As part of a reproducible workflow, caching of function calls, code chunks, and other elements of a project is a critical component. The objective of a reproducible workflow is 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 any computer, operating system, with any starting conditions, on demand. The reproducible::Cache
function is built to work with any R function.
Cache
uses 2 key the archivist
functions saveToLocalRepo
and loadFromLocalRepo
, but does not use archivist::cache
. Similar to archivist::cache
, there is some reliance on digest::digest
to determine whether the arguments are identical in subsequent iterations. It also but does many things that make standard caching with digest::digest
don’t work reliably between systems. For these, the function .robustDigest
is introduced to make caching transferable between systems. This is relevant for file paths, environments, parallel clusters, functions (which are contained within an environment), and many others (e.g., see ?.robustDigest
for methods). Cache
also adds important elements like automated tagging and the option to retrieve disk-cached values via stashed objects in memory using memoise::memoise
. This means that running Cache
1, 2, and 3 times on the same function will get progressively faster. This can be extremely useful for web apps built with, say shiny
.
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))
.
This is particularly useful for expensive operations.
library(raster)
## Loading required package: sp
library(reproducible)
tmpDir <- file.path(tempdir(), "reproducible_examples", "Cache")
checkPath(tmpDir, create = TRUE)
## [1] "/tmp/RtmpQuowAF/reproducible_examples/Cache"
ras <- raster(extent(0, 1000, 0, 1000), vals = 1:1e6, res = 1)
crs(ras) <- "+proj=lcc +lat_1=48 +lat_2=33 +lon_0=-100 +ellps=WGS84"
newCRS <- "+init=epsg:4326 +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0"
# No Cache
system.time(map1 <- projectRaster(ras, crs = newCRS))
## user system elapsed
## 2.301 0.193 2.499
# With Cache -- a little slower the first time because saving to disk
system.time(map1 <- Cache(projectRaster, ras, crs = newCRS, cacheRepo = tmpDir,
notOlderThan = Sys.time()))
## user system elapsed
## 2.457 0.197 2.810
# vastly faster the second time
system.time(map2 <- Cache(projectRaster, ras, crs = newCRS, cacheRepo = tmpDir))
## loading cached result from previous projectRaster call, adding to memoised copy
## user system elapsed
## 0.091 0.003 0.094
# even faster the third time
system.time(map3 <- Cache(projectRaster, ras, crs = newCRS, cacheRepo = tmpDir))
## loading memoised result from previous projectRaster call.
## user system elapsed
## 0.027 0.000 0.027
all.equal(map1, map2) # TRUE
## [1] TRUE
all.equal(map1, map3) # TRUE
## [1] TRUE
library(raster)
library(magrittr)
##
## Attaching package: 'magrittr'
## The following object is masked from 'package:raster':
##
## extract
try(clearCache(tmpDir, ask = FALSE), silent = TRUE) # just to make sure it is clear
ranNumsA <- Cache(rnorm, 10, 16, cacheRepo = tmpDir)
# All same
ranNumsB <- Cache(rnorm, 10, 16, cacheRepo = tmpDir) # recovers cached copy
## loading cached result from previous rnorm call, adding to memoised copy
ranNumsC <- Cache(cacheRepo = tmpDir) %C% rnorm(10, 16) # recovers cached copy
## loading memoised result from previous 'rnorm' pipe sequence call.
ranNumsD <- Cache(quote(rnorm(n = 10, 16)), cacheRepo = tmpDir) # recovers cached copy
## loading memoised result from previous rnorm call.
# Any minor change makes it different
ranNumsE <- Cache(cacheRepo = tmpDir) %C% rnorm(10, 6) # different
ranNumsA <- Cache(rnorm, 4, cacheRepo = tmpDir, userTags = "objectName:a")
ranNumsB <- Cache(runif, 4, cacheRepo = tmpDir, userTags = "objectName:b")
# access it again, from Cache
ranNumsA <- Cache(rnorm, 4, cacheRepo = tmpDir, userTags = "objectName:a")
## loading cached result from previous rnorm call, adding to memoised copy
wholeCache <- showCache(tmpDir)
## Cache size:
## Total (including Rasters): 504 bytes
## Selected objects (not including Rasters): 504 bytes
# keep only items accessed "recently" (i.e., only objectName:a)
onlyRecentlyAccessed <- showCache(tmpDir, userTags = max(wholeCache[tagKey == "accessed"]$tagValue))
## Cache size:
## Total (including Rasters): 504 bytes
## Selected objects (not including Rasters): 504 bytes
# inverse join with 2 data.tables ... using: a[!b]
# i.e., return all of wholeCache that was not recently accessed
toRemove <- unique(wholeCache[!onlyRecentlyAccessed], by = "artifact")$artifact
clearCache(tmpDir, toRemove, ask = FALSE) # remove ones not recently accessed
## Cache size:
## Total (including Rasters): 504 bytes
## Selected objects (not including Rasters): 504 bytes
showCache(tmpDir) # still has more recently accessed
## Cache size:
## Total (including Rasters): 0 bytes
## Selected objects (not including Rasters): 0 bytes
## Empty data.table (0 rows) of 3 cols: md5hash,name,createdDate
clearCache(tmpDir, ask = FALSE)
ranNumsA <- Cache(rnorm, 4, cacheRepo = tmpDir, userTags = "objectName:a")
ranNumsB <- Cache(runif, 4, cacheRepo = tmpDir, userTags = "objectName:b")
# keep only those cached items from the last 24 hours
oneDay <- 60 * 60 * 24
keepCache(tmpDir, after = Sys.time() - oneDay, ask = FALSE)
