Introduction to Cache

Eliot J. B. McIntire

August 07 2018

1 Reproducible workflow

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.

1.1 Differences with other approaches

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; however, it also uses fastdigest::fastdigest to make it substantially faster in many cases. 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.

1.2 Function-level caching

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/RtmpUaFvn0/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 
##   2.220   0.143   2.366
# 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 
##   2.474   0.144   2.743
# 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 
##   0.113   0.000   0.113
# 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 
##   0.037   0.005   0.042
all.equal(map1, map2) # TRUE
## [1] TRUE
all.equal(map1, map3) # TRUE
## [1] TRUE

1.3 Caching examples

1.3.1 Basic use

library(raster)
# magrittr, if loaded, gives an error below
  try(detach("package:magrittr", unload = TRUE), silent = TRUE)

try(clearCache(tmpDir), silent = TRUE) # just to make sure it is clear
## Cache size:
##   Total (including Rasters): 1.9 Mb
##   Selected objects (not including Rasters): 1.9 Mb
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 <- rnorm(10, 16) %>% Cache(cacheRepo = tmpDir) # 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 <- rnorm(10, 6) %>% Cache(cacheRepo = tmpDir) # different

1.4 Example 1: Basic cache use with tags

ranNumsA <- Cache(rnorm, 4, cacheRepo = tmpDir, userTags = "objectName:a")
ranNumsB <- Cache(runif, 4, cacheRepo = tmpDir, userTags = "objectName:b")

