experiment
functionOnce a simulation is properly initialized and runs correctly with the
spades function, it is likely time to do things like run
replicates. There are two functions, experiment and
experiment2 to do this. These both give opportunities to
create simulation experiments, such as through varying parameters and
modules. experiment is for simpler “fully factorial” cases,
and experiment2 can take any simList class
objects for the simulation experiment. With experiment, for
example, you can pass alternative values to parameters in modules and
the experiment will build a fully factorial experiment,
with replication and run them. This function (as with POM
and splitRaster) is parallel-aware and can either proceed
with a cluster object (cl argument) or a cluster running in
the background using the raster::beginCluster.
## Loading required package: quickPlot## Loading required package: reproducible##
## Attaching package: 'SpaDES.core'## The following objects are masked from 'package:stats':
##
## end, start## The following object is masked from 'package:utils':
##
## citation##
## Attaching package: 'SpaDES.experiment'## The following objects are masked from 'package:SpaDES.core':
##
## POM, experiment, experiment2, simInitAndExperiment# Copy Example 5 here:
mySim <- simInit(
times = list(start = 0.0, end = 2.0, timeunit = "year"),
params = list(.globals = list(stackName = "landscape", burnStats = "nPixelsBurned")),
modules = list("randomLandscapes", "fireSpread", "caribouMovement"),
paths = list(modulePath = system.file("sampleModules", package = "SpaDES.core"),
outputPath = tmpdir),
# Save final state of landscape and caribou
outputs = data.frame(objectName = c("landscape", "caribou"), stringsAsFactors = FALSE)
)## Setting:
## options(
## spades.outputPath = '/tmp/RtmpiwVfCE/experiment'
## spades.modulePath = '/github/workspace/pkglib/SpaDES.core/sampleModules'
## )## Paths set to:
## options(
## rasterTmpDir = '/tmp/RtmpiwVfCE/SpaDES/scratch/raster'
## reproducible.cachePath = '/tmp/RtmpiwVfCE/reproducible/cache'
## spades.inputPath = '/tmp/RtmpiwVfCE/SpaDES/inputs'
## spades.outputPath = '/tmp/RtmpiwVfCE/experiment'
## spades.modulePath = '/github/workspace/pkglib/SpaDES.core/sampleModules'
## spades.scratchPath = '/tmp/RtmpiwVfCE/SpaDES/scratch'
## )
## terra::terraOptions(tempdir = '/tmp/RtmpiwVfCE/SpaDES/scratch/terra'## Using GITHUB_PAT to access files on GitHub## For better security, user should use the newer way to store git credentials.
## Using a GITHUB_PAT environment variable will continue to work, but see: https://usethis.r-lib.org/articles/git-credentials.html## No packages to install/update## Loading required package: RColorBrewer## Loading required package: grid## Loading required package: sf## Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUE## Loading required package: terra## terra 1.7.83##
## Attaching package: 'terra'## The following object is masked from 'package:grid':
##
## depth## The following object is masked from 'package:SpaDES.core':
##
## time<-## The following object is masked from 'package:SpaDES.tools':
##
## wrap## Oct27 04:38:20 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.## Oct27 04:38:20 simInit randomLandscapes: module code: landscape is declared in metadata outputObjects, but is not assigned in the module## Oct27 04:38:20 simInit randomLandscapes: module code: Init: local variable 'inMemory' assigned but may not be used## Oct27 04:38:20 simInit randomLandscapes: outputObjects: Par$stackName is assigned to sim inside Init, but is not declared in metadata outputObjects## Oct27 04:38:20 simInit randomLandscapes: inputObjects: Par$stackName is used from sim inside Init, but is not declared in metadata inputObjects## Oct27 04:38:20 simInit randomLandscapes: inputObjects: Par$stackName is used from sim inside doEvent.randomLandscapes, but is not declared in metadata inputObjects## Oct27 04:38:20 simInit fireSpread: module code: landscape is declared in metadata outputObjects, but is not assigned in the module## Oct27 04:38:20 simInit fireSpread: module code: landscape, nPixelsBurned are declared