## Cache size:
## Total (including Rasters): 504 bytes
## Selected objects (not including Rasters): 504 bytes
## artifact tagKey
## 1: 41b03820fbc805b1f29f8b66ab0693cf format
## 2: 41b03820fbc805b1f29f8b66ab0693cf name
## 3: 41b03820fbc805b1f29f8b66ab0693cf class
## 4: 41b03820fbc805b1f29f8b66ab0693cf date
## 5: 41b03820fbc805b1f29f8b66ab0693cf cacheId
## 6: 41b03820fbc805b1f29f8b66ab0693cf objectName
## 7: 41b03820fbc805b1f29f8b66ab0693cf function
## 8: 41b03820fbc805b1f29f8b66ab0693cf object.size
## 9: 41b03820fbc805b1f29f8b66ab0693cf accessed
## 10: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 11: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 12: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 13: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 14: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 15: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 16: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 17: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 18: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 19: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 20: 41b03820fbc805b1f29f8b66ab0693cf preDigest
## 21: 41b03820fbc805b1f29f8b66ab0693cf preDigest
## 22: b585bc8994f5bf2762ec1d51f5a50651 format
## 23: b585bc8994f5bf2762ec1d51f5a50651 name
## 24: b585bc8994f5bf2762ec1d51f5a50651 class
## 25: b585bc8994f5bf2762ec1d51f5a50651 date
## 26: b585bc8994f5bf2762ec1d51f5a50651 cacheId
## 27: b585bc8994f5bf2762ec1d51f5a50651 objectName
## 28: b585bc8994f5bf2762ec1d51f5a50651 function
## 29: b585bc8994f5bf2762ec1d51f5a50651 object.size
## 30: b585bc8994f5bf2762ec1d51f5a50651 accessed
## 31: b585bc8994f5bf2762ec1d51f5a50651 otherFunctions
## 32: b585bc8994f5bf2762ec1d51f5a50651 otherFunctions
## 33: b585bc8994f5bf2762ec1d51f5a50651 otherFunctions
## 34: b585bc8994f5bf2762ec1d51f5a50651 otherFunctions
## 35: b585bc8994f5bf2762ec1d51f5a50651 otherFunctions
## 36: b585bc8994f5bf2762ec1d51f5a50651 otherFunctions
## 37: b585bc8994f5bf2762ec1d51f5a50651 otherFunctions
## 38: b585bc8994f5bf2762ec1d51f5a50651 otherFunctions
## 39: b585bc8994f5bf2762ec1d51f5a50651 otherFunctions
## 40: b585bc8994f5bf2762ec1d51f5a50651 otherFunctions
## 41: b585bc8994f5bf2762ec1d51f5a50651 preDigest
## 42: b585bc8994f5bf2762ec1d51f5a50651 preDigest
## artifact tagKey
## tagValue createdDate
## 1: rda 2019-01-28 11:00:06
## 2: 41b03820fbc805b1f29f8b66ab0693cf 2019-01-28 11:00:06
## 3: numeric 2019-01-28 11:00:06
## 4: 2019-01-28 11:00:06 2019-01-28 11:00:06
## 5: f7bee22047b8d0c1 2019-01-28 11:00:06
## 6: a 2019-01-28 11:00:06
## 7: rnorm 2019-01-28 11:00:06
## 8: 1008 2019-01-28 11:00:06
## 9: 2019-01-28 11:00:06 2019-01-28 11:00:06
## 10: vweave_rmarkdown 2019-01-28 11:00:06
## 11: process_file 2019-01-28 11:00:06
## 12: process_group 2019-01-28 11:00:06
## 13: process_group.block 2019-01-28 11:00:06
## 14: call_block 2019-01-28 11:00:06
## 15: block_exec 2019-01-28 11:00:06
## 16: in_dir 2019-01-28 11:00:06
## 17: timing_fn 2019-01-28 11:00:06
## 18: handle 2019-01-28 11:00:06
## 19: withVisible 2019-01-28 11:00:06
## 20: n:7eef4eae85fd9229 2019-01-28 11:00:06
## 21: .FUN:4f604aa46882b368 2019-01-28 11:00:06
## 22: rda 2019-01-28 11:00:06
## 23: b585bc8994f5bf2762ec1d51f5a50651 2019-01-28 11:00:06
## 24: numeric 2019-01-28 11:00:06
## 25: 2019-01-28 11:00:06 2019-01-28 11:00:06
## 26: 3aef38d1fc02aee5 2019-01-28 11:00:06
## 27: b 2019-01-28 11:00:06
## 28: runif 2019-01-28 11:00:06
## 29: 1008 2019-01-28 11:00:06
## 30: 2019-01-28 11:00:06 2019-01-28 11:00:06
## 31: vweave_rmarkdown 2019-01-28 11:00:06
## 32: process_file 2019-01-28 11:00:06
## 33: process_group 2019-01-28 11:00:06
## 34: process_group.block 2019-01-28 11:00:06
## 35: call_block 2019-01-28 11:00:06
## 36: block_exec 2019-01-28 11:00:06
## 37: in_dir 2019-01-28 11:00:06
## 38: timing_fn 2019-01-28 11:00:06
## 39: handle 2019-01-28 11:00:06
## 40: withVisible 2019-01-28 11:00:06
## 41: n:7eef4eae85fd9229 2019-01-28 11:00:06
## 42: .FUN:881ec847b7161f3c 2019-01-28 11:00:06
## tagValue createdDate
# Keep all Cache items created with an rnorm() call
keepCache(tmpDir, userTags = "rnorm", ask = FALSE)
## Cache size:
## Total (including Rasters): 504 bytes
## Selected objects (not including Rasters): 252 bytes
## artifact tagKey
## 1: 41b03820fbc805b1f29f8b66ab0693cf format
## 2: 41b03820fbc805b1f29f8b66ab0693cf name
## 3: 41b03820fbc805b1f29f8b66ab0693cf class
## 4: 41b03820fbc805b1f29f8b66ab0693cf date
## 5: 41b03820fbc805b1f29f8b66ab0693cf cacheId
## 6: 41b03820fbc805b1f29f8b66ab0693cf objectName
## 7: 41b03820fbc805b1f29f8b66ab0693cf function
## 8: 41b03820fbc805b1f29f8b66ab0693cf object.size
## 9: 41b03820fbc805b1f29f8b66ab0693cf accessed
## 10: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 11: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 12: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 13: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 14: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 15: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 16: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 17: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 18: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 19: 41b03820fbc805b1f29f8b66ab0693cf otherFunctions
## 20: 41b03820fbc805b1f29f8b66ab0693cf preDigest
## 21: 41b03820fbc805b1f29f8b66ab0693cf preDigest
## artifact tagKey
## tagValue createdDate
## 1: rda 2019-01-28 11:00:06
## 2: 