showCache(tmpDir, userTags = c("objectName"))
## Cache size:
##   Total (including Rasters): 1000 bytes
##   Selected objects (not including Rasters): 476 bytes
##                             artifact         tagKey
##  1: 938deef22a8e88822aca17080dc762de         format
##  2: 938deef22a8e88822aca17080dc762de           name
##  3: 938deef22a8e88822aca17080dc762de          class
##  4: 938deef22a8e88822aca17080dc762de           date
##  5: 938deef22a8e88822aca17080dc762de        cacheId
##  6: 938deef22a8e88822aca17080dc762de     objectName
##  7: 938deef22a8e88822aca17080dc762de       function
##  8: 938deef22a8e88822aca17080dc762de    object.size
##  9: 938deef22a8e88822aca17080dc762de       accessed
## 10: 938deef22a8e88822aca17080dc762de otherFunctions
## 11: 938deef22a8e88822aca17080dc762de otherFunctions
## 12: 938deef22a8e88822aca17080dc762de otherFunctions
## 13: 938deef22a8e88822aca17080dc762de otherFunctions
## 14: 938deef22a8e88822aca17080dc762de otherFunctions
## 15: 938deef22a8e88822aca17080dc762de      preDigest
## 16: 938deef22a8e88822aca17080dc762de      preDigest
## 17: ab21c48380f08a4e9f4f399caa630da8         format
## 18: ab21c48380f08a4e9f4f399caa630da8           name
## 19: ab21c48380f08a4e9f4f399caa630da8          class
## 20: ab21c48380f08a4e9f4f399caa630da8           date
## 21: ab21c48380f08a4e9f4f399caa630da8        cacheId
## 22: ab21c48380f08a4e9f4f399caa630da8     objectName
## 23: ab21c48380f08a4e9f4f399caa630da8       function
## 24: ab21c48380f08a4e9f4f399caa630da8    object.size
## 25: ab21c48380f08a4e9f4f399caa630da8       accessed
## 26: ab21c48380f08a4e9f4f399caa630da8 otherFunctions
## 27: ab21c48380f08a4e9f4f399caa630da8 otherFunctions
## 28: ab21c48380f08a4e9f4f399caa630da8 otherFunctions
## 29: ab21c48380f08a4e9f4f399caa630da8 otherFunctions
## 30: ab21c48380f08a4e9f4f399caa630da8 otherFunctions
## 31: ab21c48380f08a4e9f4f399caa630da8      preDigest
## 32: ab21c48380f08a4e9f4f399caa630da8      preDigest
##                             artifact         tagKey
##                                  tagValue         createdDate
##  1:                                   rda 2018-08-07 11:05:59
##  2:      938deef22a8e88822aca17080dc762de 2018-08-07 11:05:59
##  3:                               numeric 2018-08-07 11:05:59
##  4:                   2018-08-07 11:05:59 2018-08-07 11:05:59
##  5:      85874f26b2e0c1ef689a7d379d275ebf 2018-08-07 11:05:59
##  6:                                     a 2018-08-07 11:05:59
##  7:                                 rnorm 2018-08-07 11:05:59
##  8:                                   952 2018-08-07 11:05:59
##  9:                   2018-08-07 11:05:59 2018-08-07 11:05:59
## 10:                          process_file 2018-08-07 11:05:59
## 11:                         process_group 2018-08-07 11:05:59
## 12:                   process_group.block 2018-08-07 11:05:59
## 13:                            call_block 2018-08-07 11:05:59
## 14:                            block_exec 2018-08-07 11:05:59
## 15:    n:969a49ec15bcd4323ff31538af321264 2018-08-07 11:05:59
## 16: .FUN:7e9a928f110f80b3612e71883a6ec1f4 2018-08-07 11:05:59
## 17:                                   rda 2018-08-07 11:05:59
## 18:      ab21c48380f08a4e9f4f399caa630da8 2018-08-07 11:05:59
## 19:                               numeric 2018-08-07 11:05:59
## 20:                   2018-08-07 11:05:59 2018-08-07 11:05:59
## 21:      e37bb635c97bc2eeecab63816b881bbc 2018-08-07 11:05:59
## 22:                                     b 2018-08-07 11:05:59
## 23:                                 runif 2018-08-07 11:05:59
## 24:                                   952 2018-08-07 11:05:59
## 25:                   2018-08-07 11:05:59 2018-08-07 11:05:59
## 26:                          process_file 2018-08-07 11:05:59
## 27:                         process_group 2018-08-07 11:05:59
## 28:                   process_group.block 2018-08-07 11:05:59
## 29:                            call_block 2018-08-07 11:05:59
## 30:                            block_exec 2018-08-07 11:05:59
## 31:    n:969a49ec15bcd4323ff31538af321264 2018-08-07 11:05:59
## 32: .FUN:d2631d24c3b38b89c7bdd4ab7faaaac3 2018-08-07 11:05:59
##                                  tagValue         createdDate
showCache(tmpDir, userTags = c("^a$")) # regular expression ... "a" exactly
