30:21 chckpn:init 0 checkpoint init 0
## Nov12 06:30:21 save :init 0 save init 0
## Nov12 06:30:21 prgrss:init 0 progress init 0
## Nov12 06:30:21 load :init 0 load init 0
## Nov12 06:30:21 rndmLn:init 0 randomLandscapes init 1
## Nov12 06:30:21 rndmLn:init Object to retrieve (fn: doEvent.randomLandscapes,
## Nov12 06:30:21 rndmLn:init 7a1e1fac75a91549.rds) ...
## Nov12 06:30:21 rndmLn:init Loaded! Cached result from previous doEvent.randomLandscapes call
## Nov12 06:30:21 rndmLn:init for init event in randomLandscapes module
## Nov12 06:30:21 rndmLn:init randomLandscapes
## Nov12 06:30:21 rndmLn:init New objects created:
## Nov12 06:30:21 rndmLn:init <char>
## Nov12 06:30:21 rndmLn:init 1: landscape
## Nov12 06:30:21 frSprd:init 0 fireSpread init 1
## Nov12 06:30:22 frSprd:init Object to retrieve (fn: doEvent.fireSpread, 26e10df22356beb4.rds) ...
## Nov12 06:30:22 frSprd:init Loaded! Cached result from previous doEvent.fireSpread call
## Nov12 06:30:22 frSprd:init for init event in fireSpread module
## Nov12 06:30:22 frSprd:init fireSpread
## Nov12 06:30:22 frSprd:burn 1 fireSpread burn 5
## Nov12 06:30:22 frSprd:stats 1 fireSpread stats 5
## Nov12 06:30:22 frSprd:stats fireSpread
## Nov12 06:30:22 frSprd:stats New objects created:
## Nov12 06:30:22 frSprd:stats <char>
## Nov12 06:30:22 frSprd:stats 1: testStats
## Nov12 06:30:22 frSprd:burn 2 fireSpread burn 5
## Nov12 06:30:22 frSprd:stats 2 fireSpread stats 5
## Nov12 06:30:22 frSprd:stats fireSpread
## Nov12 06:30:22 frSprd:burn 3 fireSpread burn 5
## Nov12 06:30:22 frSprd:stats 3 fireSpread stats 5
## Nov12 06:30:22 frSprd:stats fireSpread
## simList saved in
## SpaDES.core:::savedSimEnv()$.sim
## It will be deleted at next spades() call.
## user system elapsed
## 1.190 0.008 1.202
Any function can be cached using:
Cache(FUN = functionName, ...)
.
This will be a slight change to a function call, such as:
projectRaster(raster, crs = crs(newRaster))
to
Cache(projectRaster, raster, crs = crs(newRaster))
.
ras <- terra::rast(terra::ext(0, 1e3, 0, 1e3), res = 1, vals = 1)
system.time({
map <- Cache(SpaDES.tools::neutralLandscapeMap(ras),
cachePath = cachePath(mySim),
userTags = "neutralLandscapeMap",
notOlderThan = Sys.time())
})
## Warning: In (SpaDES.tools::neutralLandscapeMap(ras))(): nlm_mpd changes the
## dimensions of the RasterLayer if even ncols/nrows are choosen.
## Saving large object (fn: SpaDES.tools::neutralLandscapeMap, cacheId:
## 94d035af43fc613d) to Cache: 17.1 Mb
## Done!
## Saved! Cache file: 94d035af43fc613d.rds; fn:
## SpaDES.tools::neutralLandscapeMap
## user system elapsed
## 2.163 0.040 2.211
# faster the second time
system.time({
mapCached <- Cache(SpaDES.tools::neutralLandscapeMap(ras),
cachePath = cachePath(mySim),
userTags = "neutralLandscapeMap")
})
## Object to retrieve (fn: SpaDES.tools::neutralLandscapeMap,
## 94d035af43fc613d.rds) ...
## Loaded! Cached result from previous
## SpaDES.tools::neutralLandscapeMap call
## user system elapsed
## 0.537 0.004 0.543
## NOTE: can't use all.equal on SpatRaster (they are pointers); use compareGeom()
all.equal(map[], mapCached[])
## [1] TRUE
Since the cache is simply a DBI
database table, all
DBI
functions will work as is. In addition, there are
several helpers in the reproducible
package, including
showCache
, keepCache
and
clearCache
, and the more advanced createCache
,
loadFromCache
, rmFromCache
, and
saveToCache
that may be useful. Also, one can access cached
items manually (rather than simply rerunning the same Cache
function again).
## Cache size:
## Total (including Rasters): 4.3 Mb
## Selected objects (not including Rasters): 4.3 Mb
## get the RasterLayer that was produced with neutralLandscapeMap()
map <- loadFromCache(cacheId = cacheDB$cacheId, cachePath = cachePath(mySim))
## Loaded! Cached result from previous call
In general, we feel that a liberal use of Cache
will
make a reusable and reproducible work flow. shiny
apps can
be made, taking advantage of Cache
. Indeed, much of the
difficulty in managing data sets and saving them for future use, can be
accommodated by caching.
simInit() --> many .inputObjects calls
spades() call --> many module calls --> many event calls --> many function calls
Lets say we start to introduce caching to this structure. We start
from the “inner” most functions that we could imaging Caching would be
useful. Lets say there are some GIS operations, like
raster::projectRaster
, which operates on an input
shapefile. We can Cache the projectRaster
call to make this
much faster, since it will always be the same result for a given input
raster.
If we look back at our structure above, we see that we still have
LOTS of places that are not Cached. That means that the
spades()
call will still spawn many module calls, and many
event calls, just to get to the one Cache(projectRaster)
call which is cached. This function will likely be called many times.
This is good, but Cache
does take some
time. So, even if Cache(projectRaster)
takes only
0.02 seconds, calling it hundreds of times means maybe 4 seconds. If we
are doing this for many functions, then this will be too slow for some
purposes.
We can start putting Cache
all up the sequence of calls.
Unfortunately, the way we use Cache at each of these levels is a bit
different, so we need a slightly different approach for each.
spades
callspades(cache = TRUE)
This will cache the spades
call, causing
stochasticity/randomness to be frozen.
Pass .useCache = TRUE
as a parameter to the module,
during the simInit
Some modules are inherently non-random, such as GIS modules, or parameter fitting statistical modules. We expect these to be identical results each time, so we can safely cache the entire module.
parameters = list(
FireModule = list(.useCache = TRUE)
)
mySim <- simInit(..., params = parameters)
mySimOut <- spades(mySim)
The messaging should indicate the caching is happening on every event in that module.
Note: This option REQUIRES that the metadata in inputs
and outputs be exactly correct, i.e., all inputObjects
and
outputObjects
must be correctly identified and listed in
the defineModule
metadata
If the module is cached, and there are errors when it is
run, it almost is guaranteed to be a problem with the
inputObjects
and outputObjects
incorrectly
specified.
Cache(<functionName>, <other arguments>)
This will allow fine scale control of individual function calls.
Once nested Caching is used all the way up to the
experiment
(see SpaDES.experiment
package)
level and even further up (e.g., if there is a shiny
module), then even very complex models can be put into a complete
workflow.
The current vision for SpaDES
is that it will allow this
type of “data to decisions” complete workflow that allows for deep,
robust models, across disciplines, with easily accessible front ends,
that are quick and responsive to users, yet can handle data changes,
module changes, etc.