in metadata inputObjects, but no default(s) are provided in .inputObjects## Oct27 04:38:20 simInit fireSpread: module code: landscape is declared in metadata inputObjects, but is not used in the module## Oct27 04:38:20 simInit fireSpread: outputObjects: Par$stackName is assigned to sim inside Burn, but is not declared in metadata outputObjects## Oct27 04:38:20 simInit fireSpread: outputObjects: Par$stackName is assigned to sim inside Init, but is not declared in metadata outputObjects## Oct27 04:38:20 simInit fireSpread: outputObjects: Par$stackName is assigned to sim inside doEvent.fireSpread, but is not declared in metadata outputObjects## Oct27 04:38:20 simInit fireSpread: inputObjects: Par$stackName is used from sim inside Burn, but is not declared in metadata inputObjects## Oct27 04:38:20 simInit fireSpread: inputObjects: Par$stackName is used from sim inside Init, but is not declared in metadata inputObjects## Oct27 04:38:20 simInit fireSpread: inputObjects: Par$stackName is used from sim inside Stats, but is not declared in metadata inputObjects## Oct27 04:38:20 simInit fireSpread: inputObjects: Par$stackName, DEM, Fires are used from sim inside doEvent.fireSpread, but are not declared in metadata inputObjects## Oct27 04:38:20 simInit caribouMovement: module code: landscape, caribou are declared in metadata inputObjects, but no default(s) are provided in .inputObjects## Oct27 04:38:20 simInit caribouMovement: module code: landscape is declared in metadata inputObjects, but is not used in the module## Oct27 04:38:20 simInit caribouMovement: inputObjects: Par$stackName is used from sim inside Init, but is not declared in metadata inputObjects## Oct27 04:38:20 simInit caribouMovement: inputObjects: Par$stackName is used from sim inside Move, but is not declared in metadata inputObjects## Oct27 04:38:20 simInit The following .globals were used:## Oct27 04:38:20 simInit Key: <global, module>
## Oct27 04:38:20 simInit module global
## Oct27 04:38:20 simInit <char> <char>
## Oct27 04:38:20 simInit 1: fireSpread burnStats
## Oct27 04:38:20 simInit 2: caribouMovement stackName
## Oct27 04:38:20 simInit 3: fireSpread stackName
## Oct27 04:38:20 simInit 4: randomLandscapes stackName## Elapsed time for simInit: 3.363291 secs## No packages to install/update## Oct27 04:38:21 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.## Oct27 04:38:21 chckpn:init total elpsd: 3.4 secs | 0 checkpoint init 0## Oct27 04:38:21 save :init total elpsd: 3.4 secs | 0 save init 0## Oct27 04:38:21 prgrss:init total elpsd: 3.4 secs | 0 progress init 0## Oct27 04:38:21 load :init total elpsd: 3.4 secs | 0 load init 0## Oct27 04:38:21 rndmLn:init total elpsd: 3.4 secs | 0 randomLandscapes init 1## Oct27 04:38:21 rndmLn:init New objects created:## Oct27 04:38:21 rndmLn:init <char>
## Oct27 04:38:21 rndmLn:init 1: landscape## Oct27 04:38:21 frSprd:init total elpsd: 3.8 secs | 0 fireSpread init 1## Oct27 04:38:21 frSprd:init fireSpread## Oct27 04:38:21 frSprd:init New objects created:## Oct27 04:38:21 frSprd:init <char>
## Oct27 04:38:21 frSprd:init 1: nPixelsBurned## Oct27 04:38:21 crbMvm:init total elpsd: 3.9 secs | 0 caribouMovement init 1## Oct27 04:38:21 crbMvm:init New objects created:## Oct27 04:38:21 crbMvm:init <char>
## Oct27 04:38:21 crbMvm:init 1: caribou## Oct27 04:38:21 frSprd:burn total elpsd: 3.9 secs | 1 fireSpread burn 5## Oct27 04:38:21 crbMvm:move total elpsd: 4 secs | 1 caribouMovement move 5## Oct27 04:38:21 crbMvm:move New objects created:## Oct27 04:38:21 crbMvm:move <char>
## Oct27 04:38:21 crbMvm:move 1: habitatQuality## Oct27 04:38:21 frSprd:stats total elpsd: 4 secs | 1 fireSpread stats 5## Oct27 04:38:21 frSprd:stats fireSpread## Oct27 04:38:21 crbMvm:move total elpsd: 4 secs | 1.083 caribouMovement move 5## Oct27 04:38:21 crbMvm:move total elpsd: 4.1 secs | 1.167 caribouMovement move## Oct27 04:38:21 crbMvm:move total elpsd: 4.1 secs | 1.25 caribouMovement move## Oct27 04:38:21 crbMvm:move total elpsd: 4.1 secs | 1.333 caribouMovement move## Oct27 04:38:21 crbMvm:move total elpsd: 4.1 secs | 1.417 caribouMovement move## Oct27 04:38:21 crbMvm:move total