41b03820fbc805b1f29f8b66ab0693cf 2019-01-28 11:00:06
## 3: numeric 2019-01-28 11:00:06
## 4: 2019-01-28 11:00:06 2019-01-28 11:00:06
## 5: f7bee22047b8d0c1 2019-01-28 11:00:06
## 6: a 2019-01-28 11:00:06
## 7: rnorm 2019-01-28 11:00:06
## 8: 1008 2019-01-28 11:00:06
## 9: 2019-01-28 11:00:06 2019-01-28 11:00:06
## 10: vweave_rmarkdown 2019-01-28 11:00:06
## 11: process_file 2019-01-28 11:00:06
## 12: process_group 2019-01-28 11:00:06
## 13: process_group.block 2019-01-28 11:00:06
## 14: call_block 2019-01-28 11:00:06
## 15: block_exec 2019-01-28 11:00:06
## 16: in_dir 2019-01-28 11:00:06
## 17: timing_fn 2019-01-28 11:00:06
## 18: handle 2019-01-28 11:00:06
## 19: withVisible 2019-01-28 11:00:06
## 20: n:7eef4eae85fd9229 2019-01-28 11:00:06
## 21: .FUN:4f604aa46882b368 2019-01-28 11:00:06
## tagValue createdDate
# Remove all Cache items that happened within a rnorm() call
clearCache(tmpDir, userTags = "rnorm", ask = FALSE)
## Cache size:
## Total (including Rasters): 252 bytes
## Selected objects (not including Rasters): 252 bytes
showCache(tmpDir) ## empty
## Cache size:
## Total (including Rasters): 0 bytes
## Selected objects (not including Rasters): 0 bytes
## Empty data.table (0 rows) of 3 cols: md5hash,name,createdDate
# default userTags is "and" matching; for "or" matching use |
ranNumsA <- Cache(runif, 4, cacheRepo = tmpDir, userTags = "objectName:a")
ranNumsB <- Cache(rnorm, 4, cacheRepo = tmpDir, userTags = "objectName:b")
# show all objects (runif and rnorm in this case)
showCache(tmpDir)
## Cache size:
## Total (including Rasters): 504 bytes
## Selected objects (not including Rasters): 504 bytes
## artifact tagKey
## 1: 4f2eec101161fba7326da197d793b4a6 format
## 2: 4f2eec101161fba7326da197d793b4a6 name
## 3: 4f2eec101161fba7326da197d793b4a6 class
## 4: 4f2eec101161fba7326da197d793b4a6 date
## 5: 4f2eec101161fba7326da197d793b4a6 cacheId
## 6: 4f2eec101161fba7326da197d793b4a6 objectName
## 7: 4f2eec101161fba7326da197d793b4a6 function
## 8: 4f2eec101161fba7326da197d793b4a6 object.size
## 9: 4f2eec101161fba7326da197d793b4a6 accessed
## 10: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 11: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 12: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 13: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 14: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 15: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 16: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 17: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 18: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 19: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 20: 4f2eec101161fba7326da197d793b4a6 preDigest
## 21: 4f2eec101161fba7326da197d793b4a6 preDigest
## 22: aefa8fdeb9be6b1f06243d5536fc0b8c format
## 23: aefa8fdeb9be6b1f06243d5536fc0b8c name
## 24: aefa8fdeb9be6b1f06243d5536fc0b8c class
## 25: aefa8fdeb9be6b1f06243d5536fc0b8c date
## 26: aefa8fdeb9be6b1f06243d5536fc0b8c cacheId
## 27: aefa8fdeb9be6b1f06243d5536fc0b8c objectName
## 28: aefa8fdeb9be6b1f06243d5536fc0b8c function
## 29: aefa8fdeb9be6b1f06243d5536fc0b8c object.size
## 30: aefa8fdeb9be6b1f06243d5536fc0b8c accessed
## 31: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 32: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 33: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 34: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 35: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 36: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 37: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 38: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 39: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 40: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 41: aefa8fdeb9be6b1f06243d5536fc0b8c preDigest
## 42: aefa8fdeb9be6b1f06243d5536fc0b8c preDigest
## artifact tagKey
## tagValue createdDate
## 1: rda 2019-01-28 11:00:07
## 2: 4f2eec101161fba7326da197d793b4a6 2019-01-28 11:00:07
## 3: numeric 2019-01-28 11:00:07
## 4: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 5: f7bee22047b8d0c1 2019-01-28 11:00:07
## 6: b 2019-01-28 11:00:07
## 7: rnorm 2019-01-28 11:00:07
## 8: 1008 2019-01-28 11:00:07
## 9: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 10: vweave_rmarkdown 2019-01-28 11:00:07
## 11: process_file 2019-01-28 11:00:07
## 12: process_group 2019-01-28 11:00:07
## 13: process_group.block 2019-01-28 11:00:07
## 14: call_block 2019-01-28 11:00:07
## 15: block_exec 2019-01-28 11:00:07
## 16: in_dir 2019-01-28 11:00:07
## 17: timing_fn 2019-01-28 11:00:07
## 18: handle 2019-01-28 11:00:07
## 19: withVisible 2019-01-28 11:00:07
## 20: n:7eef4eae85fd9229 2019-01-28 11:00:07
## 21: .FUN:4f604aa46882b368 2019-01-28 11:00:07
## 22: rda 2019-01-28 11:00:07
## 23: aefa8fdeb9be6b1f06243d5536fc0b8c 2019-01-28 11:00:07
## 24: numeric 2019-01-28 11:00:07
## 25: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 26: 3aef38d1fc02aee5 2019-01-28 11:00:07
## 27: a 2019-01-28 11:00:07
## 28: runif 2019-01-28 11:00:07
## 29: 1008 2019-01-28 11:00:07
## 30: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 31: vweave_rmarkdown 2019-01-28 11:00:07
## 32: process_file 2019-01-28 11:00:07
## 33: process_group 2019-01-28 11:00:07
## 34: process_group.block 2019-01-28 11:00:07
## 35: call_block 2019-01-28 11:00:07
## 36: block_exec 2019-01-28 11:00:07
## 37: in_dir 2019-01-28 11:00:07
## 38: timing_fn 2019-01-28 11:00:07
## 39: handle 2019-01-28 11:00:07
## 40: withVisible 2019-01-28 11:00:07
## 41: n:7eef4eae85fd9229 2019-01-28 11:00:07
## 42: .FUN:881ec847b7161f3c 2019-01-28 11:00:07
## tagValue createdDate
# show objects that are both runif and rnorm
# (i.e., none in this case, because objecs are either or, not both)
showCache(tmpDir, userTags = c("runif", "rnorm")) ## empty