## Cache size:
##   Total (including Rasters): 1000 bytes
##   Selected objects (not including Rasters): 238 bytes
##                             artifact         tagKey
##  1: 938deef22a8e88822aca17080dc762de         format
##  2: 938deef22a8e88822aca17080dc762de           name
##  3: 938deef22a8e88822aca17080dc762de          class
##  4: 938deef22a8e88822aca17080dc762de           date
##  5: 938deef22a8e88822aca17080dc762de        cacheId
##  6: 938deef22a8e88822aca17080dc762de     objectName
##  7: 938deef22a8e88822aca17080dc762de       function
##  8: 938deef22a8e88822aca17080dc762de    object.size
##  9: 938deef22a8e88822aca17080dc762de       accessed
## 10: 938deef22a8e88822aca17080dc762de otherFunctions
## 11: 938deef22a8e88822aca17080dc762de otherFunctions
## 12: 938deef22a8e88822aca17080dc762de otherFunctions
## 13: 938deef22a8e88822aca17080dc762de otherFunctions
## 14: 938deef22a8e88822aca17080dc762de otherFunctions
## 15: 938deef22a8e88822aca17080dc762de      preDigest
## 16: 938deef22a8e88822aca17080dc762de      preDigest
##                                  tagValue         createdDate
##  1:                                   rda 2018-08-07 11:05:59
##  2:      938deef22a8e88822aca17080dc762de 2018-08-07 11:05:59
##  3:                               numeric 2018-08-07 11:05:59
##  4:                   2018-08-07 11:05:59 2018-08-07 11:05:59
##  5:      85874f26b2e0c1ef689a7d379d275ebf 2018-08-07 11:05:59
##  6:                                     a 2018-08-07 11:05:59
##  7:                                 rnorm 2018-08-07 11:05:59
##  8:                                   952 2018-08-07 11:05:59
##  9:                   2018-08-07 11:05:59 2018-08-07 11:05:59
## 10:                          process_file 2018-08-07 11:05:59
## 11:                         process_group 2018-08-07 11:05:59
## 12:                   process_group.block 2018-08-07 11:05:59
## 13:                            call_block 2018-08-07 11:05:59
## 14:                            block_exec 2018-08-07 11:05:59
## 15:    n:969a49ec15bcd4323ff31538af321264 2018-08-07 11:05:59
## 16: .FUN:7e9a928f110f80b3612e71883a6ec1f4 2018-08-07 11:05:59
showCache(tmpDir, userTags = c("runif")) # show only cached objects made during runif call
## Cache size:
##   Total (including Rasters): 1000 bytes
##   Selected objects (not including Rasters): 238 bytes
##                             artifact         tagKey
##  1: ab21c48380f08a4e9f4f399caa630da8         format
##  2: ab21c48380f08a4e9f4f399caa630da8           name
##  3: ab21c48380f08a4e9f4f399caa630da8          class
##  4: ab21c48380f08a4e9f4f399caa630da8           date
##  5: ab21c48380f08a4e9f4f399caa630da8        cacheId
##  6: ab21c48380f08a4e9f4f399caa630da8     objectName
##  7: ab21c48380f08a4e9f4f399caa630da8       function
##  8: ab21c48380f08a4e9f4f399caa630da8    object.size
##  9: ab21c48380f08a4e9f4f399caa630da8       accessed
## 10: ab21c48380f08a4e9f4f399caa630da8 otherFunctions
## 11: ab21c48380f08a4e9f4f399caa630da8 otherFunctions
## 12: ab21c48380f08a4e9f4f399caa630da8 otherFunctions
## 13: ab21c48380f08a4e9f4f399caa630da8 otherFunctions
## 14: ab21c48380f08a4e9f4f399caa630da8 otherFunctions
## 15: ab21c48380f08a4e9f4f399caa630da8      preDigest
## 16: ab21c48380f08a4e9f4f399caa630da8      preDigest
##                                  tagValue         createdDate
##  1:                                   rda 2018-08-07 11:05:59
##  2:      ab21c48380f08a4e9f4f399caa630da8 2018-08-07 