elpsd: 4.1 secs | 1.5 caribouMovement move 5## Oct27 04:38:21 crbMvm:move total elpsd: 4.1 secs | 1.583 caribouMovement move## Oct27 04:38:21 crbMvm:move total elpsd: 4.2 secs | 1.667 caribouMovement move## Oct27 04:38:21 crbMvm:move total elpsd: 4.2 secs | 1.75 caribouMovement move## Oct27 04:38:21 crbMvm:move total elpsd: 4.2 secs | 1.833 caribouMovement move## Oct27 04:38:21 crbMvm:move total elpsd: 4.2 secs | 1.917 caribouMovement move## Oct27 04:38:21 frSprd:burn total elpsd: 4.2 secs | 2 fireSpread burn 5## Oct27 04:38:21 crbMvm:move total elpsd: 4.3 secs | 2 caribouMovement move 5## Oct27 04:38:21 frSprd:stats total elpsd: 4.3 secs | 2 fireSpread stats 5## Oct27 04:38:21 frSprd:stats fireSpread## Oct27 04:38:21 save :spades total elpsd: 4.3 secs | 2 save spades 10## simList saved in
## SpaDES.core:::savedSimEnv()$.sim
## It will be deleted at next spades() call.## No packages to install/update## Oct27 04:38:24 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.## Oct27 04:38:24 chckpn:init total elpsd: 3.4 secs | 0 checkpoint init 0## Oct27 04:38:24 save :init total elpsd: 3.4 secs | 0 save init 0## Oct27 04:38:24 prgrss:init total elpsd: 3.4 secs | 0 progress init 0## Oct27 04:38:24 load :init total elpsd: 3.4 secs | 0 load init 0## Oct27 04:38:24 rndmLn:init total elpsd: 3.4 secs | 0 randomLandscapes init 1## Oct27 04:38:24 rndmLn:init New objects created:## Oct27 04:38:24 rndmLn:init <char>
## Oct27 04:38:24 rndmLn:init 1: landscape## Oct27 04:38:24 frSprd:init total elpsd: 3.5 secs | 0 fireSpread init 1## Oct27 04:38:24 frSprd:init fireSpread## Oct27 04:38:24 frSprd:init New objects created:## Oct27 04:38:24 frSprd:init <char>
## Oct27 04:38:24 frSprd:init 1: nPixelsBurned## Oct27 04:38:24 crbMvm:init total elpsd: 3.5 secs | 0 caribouMovement init 1## Oct27 04:38:24 crbMvm:init New objects created:## Oct27 04:38:24 crbMvm:init <char>
## Oct27 04:38:24 crbMvm:init 1: caribou## Oct27 04:38:24 frSprd:burn total elpsd: 3.5 secs | 1 fireSpread burn 5## Oct27 04:38:24 crbMvm:move total elpsd: 3.5 secs | 1 caribouMovement move 5## Oct27 04:38:24 crbMvm:move New objects created:## Oct27 04:38:24 crbMvm:move <char>
## Oct27 04:38:24 crbMvm:move 1: habitatQuality## Oct27 04:38:24 frSprd:stats total elpsd: 3.6 secs | 1 fireSpread stats 5## Oct27 04:38:24 frSprd:stats fireSpread## Oct27 04:38:24 crbMvm:move total elpsd: 3.6 secs | 1.083 caribouMovement move## Oct27 04:38:24 crbMvm:move total elpsd: 3.6 secs | 1.167 caribouMovement move## Oct27 04:38:24 crbMvm:move total elpsd: 3.6 secs | 1.25 caribouMovement move## Oct27 04:38:24 crbMvm:move total elpsd: 3.6 secs | 1.333 caribouMovement move## Oct27 04:38:24 crbMvm:move total elpsd: 3.6 secs | 1.417 caribouMovement move## Oct27 04:38:24 crbMvm:move total elpsd: 3.6 secs | 1.5 caribouMovement move 5## Oct27 04:38:24 crbMvm:move total elpsd: 3.7 secs | 1.583 caribouMovement move## Oct27 04:38:24 crbMvm:move total elpsd: 3.7 secs | 1.667 caribouMovement move## Oct27 04:38:24 crbMvm:move total elpsd: 3.7 secs | 1.75 caribouMovement move## Oct27 04:38:24 crbMvm:move total elpsd: 3.7 secs | 1.833 caribouMovement move## Oct27 04:38:24 crbMvm:move total elpsd: 3.7 secs | 1.917 caribouMovement move## Oct27 04:38:24 frSprd:burn total elpsd: 3.7 secs | 2 fireSpread burn 5## Oct27 04:38:24 crbMvm:move total elpsd: 3.8 secs | 2 caribouMovement move 5## Oct27 04:38:24 frSprd:stats total elpsd: 3.8 secs | 2 fireSpread stats 5## Oct27 04:38:24 frSprd:stats fireSpread## Oct27 04:38:24 save :spades total elpsd: 3.8 secs | 2 save spades 10## simList saved in
## SpaDES.core:::savedSimEnv()$.sim
## It will be deleted at next spades() call.## shutting down parallel nodes## modules expLevel replicate
## 1 1 1 1
## 2 1 1 2As with spades, an experiment can be
cached.
experiment levelThis functionality can be achieved within an experiment call. This
can be done 2 ways, either: “internally” through the cache argument,
which will cache each spades call; or, “externally” which will
cache the entire experiment. If there are lots of
spades calls, then the former will be slow as the
simList will be digested once per spades
call.