## Cache size:
## Total (including Rasters): 504 bytes
## Selected objects (not including Rasters): 0 bytes
## Empty data.table (0 rows) of 4 cols: artifact,tagKey,tagValue,createdDate
# show objects that are either runif or rnorm ("or" search)
showCache(tmpDir, userTags = "runif|rnorm")
## Cache size:
## Total (including Rasters): 504 bytes
## Selected objects (not including Rasters): 504 bytes
## artifact tagKey
## 1: 4f2eec101161fba7326da197d793b4a6 format
## 2: 4f2eec101161fba7326da197d793b4a6 name
## 3: 4f2eec101161fba7326da197d793b4a6 class
## 4: 4f2eec101161fba7326da197d793b4a6 date
## 5: 4f2eec101161fba7326da197d793b4a6 cacheId
## 6: 4f2eec101161fba7326da197d793b4a6 objectName
## 7: 4f2eec101161fba7326da197d793b4a6 function
## 8: 4f2eec101161fba7326da197d793b4a6 object.size
## 9: 4f2eec101161fba7326da197d793b4a6 accessed
## 10: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 11: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 12: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 13: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 14: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 15: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 16: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 17: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 18: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 19: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 20: 4f2eec101161fba7326da197d793b4a6 preDigest
## 21: 4f2eec101161fba7326da197d793b4a6 preDigest
## 22: aefa8fdeb9be6b1f06243d5536fc0b8c format
## 23: aefa8fdeb9be6b1f06243d5536fc0b8c name
## 24: aefa8fdeb9be6b1f06243d5536fc0b8c class
## 25: aefa8fdeb9be6b1f06243d5536fc0b8c date
## 26: aefa8fdeb9be6b1f06243d5536fc0b8c cacheId
## 27: aefa8fdeb9be6b1f06243d5536fc0b8c objectName
## 28: aefa8fdeb9be6b1f06243d5536fc0b8c function
## 29: aefa8fdeb9be6b1f06243d5536fc0b8c object.size
## 30: aefa8fdeb9be6b1f06243d5536fc0b8c accessed
## 31: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 32: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 33: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 34: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 35: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 36: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 37: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 38: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 39: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 40: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 41: aefa8fdeb9be6b1f06243d5536fc0b8c preDigest
## 42: aefa8fdeb9be6b1f06243d5536fc0b8c preDigest
## artifact tagKey
## tagValue createdDate
## 1: rda 2019-01-28 11:00:07
## 2: 4f2eec101161fba7326da197d793b4a6 2019-01-28 11:00:07
## 3: numeric 2019-01-28 11:00:07
## 4: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 5: f7bee22047b8d0c1 2019-01-28 11:00:07
## 6: b 2019-01-28 11:00:07
## 7: rnorm 2019-01-28 11:00:07
## 8: 1008 2019-01-28 11:00:07
## 9: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 10: vweave_rmarkdown 2019-01-28 11:00:07
## 11: process_file 2019-01-28 11:00:07
## 12: process_group 2019-01-28 11:00:07
## 13: process_group.block 2019-01-28 11:00:07
## 14: call_block 2019-01-28 11:00:07
## 15: block_exec 2019-01-28 11:00:07
## 16: in_dir 2019-01-28 11:00:07
## 17: timing_fn 2019-01-28 11:00:07
## 18: handle 2019-01-28 11:00:07
## 19: withVisible 2019-01-28 11:00:07
## 20: n:7eef4eae85fd9229 2019-01-28 11:00:07
## 21: .FUN:4f604aa46882b368 2019-01-28 11:00:07
## 22: rda 2019-01-28 11:00:07
## 23: aefa8fdeb9be6b1f06243d5536fc0b8c 2019-01-28 11:00:07
## 24: numeric 2019-01-28 11:00:07
## 25: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 26: 3aef38d1fc02aee5 2019-01-28 11:00:07
## 27: a 2019-01-28 11:00:07
## 28: runif 2019-01-28 11:00:07
## 29: 1008 2019-01-28 11:00:07
## 30: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 31: vweave_rmarkdown 2019-01-28 11:00:07
## 32: process_file 2019-01-28 11:00:07
## 33: process_group 2019-01-28 11:00:07
## 34: process_group.block 2019-01-28 11:00:07
## 35: call_block 2019-01-28 11:00:07
## 36: block_exec 2019-01-28 11:00:07
## 37: in_dir 2019-01-28 11:00:07
## 38: timing_fn 2019-01-28 11:00:07
## 39: handle 2019-01-28 11:00:07
## 40: withVisible 2019-01-28 11:00:07
## 41: n:7eef4eae85fd9229 2019-01-28 11:00:07
## 42: .FUN:881ec847b7161f3c 2019-01-28 11:00:07
## tagValue createdDate
# keep only objects that are either runif or rnorm ("or" search)
keepCache(tmpDir, userTags = "runif|rnorm", ask = FALSE)