11:05:59
##  3:                               numeric 2018-08-07 11:05:59
##  4:                   2018-08-07 11:05:59 2018-08-07 11:05:59
##  5:      e37bb635c97bc2eeecab63816b881bbc 2018-08-07 11:05:59
##  6:                                     b 2018-08-07 11:05:59
##  7:                                 runif 2018-08-07 11:05:59
##  8:                                   952 2018-08-07 11:05:59
##  9:                   2018-08-07 11:05:59 2018-08-07 11:05:59
## 10:                          process_file 2018-08-07 11:05:59
## 11:                         process_group 2018-08-07 11:05:59
## 12:                   process_group.block 2018-08-07 11:05:59
## 13:                            call_block 2018-08-07 11:05:59
## 14:                            block_exec 2018-08-07 11:05:59
## 15:    n:969a49ec15bcd4323ff31538af321264 2018-08-07 11:05:59
## 16: .FUN:d2631d24c3b38b89c7bdd4ab7faaaac3 2018-08-07 11:05:59
clearCache(tmpDir, userTags = c("runif")) # remove only cached objects made during runif call
## Cache size:
##   Total (including Rasters): 1000 bytes
##   Selected objects (not including Rasters): 238 bytes
showCache(tmpDir) # only those made during rnorm call
## Cache size:
##   Total (including Rasters): 762 bytes
##   Selected objects (not including Rasters): 762 bytes
##                             artifact         tagKey
##  1: 09a1d11b79d46e10c07d5fd6504ac60f         format
##  2: 09a1d11b79d46e10c07d5fd6504ac60f           name
##  3: 09a1d11b79d46e10c07d5fd6504ac60f          class
##  4: 09a1d11b79d46e10c07d5fd6504ac60f           date
##  5: 09a1d11b79d46e10c07d5fd6504ac60f        cacheId
##  6: 09a1d11b79d46e10c07d5fd6504ac60f       function
##  7: 09a1d11b79d46e10c07d5fd6504ac60f    object.size
##  8: 09a1d11b79d46e10c07d5fd6504ac60f       accessed
##  9: 09a1d11b79d46e10c07d5fd6504ac60f otherFunctions
## 10: 09a1d11b79d46e10c07d5fd6504ac60f otherFunctions
## 11: 09a1d11b79d46e10c07d5fd6504ac60f otherFunctions
## 12: 09a1d11b79d46e10c07d5fd6504ac60f otherFunctions
## 13: 09a1d11b79d46e10c07d5fd6504ac60f otherFunctions
## 14: 09a1d11b79d46e10c07d5fd6504ac60f      preDigest
## 15: 09a1d11b79d46e10c07d5fd6504ac60f      preDigest
## 16: 09a1d11b79d46e10c07d5fd6504ac60f      preDigest
## 17: 938deef22a8e88822aca17080dc762de         format
## 18: 938deef22a8e88822aca17080dc762de           name
## 19: 938deef22a8e88822aca17080dc762de          class
## 20: 938deef22a8e88822aca17080dc762de           date
## 21: 938deef22a8e88822aca17080dc762de        cacheId
## 22: 938deef22a8e88822aca17080dc762de     objectName
## 23: 938deef22a8e88822aca17080dc762de       function
## 24: 938deef22a8e88822aca17080dc762de    object.size
## 25: 938deef22a8e88822aca17080dc762de       accessed
## 26: 938deef22a8e88822aca17080dc762de otherFunctions
## 27: 938deef22a8e88822aca17080dc762de otherFunctions
## 28: 938deef22a8e88822aca17080dc762de otherFunctions
## 29: 938deef22a8e88822aca17080dc762de otherFunctions
## 30: 938deef22a8e88822aca17080dc762de otherFunctions
## 31: 938deef22a8e88822aca17080dc762de      preDigest
## 32: 938deef22a8e88822aca17080dc762de      preDigest
## 33: fbd196237f45aab26be0556be7d5ed26         format
## 34: fbd196237f45aab26be0556be7d5ed26           name
## 35: fbd196237f45aab26be0556be7d5ed26          class
## 36: fbd196237f45aab26be0556be7d5ed26           date
## 37: fbd196237f45aab26be0556be7d5ed26        cacheId
## 38: fbd196237f45aab26be0556be7d5ed26       function
## 39: fbd196237f45aab26be0556be7d5ed26    object.size
## 40: fbd196237f45aab26be0556be7d5ed26       accessed
## 41: fbd196237f45aab26be0556be7d5ed26 otherFunctions
## 42: fbd196237f45aab26be0556be7d5ed26 otherFunctions
## 43: fbd196237f45aab26be0556be7d5ed26 otherFunctions
## 44: fbd196237f45aab26be0556be7d5ed26 otherFunctions
## 45: fbd196237f45aab26be0556be7d5ed26 otherFunctions
## 46: fbd196237f45aab26be0556be7d5ed26      preDigest
## 47: fbd196237f45aab26be0556be7d5ed26      preDigest
## 48: fbd196237f45aab26be0556be7d5ed26      preDigest
## 49: fbd196237f45aab26be0556be7d5ed26       accessed
## 50: fbd196237f45aab26be0556be7d5ed26       accessed
## 51: fbd196237f45aab26be0556be7d5ed26       accessed
##                             artifact         tagKey
##                                  tagValue         createdDate
##  1:                                   rda 2018-08-07 11:05:59
##  2:      09a1d11b79d46e10c07d5fd6504ac60f 2018-08-07 11:05:59
##  3:                               numeric 2018-08-07 11:05:59
##  4:                   2018-08-07 11:05:59 2018-08-07 11:05:59
##  5:      778e2e6b9a967175d1f08811a995269d 2018-08-07 11:05:59
##  6:                   rnorm pipe sequence 2018-08-07 11:05:59
##  7:                                  1048 2018-08-07 11:05:59
##  8:                   2018-08-07 11:05:59 2018-08-07 11:05:59
##  9:                          process_file 2018-08-07 11:05:59
## 10:                         process_group 2018-08-07 11:05:59
## 11:                   process_group.block 2018-08-07 11:05:59
## 12:                            call_block 2018-08-07 11:05:59
## 13:                            block_exec 2018-08-07 11:05:59
## 14:    n:52ad08b1270ae9be9c0a12805d408433 2018-08-07 11:05:59
## 15: mean:6f529546a7c8cf6edda6081007b3d58d 2018-08-07 11:05:59
## 16: .FUN:7e9a928f110f80b3612e71883a6ec1f4 2018-08-07 11:05:59
## 17:                                   rda 2018-08-07 11:05:59
## 18:      938deef22a8e88822aca17080dc762de 2018-08-07 11:05:59
## 19:                               numeric 2018-08-07 11:05:59
## 20:                   2018-08-07 11:05:59 2018-08-07 11:05:59
## 21:      85874f26b2e0c1ef689a7d379d275ebf 2018-08-07 11:05:59
## 22:                                     a 2018-08-07 11:05:59
## 23:                                 rnorm 2018-08-07 11:05:59
## 24:                                   952 2018-08-07 11:05:59
## 25:                   2018-08-07 11:05:59 2018-08-07 11:05:59
## 26:                          process_file 2018-08-07 11:05:59
## 27:                         process_group 2018-08-07 11:05:59
## 28:                   process_group.block 2018-08-07 11:05:59
## 29:                            call_block 2018-08-07 11:05:59
## 30:                            block_exec 2018-08-07 11:05:59
## 31:    n:969a49ec15bcd4323ff31538af321264 2018-08-07 11:05:59
## 32: .FUN:7e9a928f110f80b3612e71883a6ec1f4 2018-08-07 11:05:59
## 33:                                   rda 2018-08-07 11:05:58
## 34:      fbd196237f45aab26be0556be7d5ed26 2018-08-07 11:05:58
## 35:                               numeric 2018-08-07 11:05:58
## 36:                   2018-08-07 11:05:58 2018-08-07 11:05:58
## 37:      f185e4f8cea576a595f7b81be17e63b5 2018-08-07 11:05:58
## 38:                                 rnorm 2018-08-07 11:05:58
## 39:                                  1048 2018-08-07 11:05:58
## 40:                   2018-08-07 11:05:58 2018-08-07 11:05:58
## 41:                          process_file 2018-08-07 11:05:58
## 42:                         process_group 2018-08-07 11:05:58
## 43:                   process_group.block 2018-08-07 11:05:58
## 44:                            call_block 2018-08-07 11:05:58
## 45:                            block_exec 2018-08-07 11:05:58
## 46:    n:52ad08b1270ae9be9c0a12805d408433 2018-08-07 11:05:58
## 47: mean:2c67b8e97ab3ea8d032fea4318223887 2018-08-07 11:05:58
## 48: .FUN:7e9a928f110f80b3612e71883a6ec1f4 2018-08-07 11:05:58
## 49:                   2018-08-07 11:05:59 2018-08-07 11:05:59
## 50:                   2018-08-07 11:05:59 2018-08-07 11:05:59
## 51:                   2018-08-07 11:05:59 2018-08-07 11:05:59
##                                  tagValue         createdDate
clearCache(tmpDir)
## Cache size:
##   Total (including Rasters): 762 bytes
##   Selected objects (not including Rasters): 762 bytes