## No packages to install/update## Oct27 04:38:26 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.## Oct27 04:38:26 chckpn:init total elpsd: 3.4 secs | 0 checkpoint init 0## Oct27 04:38:26 save :init total elpsd: 3.4 secs | 0 save init 0## Oct27 04:38:26 prgrss:init total elpsd: 3.4 secs | 0 progress init 0## Oct27 04:38:26 load :init total elpsd: 3.4 secs | 0 load init 0## Oct27 04:38:26 rndmLn:init total elpsd: 3.4 secs | 0 randomLandscapes init 1## Oct27 04:38:27 rndmLn:init New objects created:## Oct27 04:38:27 rndmLn:init <char>
## Oct27 04:38:27 rndmLn:init 1: landscape## Oct27 04:38:27 frSprd:init total elpsd: 3.5 secs | 0 fireSpread init 1## Oct27 04:38:27 frSprd:init fireSpread## Oct27 04:38:27 frSprd:init New objects created:## Oct27 04:38:27 frSprd:init <char>
## Oct27 04:38:27 frSprd:init 1: nPixelsBurned## Oct27 04:38:27 crbMvm:init total elpsd: 3.5 secs | 0 caribouMovement init 1## Oct27 04:38:27 crbMvm:init New objects created:## Oct27 04:38:27 crbMvm:init <char>
## Oct27 04:38:27 crbMvm:init 1: caribou## Oct27 04:38:27 frSprd:burn total elpsd: 3.5 secs | 1 fireSpread burn 5## Oct27 04:38:27 crbMvm:move total elpsd: 3.5 secs | 1 caribouMovement move 5## Oct27 04:38:27 crbMvm:move New objects created:## Oct27 04:38:27 crbMvm:move <char>
## Oct27 04:38:27 crbMvm:move 1: habitatQuality## Oct27 04:38:27 frSprd:stats total elpsd: 3.6 secs | 1 fireSpread stats 5## Oct27 04:38:27 frSprd:stats fireSpread## Oct27 04:38:27 crbMvm:move total elpsd: 3.6 secs | 1.083 caribouMovement move## Oct27 04:38:27 crbMvm:move total elpsd: 3.6 secs | 1.167 caribouMovement move## Oct27 04:38:27 crbMvm:move total elpsd: 3.6 secs | 1.25 caribouMovement move## Oct27 04:38:27 crbMvm:move total elpsd: 3.6 secs | 1.333 caribouMovement move## Oct27 04:38:27 crbMvm:move total elpsd: 3.6 secs | 1.417 caribouMovement move## Oct27 04:38:27 crbMvm:move total elpsd: 3.6 secs | 1.5 caribouMovement move 5## Oct27 04:38:27 crbMvm:move total elpsd: 3.7 secs | 1.583 caribouMovement move## Oct27 04:38:27 crbMvm:move total elpsd: 3.7 secs | 1.667 caribouMovement move## Oct27 04:38:27 crbMvm:move total elpsd: 3.7 secs | 1.75 caribouMovement move## Oct27 04:38:27 crbMvm:move total elpsd: 3.7 secs | 1.833 caribouMovement move## Oct27 04:38:27 crbMvm:move total elpsd: 3.7 secs | 1.917 caribouMovement move## Oct27 04:38:27 frSprd:burn total elpsd: 3.7 secs | 2 fireSpread burn 5## Oct27 04:38:27 crbMvm:move total elpsd: 3.8 secs | 2 caribouMovement move 5## Oct27 04:38:27 frSprd:stats total elpsd: 3.8 secs | 2 fireSpread stats 5## Oct27 04:38:27 frSprd:stats fireSpread## Oct27 04:38:27 save :spades total elpsd: 3.8 secs | 2 save spades 10## simList saved in
## SpaDES.core:::savedSimEnv()$.sim
## It will be deleted at next spades() call.## Saving large object (fn: spades, cacheId: 9509f09db39d467f) to
## Cache: 10.5 Mb## Done!## Saved! Cache file: 9509f09db39d467f.rds; fn: spades## Object to retrieve (fn: spades, 9509f09db39d467f.rds) ...## Loaded! Cached result from previous spades call## from module## shutting down parallel nodes## user system elapsed
## 5.594 0.232 5.840# internal -- second time faster
system.time({
sims2 <- experiment(mySim, replicates = 2, cache = TRUE, .plotInitialTime = NA)
})## Object to retrieve (fn: spades, 9509f09db39d467f.rds) ...## Loaded! Cached result from previous spades call## from module## Object to retrieve (fn: spades, 9509f09db39d467f.rds) ...## Loaded! Cached result from previous spades call## from module## shutting down parallel nodes## user system elapsed
## 1.097 0.004 1.102## [1] "Component 1: Names: 5 string mismatches"
## [2] "Component 1: Length mismatch: comparison on first 6 components"
## [3] "Component 1: Component 2: Modes: numeric, NULL"
## [4] "Component 1: Component 2: Lengths: 4, 0"
## [5] "Component 1: Component 2: target is numeric, current is NULL"
## [6] "Component 1: Component 3: target is NULL, current is PackedSpatVector"
## [7] "Component 1: Component 4: Attributes: < Names: 3 string mismatches >"
## [8] "Component 1: Component 4: Attributes: < Length mismatch: comparison on first 5 components >"
## [9] "Component 1: Component 4: Attributes: < Component 1: Names: 1 string mismatch >"
## [10] "Component 1: Component 4: Attributes: < Component 1: Attributes: < names for target but not for current > >"
## [11] "Component 1: Component 4: Attributes: < Component 1: Attributes: < Length mismatch: comparison on first 0 components > >"
## [12] "Component 1: Component 4: Attributes: < Component 1: Length mismatch: comparison on first 1 components >"
## [13] "Component 1: Component 4: Attributes: < Component 1: Component 1: Modes: character, list >"
## [14] "Component 1: Component 4: Attributes: < Component 1: Component 1: Lengths: 84, 1 >"
## [15] "Component 1: Component 4: Attributes: < Component 1: Component 1: target is character, current is list >"
## [16] "Component 1: Component 4: Attributes: < Component 2: 1 string mismatch >"
## [17] "Component 1: Component 4: Attributes: < Component 3: Modes: numeric, character >"
## [18] "Component 1: Component 4: Attributes: < Component 3: Lengths: 168, 1 >"
## [19] "Component 1: Component 4: Attributes: < Component 3: Attributes: < Modes: list, NULL > >"
## [20] "Component 1: Component 4: Attributes: < Component 3: Attributes: < Lengths: 2, 0 > >"
## [21] "Component 1: Component 4: Attributes: < Component 3: Attributes: < names for target but not for current > >"
## [22] "Component 1: Component 4: Attributes: < Component 3: Attributes: < current is not list-like > >"
## [23] "Component 1: Component 4: Attributes: < Component 3: target is matrix, current is character >"
## [24] "Component 1: Component 4: Attributes: < Component 4: Modes: character, S4 >"
## [25] "Component 1: Component 4: Attributes: < Component 4: names for current but not for target >"
## [26] "Component 1: Component 4: Attributes: < Component 4: Attributes: < target is NULL, current is list > >"
## [27] "Component 1: Component 4: Attributes: < Component 4: target is character, current is Rcpp_SpatRaster >"
## [28] "Component 1: Component 4: Attributes: < Component 5: Attributes: < Component 1: Mean relative difference: 112.7159 > >"
## [29] "Component 1: Component 4: Attributes: < Component 5: Attributes: < Component 2: Component 2: 1 string mismatch > >"
## [30] "Component 1: Component 4: Attributes: < Component 5: Numeric: lengths (336, 10000) differ >"
## [31] "Component 1: Component 5: Attributes: < Component 1: Component 1: Length mismatch: comparison on first 1 components >"
## [32] "Component 1: Component 5: Attributes: < Component 1: Component 1: Component 1: Attributes: < Component \"row.names\": Numeric: lengths (8, 9) differ > >"
## [33] "Component 1: Component 5: Attributes: < Component 1: Component 1: Component 1: Component 1: Numeric: lengths (8, 9) differ >"
## [34] "Component 1: Component 5: Attributes: < Component 1: Component 1: Component 1: Component 2: Numeric: lengths (8, 9) differ >"
## [35] "Component 1: Component 5: Attributes: < Component 1: Component 1: Component 1: Component 3: Numeric: lengths (8, 9) differ >"
## [36] "Component 1: Component 5: Attributes: < Component 1: Component 1: Component 1: Component 4: Numeric: lengths (8, 9) differ >"
## [37] "Component 1: Component 5: Attributes: < Component 1: Component 1: Component 1: Component 5: Numeric: lengths (8, 9) differ >"
## [38] "Component 1: Component 5: Attributes: < Component 3: 1 string mismatch >"
## [39] "Component 1: Component 5: Attributes: < Component 4: Component 2: Numeric: lengths (1, 5) differ >"
## [40] "Component 1: Component 5: Attributes: < Component 4: Component 4: Lengths (1, 5) differ (comparison on first 1 components) >"
## [41] "Component 1: Component 5: Attributes: < Component 4: Component 10: Lengths (1, 5) differ (string compare on first 1) >"
## [42] "Component 1: Component 5: Attributes: < Component 4: Component 10: 1 string mismatch >"
## [43] "Component 1: Component 5: Attributes: < Component 4: Component 12: Numeric: lengths (1, 5) differ >"
## [44] "Component 1: Component 5: Attributes: < Component 4: Component 13: Numeric: lengths (1, 5) differ >"
## [45] "Component 1: Component 5: Attributes: < Component 4: Component 17: Numeric: lengths (1, 5) differ >"
## [46] "Component 1: Component 5: Attributes: < Component 4: Component 18: 1 string mismatch >"
## [47] "Component 1: Component 5: Attributes: < Component 4: Component 20: Lengths (1, 5) differ (string compare on first 1) >"
## [48] "Component 1: Component 5: Attributes: < Component 5: Attributes: < Component 1: Mean relative difference: 4 > >"
## [49] "Component 1: Component 5: Attributes: < Component 5: Attributes: < Component 2: Component 2: 1 string mismatch > >"
## [50] "Component 1: Component 5: Attributes: < Component 5: Numeric: lengths (10000, 50000) differ >"
## [51] "Component 1: Component 6: Modes: S4, numeric"
## [52] "Component 1: Component 6: Lengths: 1, 2"
## [53] "Component 1: Component 6: Attributes: < Modes: list, NULL >"
## [54] "Component 1: Component 6: Attributes: < Lengths: 5, 0 >"
## [55] "Component 1: Component 6: Attributes: < names for target but not for current >"
## [56] "Component 1: Component 6: Attributes: < current is not list-like >"experiment with CacheHere, the simList (and other arguments to experiment) is
hashed once, and if it is found to be the same as previous, then the
returned list of simList objects is recovered. This means
that even a very large experiment, with many replicates and combinations
of parameters and modules can be recovered very quickly. Here we show
that you can output objects to disk, so the list of simList
objects doesn’t get too big. Then, when we recover it in the Cached
version, all the files are still there, the list of simList
objects is small, so very fast to recover.