## Cache size:
## Total (including Rasters): 504 bytes
## Selected objects (not including Rasters): 504 bytes
## artifact tagKey
## 1: 4f2eec101161fba7326da197d793b4a6 format
## 2: 4f2eec101161fba7326da197d793b4a6 name
## 3: 4f2eec101161fba7326da197d793b4a6 class
## 4: 4f2eec101161fba7326da197d793b4a6 date
## 5: 4f2eec101161fba7326da197d793b4a6 cacheId
## 6: 4f2eec101161fba7326da197d793b4a6 objectName
## 7: 4f2eec101161fba7326da197d793b4a6 function
## 8: 4f2eec101161fba7326da197d793b4a6 object.size
## 9: 4f2eec101161fba7326da197d793b4a6 accessed
## 10: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 11: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 12: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 13: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 14: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 15: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 16: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 17: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 18: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 19: 4f2eec101161fba7326da197d793b4a6 otherFunctions
## 20: 4f2eec101161fba7326da197d793b4a6 preDigest
## 21: 4f2eec101161fba7326da197d793b4a6 preDigest
## 22: aefa8fdeb9be6b1f06243d5536fc0b8c format
## 23: aefa8fdeb9be6b1f06243d5536fc0b8c name
## 24: aefa8fdeb9be6b1f06243d5536fc0b8c class
## 25: aefa8fdeb9be6b1f06243d5536fc0b8c date
## 26: aefa8fdeb9be6b1f06243d5536fc0b8c cacheId
## 27: aefa8fdeb9be6b1f06243d5536fc0b8c objectName
## 28: aefa8fdeb9be6b1f06243d5536fc0b8c function
## 29: aefa8fdeb9be6b1f06243d5536fc0b8c object.size
## 30: aefa8fdeb9be6b1f06243d5536fc0b8c accessed
## 31: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 32: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 33: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 34: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 35: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 36: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 37: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 38: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 39: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 40: aefa8fdeb9be6b1f06243d5536fc0b8c otherFunctions
## 41: aefa8fdeb9be6b1f06243d5536fc0b8c preDigest
## 42: aefa8fdeb9be6b1f06243d5536fc0b8c preDigest
## artifact tagKey
## tagValue createdDate
## 1: rda 2019-01-28 11:00:07
## 2: 4f2eec101161fba7326da197d793b4a6 2019-01-28 11:00:07
## 3: numeric 2019-01-28 11:00:07
## 4: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 5: f7bee22047b8d0c1 2019-01-28 11:00:07
## 6: b 2019-01-28 11:00:07
## 7: rnorm 2019-01-28 11:00:07
## 8: 1008 2019-01-28 11:00:07
## 9: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 10: vweave_rmarkdown 2019-01-28 11:00:07
## 11: process_file 2019-01-28 11:00:07
## 12: process_group 2019-01-28 11:00:07
## 13: process_group.block 2019-01-28 11:00:07
## 14: call_block 2019-01-28 11:00:07
## 15: block_exec 2019-01-28 11:00:07
## 16: in_dir 2019-01-28 11:00:07
## 17: timing_fn 2019-01-28 11:00:07
## 18: handle 2019-01-28 11:00:07
## 19: withVisible 2019-01-28 11:00:07
## 20: n:7eef4eae85fd9229 2019-01-28 11:00:07
## 21: .FUN:4f604aa46882b368 2019-01-28 11:00:07
## 22: rda 2019-01-28 11:00:07
## 23: aefa8fdeb9be6b1f06243d5536fc0b8c 2019-01-28 11:00:07
## 24: numeric 2019-01-28 11:00:07
## 25: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 26: 3aef38d1fc02aee5 2019-01-28 11:00:07
## 27: a 2019-01-28 11:00:07
## 28: runif 2019-01-28 11:00:07
## 29: 1008 2019-01-28 11:00:07
## 30: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 31: vweave_rmarkdown 2019-01-28 11:00:07
## 32: process_file 2019-01-28 11:00:07
## 33: process_group 2019-01-28 11:00:07
## 34: process_group.block 2019-01-28 11:00:07
## 35: call_block 2019-01-28 11:00:07
## 36: block_exec 2019-01-28 11:00:07
## 37: in_dir 2019-01-28 11:00:07
## 38: timing_fn 2019-01-28 11:00:07
## 39: handle 2019-01-28 11:00:07
## 40: withVisible 2019-01-28 11:00:07
## 41: n:7eef4eae85fd9229 2019-01-28 11:00:07
## 42: .FUN:881ec847b7161f3c 2019-01-28 11:00:07
## tagValue createdDate
clearCache(tmpDir, ask = FALSE)
ras <- raster(extent(0, 5, 0, 5), res = 1,
vals = sample(1:5, replace = TRUE, size = 25),
crs = "+proj=lcc +lat_1=48 +lat_2=33 +lon_0=-100 +ellps=WGS84")
# A slow operation, like GIS operation
notCached <- suppressWarnings(
# project raster generates warnings when run non-interactively
projectRaster(ras, crs = crs(ras), res = 5, cacheRepo = tmpDir)
)
cached <- suppressWarnings(
# project raster generates warnings when run non-interactively
# using quote works also
Cache(projectRaster, ras, crs = crs(ras), res = 5, cacheRepo = tmpDir)
)
# second time is much faster
reRun <- suppressWarnings(
# project raster generates warnings when run non-interactively
Cache(projectRaster, ras, crs = crs(ras), res = 5, cacheRepo = tmpDir)
)
## loading cached result from previous projectRaster call, adding to memoised copy
# recovered cached version is same as non-cached version
all.equal(notCached, reRun) ## TRUE
## [1] TRUE
Nested caching, which is when Caching of a function occurs inside an outer function, which is itself cached. This is a critical element to working within a reproducible work flow. It is not enough during development to cache flat code chunks, as there will be many levels of “slow” functions. Ideally, at all points in a development cycle, it should be possible to get to any line of code starting from the very initial steps, running through everything up to that point, in less that 1 second. If the workflow can be kept very fast like this, then there is a guarantee that it will work at any point.
##########################
## Nested Caching
# Make 2 functions
inner <- function(mean) {
d <- 1