1.5 Example 2: using the “accessed” tag

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): 476 bytes
##   Selected objects (not including Rasters): 476 bytes
# keep only items accessed "recently" (i.e., only objectName:a)
onlyRecentlyAccessed <- showCache(tmpDir, userTags = max(wholeCache[tagKey == "accessed"]$tagValue))
## Cache size:
##   Total (including Rasters): 476 bytes
##   Selected objects (not including Rasters): 476 bytes
# inverse join with 2 data.tables ... using: a[!b]
# i.e., return all of wholeCache that was not recently accessed
toRemove <- unique(wholeCache[!onlyRecentlyAccessed], by = "artifact")$artifact
clearCache(tmpDir, toRemove) # remove ones not recently accessed
## Cache size:
##   Total (including Rasters): 476 bytes
##   Selected objects (not including Rasters): 476 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)
## Cache size:
##   Total (including Rasters): 0 bytes
##   Selected objects (not including Rasters): 0 bytes

1.6 Example 3: using keepCache

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)
## Cache size:
##   Total (including Rasters): 476 bytes
##   Selected objects (not including Rasters): 476 bytes
##                             artifact         tagKey
##  1: 129c4fbd611bb1c66a677fa2e8f6e860         format
##  2: 129c4fbd611bb1c66a677fa2e8f6e860           name
##  3: 129c4fbd611bb1c66a677fa2e8f6e860          class
##  4: 129c4fbd611bb1c66a677fa2e8f6e860           date
##  5: 129c4fbd611bb1c66a677fa2e8f6e860        cacheId
##  6: 129c4fbd611bb1c66a677fa2e8f6e860     objectName
##  7: 129c4fbd611bb1c66a677fa2e8f6e860       function
##  8: 129c4fbd611bb1c66a677fa2e8f6e860    object.size
##  9: 129c4fbd611bb1c66a677fa2e8f6e860       accessed
## 10: 129c4fbd611bb1c66a677fa2e8f6e860 otherFunctions
## 11: 129c4fbd611bb1c66a677fa2e8f6e860 otherFunctions
## 12: 129c4fbd611bb1c66a677fa2e8f6e860 otherFunctions
## 13: 129c4fbd611bb1c66a677fa2e8f6e860 otherFunctions
## 14: 129c4fbd611bb1c66a677fa2e8f6e860 otherFunctions
## 15: 129c4fbd611bb1c66a677fa2e8f6e860      preDigest
## 16: 129c4fbd611bb1c66a677fa2e8f6e860      preDigest
## 17: b25cd11467694fc736ec444b8c25c187         format
## 18: b25cd11467694fc736ec444b8c25c187           name
## 19: b25cd11467694fc736ec444b8c25c187          class
## 20: b25cd11467694fc736ec444b8c25c187           date
## 21: b25cd11467694fc736ec444b8c25c187        cacheId
## 22: b25cd11467694fc736ec444b8c25c187     objectName
## 23: b25cd11467694fc736ec444b8c25c187       function
## 24: b25cd11467694fc736ec444b8c25c187    object.size
## 25: b25cd11467694fc736ec444b8c25c187       accessed
## 26: b25cd11467694fc736ec444b8c25c187 otherFunctions
## 27: b25cd11467694fc736ec444b8c25c187 otherFunctions
## 28: b25cd11467694fc736ec444b8c25c187 otherFunctions
## 29: b25cd11467694fc736ec444b8c25c187 otherFunctions
## 30: b25cd11467694fc736ec444b8c25c187 otherFunctions
## 31: b25cd11467694fc736ec444b8c25c187      preDigest
## 32: b25cd11467694fc736ec444b8c25c187      preDigest
##                             artifact         tagKey
##                                  tagValue         createdDate
##  1:                                   rda 2018-08-07 11:05:59
##  2:      129c4fbd611bb1c66a677fa2e8f6e860 2018-08-07 11:05:59
##  3:                               numeric 2018-08-07 11:05:59
##  4:                   2018-08-07 11:05:59 2018-08-07 11:05:59
##  5:      e37bb635c97bc2eeecab63816b881bbc 2018-08-07 11:05:59
##  6:                                     b 2018-08-07 11:05:59
##  7:                                 runif 2018-08-07 11:05:59
##  8:                                   952 2018-08-07 11:05:59
##  9:                   2018-08-07 11:05:59 2018-08-07 11:05:59
## 10:                          process_file 2018-08-07 11:05:59
## 11:                         process_group 2018-08-07 11:05:59
## 12:                   process_group.block 2018-08-07 