# External
outputs(mySim) <- data.frame(objectName = "landscape")
system.time({
sims3 <- Cache(experiment, mySim, replicates = 3, .plotInitialTime = NA,
clearSimEnv = TRUE)
})## No packages to install/update## Oct27 04:38:34 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.## Oct27 04:38:34 chckpn:init total elpsd: 3.4 secs | 0 checkpoint init 0## Oct27 04:38:34 save :init total elpsd: 3.4 secs | 0 save init 0## Oct27 04:38:34 prgrss:init total elpsd: 3.4 secs | 0 progress init 0## Oct27 04:38:34 load :init total elpsd: 3.4 secs | 0 load init 0## Oct27 04:38:34 rndmLn:init total elpsd: 3.4 secs | 0 randomLandscapes init 1## Oct27 04:38:34 rndmLn:init New objects created:## Oct27 04:38:34 rndmLn:init <char>
## Oct27 04:38:34 rndmLn:init 1: landscape## Oct27 04:38:34 frSprd:init total elpsd: 3.5 secs | 0 fireSpread init 1## Oct27 04:38:34 frSprd:init fireSpread## Oct27 04:38:34 frSprd:init New objects created:## Oct27 04:38:34 frSprd:init <char>
## Oct27 04:38:34 frSprd:init 1: nPixelsBurned## Oct27 04:38:34 crbMvm:init total elpsd: 3.5 secs | 0 caribouMovement init 1## Oct27 04:38:34 crbMvm:init New objects created:## Oct27 04:38:34 crbMvm:init <char>
## Oct27 04:38:34 crbMvm:init 1: caribou## Oct27 04:38:34 frSprd:burn total elpsd: 3.5 secs | 1 fireSpread burn 5## Oct27 04:38:34 crbMvm:move total elpsd: 3.5 secs | 1 caribouMovement move 5## Oct27 04:38:34 crbMvm:move New objects created:## Oct27 04:38:34 crbMvm:move <char>
## Oct27 04:38:34 crbMvm:move 1: habitatQuality## Oct27 04:38:34 frSprd:stats total elpsd: 3.6 secs | 1 fireSpread stats 5## Oct27 04:38:34 frSprd:stats fireSpread## Oct27 04:38:34 crbMvm:move total elpsd: 3.6 secs | 1.083 caribouMovement move## Oct27 04:38:34 crbMvm:move total elpsd: 3.6 secs | 1.167 caribouMovement move## Oct27 04:38:34 crbMvm:move total elpsd: 3.6 secs | 1.25 caribouMovement move## Oct27 04:38:34 crbMvm:move total elpsd: 3.6 secs | 1.333 caribouMovement move## Oct27 04:38:35 crbMvm:move total elpsd: 3.6 secs | 1.417 caribouMovement move## Oct27 04:38:35 crbMvm:move total elpsd: 3.6 secs | 1.5 caribouMovement move 5## Oct27 04:38:35 crbMvm:move total elpsd: 3.7 secs | 1.583 caribouMovement move## Oct27 04:38:35 crbMvm:move total elpsd: 3.7 secs | 1.667 caribouMovement move## Oct27 04:38:35 crbMvm:move total elpsd: 3.7 secs | 1.75 caribouMovement move## Oct27 04:38:35 crbMvm:move total elpsd: 3.7 secs | 1.833 caribouMovement move## Oct27 04:38:35 crbMvm:move total elpsd: 3.7 secs | 1.917 caribouMovement move## Oct27 04:38:35 frSprd:burn total elpsd: 3.7 secs | 2 fireSpread burn 5## Oct27 04:38:35 crbMvm:move total elpsd: 3.8 secs | 2 caribouMovement move 5## Oct27 04:38:35 frSprd:stats total elpsd: 3.8 secs | 2 fireSpread stats 5## Oct27 04:38:35 frSprd:stats fireSpread## Oct27 04:38:35 save :spades total elpsd: 3.8 secs | 2 save spades 10## simList saved in
## SpaDES.core:::savedSimEnv()$.sim
## It will be deleted at next spades() call.## No packages to install/update## Oct27 04:38:36 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.## Oct27 04:38:36 chckpn:init total elpsd: 3.4 secs | 0 checkpoint init 0## Oct27 04:38:36 save :init total elpsd: 3.4 secs | 0 save init 0## Oct27 04:38:36 prgrss:init total elpsd: 3.4 secs | 0 progress init 0## Oct27 04:38:36 load :init total elpsd: 3.4 secs | 0 load init 0## Oct27 04:38:36 rndmLn:init total elpsd: 3.4 secs | 0 randomLandscapes init 1## Oct27 04:38:36 rndmLn:init New objects created:## Oct27 04:38:36 rndmLn:init <char>
## Oct27 04:38:36 rndmLn:init 1: landscape## Oct27 04:38:36 frSprd:init total elpsd: 3.5 secs | 0 fireSpread init 1## Oct27 04:38:36 frSprd:init fireSpread## Oct27 04:38:36 frSprd:init New objects created:## Oct27 04:38:36 frSprd:init <char>
## Oct27 04:38:36 frSprd:init 1: nPixelsBurned## Oct27 04:38:36 crbMvm:init total elpsd: 3.5 secs | 0 caribouMovement