Cache(rnorm, n = 3, mean = mean)
}
outer <- function(n) {
Cache(inner, 0.1, cacheRepo = tmpdir2)
}
# make 2 different cache paths
tmpdir1 <- file.path(tempdir(), "first")
tmpdir2 <- file.path(tempdir(), "second")
# Run the Cache ... notOlderThan propagates to all 3 Cache calls,
# but cacheRepo is tmpdir1 in top level Cache and all nested
# Cache calls, unless individually overridden ... here inner
# uses tmpdir2 repository
Cache(outer, n = 2, cacheRepo = tmpdir1, notOlderThan = Sys.time())
## [1] -1.4258265 -1.4687567 0.9123924
## attr(,".Cache")
## attr(,".Cache")$newCache
## [1] TRUE
##
## attr(,"tags")
## [1] "cacheId:a7af5367c13aba8f"
## attr(,"call")
## [1] ""
showCache(tmpdir1) # 2 function calls
## Cache size:
## Total (including Rasters): 504 bytes
## Selected objects (not including Rasters): 504 bytes
## artifact tagKey
## 1: 4571083d4dbddfba7362b1236be88944 format
## 2: 4571083d4dbddfba7362b1236be88944 name
## 3: 4571083d4dbddfba7362b1236be88944 class
## 4: 4571083d4dbddfba7362b1236be88944 date
## 5: 4571083d4dbddfba7362b1236be88944 cacheId
## 6: 4571083d4dbddfba7362b1236be88944 function
## 7: 4571083d4dbddfba7362b1236be88944 object.size
## 8: 4571083d4dbddfba7362b1236be88944 accessed
## 9: 4571083d4dbddfba7362b1236be88944 otherFunctions
## 10: 4571083d4dbddfba7362b1236be88944 otherFunctions
## 11: 4571083d4dbddfba7362b1236be88944 otherFunctions
## 12: 4571083d4dbddfba7362b1236be88944 otherFunctions
## 13: 4571083d4dbddfba7362b1236be88944 otherFunctions
## 14: 4571083d4dbddfba7362b1236be88944 otherFunctions
## 15: 4571083d4dbddfba7362b1236be88944 otherFunctions
## 16: 4571083d4dbddfba7362b1236be88944 otherFunctions
## 17: 4571083d4dbddfba7362b1236be88944 otherFunctions
## 18: 4571083d4dbddfba7362b1236be88944 otherFunctions
## 19: 4571083d4dbddfba7362b1236be88944 preDigest
## 20: 4571083d4dbddfba7362b1236be88944 preDigest
## 21: 4571083d4dbddfba7362b1236be88944 preDigest
## 22: 8a4e81fc565841d5cbdd42362704d996 format
## 23: 8a4e81fc565841d5cbdd42362704d996 name
## 24: 8a4e81fc565841d5cbdd42362704d996 class
## 25: 8a4e81fc565841d5cbdd42362704d996 date
## 26: 8a4e81fc565841d5cbdd42362704d996 cacheId
## 27: 8a4e81fc565841d5cbdd42362704d996 function
## 28: 8a4e81fc565841d5cbdd42362704d996 object.size
## 29: 8a4e81fc565841d5cbdd42362704d996 accessed
## 30: 8a4e81fc565841d5cbdd42362704d996 otherFunctions
## 31: 8a4e81fc565841d5cbdd42362704d996 otherFunctions
## 32: 8a4e81fc565841d5cbdd42362704d996 otherFunctions
## 33: 8a4e81fc565841d5cbdd42362704d996 otherFunctions
## 34: 8a4e81fc565841d5cbdd42362704d996 otherFunctions
## 35: 8a4e81fc565841d5cbdd42362704d996 otherFunctions
## 36: 8a4e81fc565841d5cbdd42362704d996 otherFunctions
## 37: 8a4e81fc565841d5cbdd42362704d996 otherFunctions
## 38: 8a4e81fc565841d5cbdd42362704d996 otherFunctions
## 39: 8a4e81fc565841d5cbdd42362704d996 otherFunctions
## 40: 8a4e81fc565841d5cbdd42362704d996 preDigest
## 41: 8a4e81fc565841d5cbdd42362704d996 preDigest
## artifact tagKey
## tagValue createdDate
## 1: rda 2019-01-28 11:00:07
## 2: 4571083d4dbddfba7362b1236be88944 2019-01-28 11:00:07
## 3: numeric 2019-01-28 11:00:07
## 4: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 5: 4ac2b7c0f42d1e46 2019-01-28 11:00:07
## 6: rnorm 2019-01-28 11:00:07
## 7: 1008 2019-01-28 11:00:07
## 8: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 9: vweave_rmarkdown 2019-01-28 11:00:07
## 10: process_file 2019-01-28 11:00:07
## 11: process_group 2019-01-28 11:00:07
## 12: process_group.block 2019-01-28 11:00:07
## 13: call_block 2019-01-28 11:00:07
## 14: block_exec 2019-01-28 11:00:07
## 15: in_dir 2019-01-28 11:00:07
## 16: timing_fn 2019-01-28 11:00:07
## 17: handle 2019-01-28 11:00:07
## 18: withVisible 2019-01-28 11:00:07
## 19: n:7f12988bd88a0fb8 2019-01-28 11:00:07
## 20: mean:22413394efd9f6a3 2019-01-28 11:00:07
## 21: .FUN:4f604aa46882b368 2019-01-28 11:00:07
## 22: rda 2019-01-28 11:00:07
## 23: 8a4e81fc565841d5cbdd42362704d996 2019-01-28 11:00:07
## 24: numeric 2019-01-28 11:00:07
## 25: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 26: a7af5367c13aba8f 2019-01-28 11:00:07
## 27: outer 2019-01-28 11:00:07
## 28: 1008 2019-01-28 11:00:07
## 29: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 30: vweave_rmarkdown 2019-01-28 11:00:07
## 31: process_file 2019-01-28 11:00:07
## 32: process_group 2019-01-28 11:00:07
## 33: process_group.block 2019-01-28 11:00:07
## 34: call_block 2019-01-28 11:00:07
## 35: block_exec 2019-01-28 11:00:07
## 36: in_dir 2019-01-28 11:00:07
## 37: timing_fn 2019-01-28 11:00:07
## 38: handle 2019-01-28 11:00:08
## 39: withVisible 2019-01-28 11:00:08
## 40: n:82dc709f2b91918a 2019-01-28 11:00:08
## 41: .FUN:892a6afc47a63a90 2019-01-28 11:00:08
## tagValue createdDate
showCache(tmpdir2) # 1 function call