11:05:59
## 13:                            call_block 2018-08-07 11:05:59
## 14:                            block_exec 2018-08-07 11:05:59
## 15:    n:969a49ec15bcd4323ff31538af321264 2018-08-07 11:05:59
## 16: .FUN:d2631d24c3b38b89c7bdd4ab7faaaac3 2018-08-07 11:05:59
## 17:                                   rda 2018-08-07 11:05:59
## 18:      b25cd11467694fc736ec444b8c25c187 2018-08-07 11:05:59
## 19:                               numeric 2018-08-07 11:05:59
## 20:                   2018-08-07 11:05:59 2018-08-07 11:05:59
## 21:      85874f26b2e0c1ef689a7d379d275ebf 2018-08-07 11:05:59
## 22:                                     a 2018-08-07 11:05:59
## 23:                                 rnorm 2018-08-07 11:05:59
## 24:                                   952 2018-08-07 11:05:59
## 25:                   2018-08-07 11:05:59 2018-08-07 11:05:59
## 26:                          process_file 2018-08-07 11:05:59
## 27:                         process_group 2018-08-07 11:05:59
## 28:                   process_group.block 2018-08-07 11:05:59
## 29:                            call_block 2018-08-07 11:05:59
## 30:                            block_exec 2018-08-07 11:05:59
## 31:    n:969a49ec15bcd4323ff31538af321264 2018-08-07 11:05:59
## 32: .FUN:7e9a928f110f80b3612e71883a6ec1f4 2018-08-07 11:05:59
##                                  tagValue         createdDate
# Keep all Cache items created with an rnorm() call
keepCache(tmpDir, userTags = "rnorm")
## Cache size:
##   Total (including Rasters): 476 bytes
##   Selected objects (not including Rasters): 238 bytes
##                             artifact         tagKey
##  1: b25cd11467694fc736ec444b8c25c187         format
##  2: b25cd11467694fc736ec444b8c25c187           name
##  3: b25cd11467694fc736ec444b8c25c187          class
##  4: b25cd11467694fc736ec444b8c25c187           date
##  5: b25cd11467694fc736ec444b8c25c187        cacheId
##  6: b25cd11467694fc736ec444b8c25c187     objectName
##  7: b25cd11467694fc736ec444b8c25c187       function
##  8: b25cd11467694fc736ec444b8c25c187    object.size
##  9: b25cd11467694fc736ec444b8c25c187       accessed
## 10: b25cd11467694fc736ec444b8c25c187 otherFunctions
## 11: b25cd11467694fc736ec444b8c25c187 otherFunctions
## 12: b25cd11467694fc736ec444b8c25c187 otherFunctions
## 13: b25cd11467694fc736ec444b8c25c187 otherFunctions
## 14: b25cd11467694fc736ec444b8c25c187 otherFunctions
## 15: b25cd11467694fc736ec444b8c25c187      preDigest
## 16: b25cd11467694fc736ec444b8c25c187      preDigest
##                                  tagValue         createdDate
##  1:                                   rda 2018-08-07 11:05:59
##  2:      b25cd11467694fc736ec444b8c25c187 2018-08-07 11:05:59
##  3:                               numeric 2018-08-07 11:05:59
##  4:                   2018-08-07 11:05:59 2018-08-07 11:05:59
##  5:      85874f26b2e0c1ef689a7d379d275ebf 2018-08-07 11:05:59
##  6:                                     a 2018-08-07 11:05:59
##  7:                                 rnorm 2018-08-07 11:05:59
##  8:                                   952 2018-08-07 11:05:59
##  9:                   2018-08-07 11:05:59 2018-08-07 11:05:59
## 10:                          process_file 2018-08-07 11:05:59
## 11:                         process_group 2018-08-07 11:05:59
## 12:                   process_group.block 2018-08-07 11:05:59
## 13:                            call_block 2018-08-07 11:05:59
## 14:                            block_exec 2018-08-07 11:05:59
## 15:    n:969a49ec15bcd4323ff31538af321264 2018-08-07 11:05:59
## 16: .FUN:7e9a928f110f80b3612e71883a6ec1f4 2018-08-07 11:05:59
# Remove all Cache items that happened within a rnorm() call
clearCache(tmpDir, userTags = "rnorm")
## Cache size:
##   Total (including Rasters): 238 bytes
##   Selected objects (not including Rasters): 238 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