init 1## Oct27 04:38:36 crbMvm:init New objects created:## Oct27 04:38:36 crbMvm:init <char>
## Oct27 04:38:36 crbMvm:init 1: caribou## Oct27 04:38:36 frSprd:burn total elpsd: 3.5 secs | 1 fireSpread burn 5## Oct27 04:38:36 crbMvm:move total elpsd: 3.5 secs | 1 caribouMovement move 5## Oct27 04:38:36 crbMvm:move New objects created:## Oct27 04:38:36 crbMvm:move <char>
## Oct27 04:38:36 crbMvm:move 1: habitatQuality## Oct27 04:38:36 frSprd:stats total elpsd: 3.6 secs | 1 fireSpread stats 5## Oct27 04:38:36 frSprd:stats fireSpread## Oct27 04:38:36 crbMvm:move total elpsd: 3.6 secs | 1.083 caribouMovement move## Oct27 04:38:36 crbMvm:move total elpsd: 3.6 secs | 1.167 caribouMovement move## Oct27 04:38:36 crbMvm:move total elpsd: 3.6 secs | 1.25 caribouMovement move## Oct27 04:38:36 crbMvm:move total elpsd: 3.6 secs | 1.333 caribouMovement move## Oct27 04:38:36 crbMvm:move total elpsd: 3.6 secs | 1.417 caribouMovement move## Oct27 04:38:36 crbMvm:move total elpsd: 3.6 secs | 1.5 caribouMovement move 5## Oct27 04:38:36 crbMvm:move total elpsd: 3.7 secs | 1.583 caribouMovement move## Oct27 04:38:36 crbMvm:move total elpsd: 3.7 secs | 1.667 caribouMovement move## Oct27 04:38:36 crbMvm:move total elpsd: 3.7 secs | 1.75 caribouMovement move## Oct27 04:38:36 crbMvm:move total elpsd: 3.7 secs | 1.833 caribouMovement move## Oct27 04:38:36 crbMvm:move total elpsd: 3.7 secs | 1.917 caribouMovement move## Oct27 04:38:36 frSprd:burn total elpsd: 3.7 secs | 2 fireSpread burn 5## Oct27 04:38:36 crbMvm:move total elpsd: 3.8 secs | 2 caribouMovement move 5## Oct27 04:38:36 frSprd:stats total elpsd: 3.8 secs | 2 fireSpread stats 5## Oct27 04:38:36 frSprd:stats fireSpread## Oct27 04:38:36 save :spades total elpsd: 3.8 secs | 2 save spades 10## simList saved in
## SpaDES.core:::savedSimEnv()$.sim
## It will be deleted at next spades() call.## No packages to install/update## Oct27 04:38:37 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.## Oct27 04:38:37 chckpn:init total elpsd: 3.4 secs | 0 checkpoint init 0## Oct27 04:38:37 save :init total elpsd: 3.4 secs | 0 save init 0## Oct27 04:38:37 prgrss:init total elpsd: 3.4 secs | 0 progress init 0## Oct27 04:38:37 load :init total elpsd: 3.4 secs | 0 load init 0## Oct27 04:38:37 rndmLn:init total elpsd: 3.4 secs | 0 randomLandscapes init 1## Oct27 04:38:37 rndmLn:init New objects created:## Oct27 04:38:37 rndmLn:init <char>
## Oct27 04:38:37 rndmLn:init 1: landscape## Oct27 04:38:37 frSprd:init total elpsd: 3.5 secs | 0 fireSpread init 1## Oct27 04:38:37 frSprd:init fireSpread## Oct27 04:38:37 frSprd:init New objects created:## Oct27 04:38:37 frSprd:init <char>
## Oct27 04:38:37 frSprd:init 1: nPixelsBurned## Oct27 04:38:37 crbMvm:init total elpsd: 3.5 secs | 0 caribouMovement init 1## Oct27 04:38:37 crbMvm:init New objects created:## Oct27 04:38:37 crbMvm:init <char>
## Oct27 04:38:37 crbMvm:init 1: caribou## Oct27 04:38:37 frSprd:burn total elpsd: 3.5 secs | 1 fireSpread burn 5## Oct27 04:38:37 crbMvm:move total elpsd: 3.5 secs | 1 caribouMovement move 5## Oct27 04:38:37 crbMvm:move New objects created:## Oct27 04:38:37 crbMvm:move <char>
## Oct27 04:38:37 crbMvm:move 1: habitatQuality## Oct27 04:38:37 frSprd:stats total elpsd: 3.5 secs | 1 fireSpread stats 5## Oct27 04:38:37 frSprd:stats fireSpread## Oct27 04:38:37 crbMvm:move total elpsd: 3.6 secs | 1.083 caribouMovement move## Oct27 04:38:37 crbMvm:move total elpsd: 3.6 secs | 1.167 caribouMovement move## Oct27 04:38:37 crbMvm:move total elpsd: 3.6 secs | 1.25 caribouMovement move## Oct27 04:38:37 crbMvm:move total elpsd: 3.6 secs | 1.333 caribouMovement move## Oct27 04:38:37 crbMvm:move total elpsd: 3.6 secs | 1.417 caribouMovement move## Oct27 04:38:37 crbMvm:move total elpsd: 3.6 secs | 1.5 caribouMovement move 5## Oct27 04:38:37 crbMvm:move total elpsd: 3.6 secs | 