## Cache size:
## Total (including Rasters): 252 bytes
## Selected objects (not including Rasters): 252 bytes
## artifact tagKey
## 1: e4746767371ee7e6b38f9647f9b73482 format
## 2: e4746767371ee7e6b38f9647f9b73482 name
## 3: e4746767371ee7e6b38f9647f9b73482 class
## 4: e4746767371ee7e6b38f9647f9b73482 date
## 5: e4746767371ee7e6b38f9647f9b73482 cacheId
## 6: e4746767371ee7e6b38f9647f9b73482 function
## 7: e4746767371ee7e6b38f9647f9b73482 object.size
## 8: e4746767371ee7e6b38f9647f9b73482 accessed
## 9: e4746767371ee7e6b38f9647f9b73482 otherFunctions
## 10: e4746767371ee7e6b38f9647f9b73482 otherFunctions
## 11: e4746767371ee7e6b38f9647f9b73482 otherFunctions
## 12: e4746767371ee7e6b38f9647f9b73482 otherFunctions
## 13: e4746767371ee7e6b38f9647f9b73482 otherFunctions
## 14: e4746767371ee7e6b38f9647f9b73482 otherFunctions
## 15: e4746767371ee7e6b38f9647f9b73482 otherFunctions
## 16: e4746767371ee7e6b38f9647f9b73482 otherFunctions
## 17: e4746767371ee7e6b38f9647f9b73482 otherFunctions
## 18: e4746767371ee7e6b38f9647f9b73482 otherFunctions
## 19: e4746767371ee7e6b38f9647f9b73482 preDigest
## 20: e4746767371ee7e6b38f9647f9b73482 preDigest
## tagValue createdDate
## 1: rda 2019-01-28 11:00:07
## 2: e4746767371ee7e6b38f9647f9b73482 2019-01-28 11:00:07
## 3: numeric 2019-01-28 11:00:07
## 4: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 5: 33ceb4fb525fd08f 2019-01-28 11:00:07
## 6: inner 2019-01-28 11:00:07
## 7: 1008 2019-01-28 11:00:07
## 8: 2019-01-28 11:00:07 2019-01-28 11:00:07
## 9: vweave_rmarkdown 2019-01-28 11:00:07
## 10: process_file 2019-01-28 11:00:07
## 11: process_group 2019-01-28 11:00:07
## 12: process_group.block 2019-01-28 11:00:07
## 13: call_block 2019-01-28 11:00:07
## 14: block_exec 2019-01-28 11:00:07
## 15: in_dir 2019-01-28 11:00:07
## 16: timing_fn 2019-01-28 11:00:07
## 17: handle 2019-01-28 11:00:07
## 18: withVisible 2019-01-28 11:00:07
## 19: mean:22413394efd9f6a3 2019-01-28 11:00:07
## 20: .FUN:87e2c30917a34d25 2019-01-28 11:00:07
# userTags get appended
# all items have the outer tag propagate, plus inner ones only have inner ones
clearCache(tmpdir1, ask = FALSE)
outerTag <- "outerTag"
innerTag <- "innerTag"
inner <- function(mean) {
d <- 1
Cache(rnorm, n = 3, mean = mean, notOlderThan = Sys.time() - 1e5, userTags = innerTag)
}
outer <- function(n) {
Cache(inner, 0.1)
}
aa <- Cache(outer, n = 2, cacheRepo = tmpdir1, userTags = outerTag)
showCache(tmpdir1) # rnorm function has outerTag and innerTag, inner and outer only have outerTag
## Cache size:
## Total (including Rasters): 756 bytes
## Selected objects (not including Rasters): 756 bytes
## artifact tagKey
## 1: 55ca5ec58674d9e2119c6c41b84d2d46 format
## 2: 55ca5ec58674d9e2119c6c41b84d2d46 name
## 3: 55ca5ec58674d9e2119c6c41b84d2d46 class
## 4: 55ca5ec58674d9e2119c6c41b84d2d46 date
## 5: 55ca5ec58674d9e2119c6c41b84d2d46 cacheId
## 6: 55ca5ec58674d9e2119c6c41b84d2d46 outerTag
## 7: 55ca5ec58674d9e2119c6c41b84d2d46 function
## 8: 55ca5ec58674d9e2119c6c41b84d2d46 object.size
## 9: 55ca5ec58674d9e2119c6c41b84d2d46 accessed
## 10: 55ca5ec58674d9e2119c6c41b84d2d46 otherFunctions
## 11: 55ca5ec58674d9e2119c6c41b84d2d46 otherFunctions
## 12: 55ca5ec58674d9e2119c6c41b84d2d46 otherFunctions
## 13: 55ca5ec58674d9e2119c6c41b84d2d46 otherFunctions
## 14: 55ca5ec58674d9e2119c6c41b84d2d46 otherFunctions
## 15: 55ca5ec58674d9e2119c6c41b84d2d46 otherFunctions
## 16: 55ca5ec58674d9e2119c6c41b84d2d46 otherFunctions
## 17: 55ca5ec58674d9e2119c6c41b84d2d46 otherFunctions
## 18: 55ca5ec58674d9e2119c6c41b84d2d46 otherFunctions
## 19: 55ca5ec58674d9e2119c6c41b84d2d46 otherFunctions
## 20: 55ca5ec58674d9e2119c6c41b84d2d46 preDigest
## 21: 55ca5ec58674d9e2119c6c41b84d2d46 preDigest
## 22: 8cce866a994487d14cae2bbf5e5fff3e format
## 23: 8cce866a994487d14cae2bbf5e5fff3e name
## 24: 8cce866a994487d14cae2bbf5e5fff3e class
## 25: 8cce866a994487d14cae2bbf5e5fff3e date
## 26: 8cce866a994487d14cae2bbf5e5fff3e cacheId
## 27: 8cce866a994487d14cae2bbf5e5fff3e outerTag
## 28: 8cce866a994487d14cae2bbf5e5fff3e function
## 29: 8cce866a994487d14cae2bbf5e5fff3e object.size
## 30: 8cce866a994487d14cae2bbf5e5fff3e accessed
## 31: 8cce866a994487d14cae2bbf5e5fff3e otherFunctions
## 32: 8cce866a994487d14cae2bbf5e5fff3e otherFunctions
## 33: 8cce866a994487d14cae2bbf5e5fff3e otherFunctions
## 34: 8cce866a994487d14cae2bbf5e5fff3e otherFunctions
## 35: 8cce866a994487d14cae2bbf5e5fff3e otherFunctions
## 36: 8cce866a994487d14cae2bbf5e5fff3e otherFunctions
## 37: 8cce866a994487d14cae2bbf5e5fff3e otherFunctions
## 38: 8cce866a994487d14cae2bbf5e5fff3e otherFunctions
## 39: 8cce866a994487d14cae2bbf5e5fff3e otherFunctions
## 40: 8cce866a994487d14cae2bbf5e5fff3e otherFunctions
## 41: 8cce866a994487d14cae2bbf5e5fff3e preDigest
## 42: 8cce866a994487d14cae2bbf5e5fff3e preDigest
## 43: d799f879bf686af1fba8aea59b51953f format
## 44: d799f879bf686af1fba8aea59b51953f name
## 45: d799f879bf686af1fba8aea59b51953f class
## 46: d799f879bf686af1fba8aea59b51953f date
## 47: d799f879bf686af1fba8aea59b51953f cacheId
## 48: d799f879bf686af1fba8aea59b51953f innerTag
## 49: d799f879bf686af1fba8aea59b51953f outerTag
## 50: d799f879bf686af1fba8aea59b51953f function
## 51: d799f879bf686af1fba8aea59b51953f object.size
## 52: d799f879bf686af1fba8aea59b51953f accessed
## 53: d799f879bf686af1fba8aea59b51953f otherFunctions
## 54: d799f879bf686af1fba8aea59b51953f otherFunctions
## 55: d799f879bf686af1fba8aea59b51953f otherFunctions
## 56: d799f879bf686af1fba8aea59b51953f otherFunctions
## 57: d799f879bf686af1fba8aea59b51953f otherFunctions
## 58: d799f879bf686af1fba8aea59b51953f otherFunctions
## 59: d799f879bf686af1fba8aea59b51953f otherFunctions
## 60: d799f879bf686af1fba8aea59b51953f otherFunctions
## 61: d799f879bf686af1fba8aea59b51953f otherFunctions
## 62: d799f879bf686af1fba8aea59b51953f otherFunctions
## 63: d799f879bf686af1fba8aea59b51953f preDigest
## 64: d799f879bf686af1fba8aea59b51953f preDigest
## 65: d799f879bf686af1fba8aea59b51953f preDigest
## artifact tagKey
## tagValue createdDate
## 1: rda 2019-01-28 11:00:08
## 2: 55ca5ec58674d9e2119c6c41b84d2d46 2019-01-28 11:00:08
## 3: numeric 2019-01-28 11:00:08
## 4: 2019-01-28 11:00:08 2019-01-28 11:00:08
## 5: b06af03d5a73dc7d 2019-01-28 11:00:08
## 6: outerTag 2019-01-28 11:00:08
## 7: inner 2019-01-28 11:00:08
## 8: 1008 2019-01-28 11:00:08
## 9: 2019-01-28 11:00:08 2019-01-28 11:00:08
## 10: vweave_rmarkdown 2019-01-28 11:00:08
## 11: process_file 2019-01-28 11:00:08
## 12: process_group 2019-01-28 11:00:08
## 13: process_group.block 2019-01-28 11:00:08
## 14: call_block 2019-01-28 11:00:08
## 15: block_exec 2019-01-28 11:00:08
## 16: in_dir 2019-01-28 11:00:08
## 17: timing_fn 2019-01-28 11:00:08
## 18: handle 2019-01-28 11:00:08
## 19: withVisible 2019-01-28 11:00:08
## 20: mean:22413394efd9f6a3 2019-01-28 11:00:08
## 21: .FUN:7ad10bc1ae528d8c 2019-01-28 11:00:08
## 22: rda 2019-01-28 11:00:08
## 23: 8cce866a994487d14cae2bbf5e5fff3e 2019-01-28 11:00:08
## 24: numeric 2019-01-28 11:00:08
## 25: 2019-01-28 11:00:08 2019-01-28 11:00:08
## 26: 88a34e1d033329e5 2019-01-28 11:00:08
## 27: outerTag 2019-01-28 11:00:08
## 28: outer 2019-01-28 11:00:08
## 29: 1008 2019-01-28 11:00:08
## 30: 2019-01-28 11:00:08 2019-01-28 11:00:08
## 31: vweave_rmarkdown 2019-01-28 11:00:08
## 32: process_file 2019-01-28 11:00:08
## 33: process_group 2019-01-28 11:00:08
## 34: process_group.block 2019-01-28 11:00:08
## 35: call_block 2019-01-28 11:00:08
## 36: block_exec 2019-01-28 11:00:08
## 37: in_dir 2019-01-28 11:00:08
## 38: timing_fn 2019-01-28 11:00:08
## 39: handle 2019-01-28 11:00:08
## 40: withVisible 2019-01-28 11:00:08
## 41: n:82dc709f2b91918a 2019-01-28 11:00:08
## 42: .FUN:5f06fb5fbffe9e3b 2019-01-28 11:00:08
## 43: rda 2019-01-28 11:00:08
## 44: d799f879bf686af1fba8aea59b51953f 2019-01-28 11:00:08
## 45: numeric 2019-01-28 11:00:08
## 46: 2019-01-28 11:00:08 2019-01-28 11:00:08
## 47: 4ac2b7c0f42d1e46 2019-01-28 11:00:08
## 48: innerTag 2019-01-28 11:00:08
## 49: outerTag 2019-01-28 11:00:08
## 50: rnorm 2019-01-28 11:00:08
## 51: 1008 2019-01-28 11:00:08
## 52: 2019-01-28 11:00:08 2019-01-28 11:00:08
## 53: vweave_rmarkdown 2019-01-28 11:00:08
## 54: process_file 2019-01-28 11:00:08
## 55: process_group 2019-01-28 11:00:08
## 56: process_group.block 2019-01-28 11:00:08
## 57: call_block 2019-01-28 11:00:08
## 58: block_exec 2019-01-28 11:00:08
## 59: in_dir 2019-01-28 11:00:08
## 60: timing_fn 2019-01-28 11:00:08
## 61: handle 2019-01-28 11:00:08
## 62: withVisible 2019-01-28 11:00:08
## 63: n:7f12988bd88a0fb8 2019-01-28 11:00:08
## 64: mean:22413394efd9f6a3 2019-01-28 11:00:08
## 65: .FUN:4f604aa46882b368 2019-01-28 11:00:08
## tagValue createdDate
Sometimes, it is not absolutely desirable to maintain the work flow intact because changes that are irrelevant to the analysis, such as changing messages sent to a user, may be changed, without a desire to rerun functions. The cacheId
argument is for this. Once a piece of code is run, then the cacheId
can be manually extracted (it is reported at the end of a Cache call) and manually placed in the code, passed in as, say, cacheId = "ad184ce64541972b50afd8e7b75f821b"
.
### cacheId
set.seed(1)
Cache(rnorm, 1, cacheRepo = tmpdir1)
## [1] -0.6264538
## attr(,".Cache")
## attr(,".Cache")$newCache
## [1] TRUE
##
## attr(,"tags")
## [1] "cacheId:7072c305d8c69df0"
## attr(,"call")
## [1] ""
# manually look at output attribute which shows cacheId: ad184ce64541972b50afd8e7b75f821b
Cache(rnorm, 1, cacheRepo = tmpdir1, cacheId = "ad184ce64541972b50afd8e7b75f821b") # same value
## cacheId is not same as calculated hash. Manually searching for cacheId:ad184ce64541972b50afd8e7b75f821b
## [1] 0.1836433
## attr(,".Cache")
## attr(,".Cache")$newCache
## [1] TRUE
##
## attr(,"tags")
## [1] "cacheId:ad184ce64541972b50afd8e7b75f821b"
## attr(,"call")
## [1] ""
# override even with different inputs:
Cache(rnorm, 2, cacheRepo = tmpdir1, cacheId = "ad184ce64541972b50afd8e7b75f821b")
## cacheId is not same as calculated hash. Manually searching for cacheId:ad184ce64541972b50afd8e7b75f821b
## loading cached result from previous rnorm call, adding to memoised copy
## [1] 0.1836433
## attr(,".Cache")
## attr(,".Cache")$newCache
## [1] FALSE
##
## attr(,"tags")
## [1] "cacheId:ad184ce64541972b50afd8e7b75f821b"
## attr(,"call")
## [1] ""
## cleanup
unlink(c("filename.rda", "filename1.rda"))
Since the cache is simply an archivist
repository, all archivist
functions will work as is. In addition, there are several helpers in the reproducible
package, including showCache
, keepCache
and clearCache
that may be useful. Also, one can access cached items manually (rather than simply rerunning the same Cache
function again).
if (requireNamespace("archivist")) {
# get the RasterLayer that was produced with the gaussMap function:
mapHash <- unique(showCache(tmpDir, userTags = "projectRaster")$artifact)
map <- archivist::loadFromLocalRepo(md5hash = mapHash[1], repoDir = tmpDir, value = TRUE)
plot(map)
}
## Cache size:
## Total (including Rasters): 3.3 Kb
## Selected objects (not including Rasters): 3.3 Kb
## cleanup
unlink(dirname(tmpDir), recursive = TRUE)
In general, we feel that a liberal use of Cache
will make a re-usable 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.
Cache(<functionName>, <other arguments>)
This will allow fine scale control of individual function calls.