1.583 caribouMovement move## Oct27 04:38:37 crbMvm:move total elpsd: 3.7 secs | 1.667 caribouMovement move## Oct27 04:38:37 crbMvm:move total elpsd: 3.7 secs | 1.75 caribouMovement move## Oct27 04:38:38 crbMvm:move total elpsd: 3.7 secs | 1.833 caribouMovement move## Oct27 04:38:38 crbMvm:move total elpsd: 3.7 secs | 1.917 caribouMovement move## Oct27 04:38:38 frSprd:burn total elpsd: 3.7 secs | 2 fireSpread burn 5## Oct27 04:38:38 crbMvm:move total elpsd: 3.8 secs | 2 caribouMovement move 5## Oct27 04:38:38 frSprd:stats total elpsd: 3.8 secs | 2 fireSpread stats 5## Oct27 04:38:38 frSprd:stats fireSpread## Oct27 04:38:38 save :spades total elpsd: 3.8 secs | 2 save spades 10## simList saved in
## SpaDES.core:::savedSimEnv()$.sim
## It will be deleted at next spades() call.## shutting down parallel nodes## Saved! Cache file: ad2e3e1b82d02f8c.rds; fn: experiment## user system elapsed
## 4.539 0.092 4.633The second time is way faster. We see the output files in the same location.
system.time({
sims4 <- Cache(experiment, mySim, replicates = 3, .plotInitialTime = NA,
clearSimEnv = TRUE)
})## Object to retrieve (fn: experiment, ad2e3e1b82d02f8c.rds) ...## Loaded! Cached result from previous experiment call## user system elapsed
## 0.069 0.000 0.070## [[1]]
## [1] TRUE
##
## [[2]]
## [1] TRUE## [1] "experiment.RData" "rep1/caribou_year2.rds"
## [3] "rep1/landscape_year2.rds" "rep2/caribou_year2.rds"
## [5] "rep2/landscape_year2.rds" "rep3/landscape_year2.rds"Notice that speed up can be enormous; in this case ~100 times faster.
This is a continuation of the Nested Caching section in
the iv-caching vignetted in the SpaDES.core
package. - Imagine we have large model, with many modules, with
replication and alternative module collections (e.g., alternative fire
models) - To run this would have a nested structure with the following
functions:
simInit --> many .inputObjects calls
experiment --> many spades calls --> many module calls --> many event calls --> many function callsLets 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 experiment call
will still spawn many spades calls, which 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 hundreds of times (because experiment
runs the spades call 100 times due to replication). 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.
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.
experiment callCache(experiment)
This will assess the simList (the objects, times,
modules, etc.) and if they are all the same, it will return the final
list of simLists that came from the first
experiment call. NOTE: because this can be
large, it is likely that you want clearSimEnv = TRUE, and
have all objects that are needed after the experiment call saved to
disk. Any stochasticity/randomness inside modules will be frozen. This
is likely ok if the objective is to show results in a web app (via shiny
or otherwise) or another visualization about the experiment outputs,
e.g., comparing treatments, once sufficient stochasticity has been
achieved.
mySimListOut <- Cache(experiment, mySim, clearSimEnv = TRUE)
spades calls inside
experimentexperiment(cache = TRUE)
This will cache each of the spades calls inside the
experiment call. That means that there are as many cache
events as there are replicates and experimental treatments, which, again
could be a lot. Like caching the experiment call,
stochasticity/randomness will be frozen. Note, one good use of this is
when you are making iterative, incremental replication, e.g.,
mySimOut <- experiment(mySim, replicates = 5, cache = TRUE)
You decide after waiting 10 minutes for it to finish, that you need more replication. Rather than start from zero replicates, you can just pick up where you left off:
mySimOut <- experiment(mySim, replicates = 10, cache = TRUE)
This will only add 5 more replicates.