1.7 Example 4: searching for multiple objects in the cache

# 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): 476 bytes
##   Selected objects (not including Rasters): 476 bytes
##                             artifact         tagKey
##  1: a12547f9875d9c1eed262d32532d4e9e         format
##  2: a12547f9875d9c1eed262d32532d4e9e           name
##  3: a12547f9875d9c1eed262d32532d4e9e          class
##  4: a12547f9875d9c1eed262d32532d4e9e           date
##  5: a12547f9875d9c1eed262d32532d4e9e        cacheId
##  6: a12547f9875d9c1eed262d32532d4e9e     objectName
##  7: a12547f9875d9c1eed262d32532d4e9e       function
##  8: a12547f9875d9c1eed262d32532d4e9e    object.size
##  9: a12547f9875d9c1eed262d32532d4e9e       accessed
## 10: a12547f9875d9c1eed262d32532d4e9e otherFunctions
## 11: a12547f9875d9c1eed262d32532d4e9e otherFunctions
## 12: a12547f9875d9c1eed262d32532d4e9e otherFunctions
## 13: a12547f9875d9c1eed262d32532d4e9e otherFunctions
## 14: a12547f9875d9c1eed262d32532d4e9e otherFunctions
## 15: a12547f9875d9c1eed262d32532d4e9e      preDigest
## 16: a12547f9875d9c1eed262d32532d4e9e      preDigest
## 17: fbc518cef93ac0f40d8c3a7eac57207c         format
## 18: fbc518cef93ac0f40d8c3a7eac57207c           name
## 19: fbc518cef93ac0f40d8c3a7eac57207c          class
## 20: fbc518cef93ac0f40d8c3a7eac57207c           date
## 21: fbc518cef93ac0f40d8c3a7eac57207c        cacheId
## 22: fbc518cef93ac0f40d8c3a7eac57207c     objectName
## 23: fbc518cef93ac0f40d8c3a7eac57207c       function
## 24: fbc518cef93ac0f40d8c3a7eac57207c    object.size
## 25: fbc518cef93ac0f40d8c3a7eac57207c       accessed
## 26: fbc518cef93ac0f40d8c3a7eac57207c otherFunctions
## 27: fbc518cef93ac0f40d8c3a7eac57207c otherFunctions
## 28: fbc518cef93ac0f40d8c3a7eac57207c otherFunctions
## 29: fbc518cef93ac0f40d8c3a7eac57207c otherFunctions
## 30: fbc518cef93ac0f40d8c3a7eac57207c otherFunctions
## 31: fbc518cef93ac0f40d8c3a7eac57207c      preDigest
## 32: fbc518cef93ac0f40d8c3a7eac57207c      preDigest
##                             artifact         tagKey
##                                  tagValue         createdDate
##  1:                                   rda 2018-08-07 11:06:00
##  2:      a12547f9875d9c1eed262d32532d4e9e 2018-08-07 11:06:00
##  3:                               numeric 2018-08-07 11:06:00
##  4:                   2018-08-07 11:06:00 2018-08-07 11:06:00
##  5:      e37bb635c97bc2eeecab63816b881bbc 2018-08-07 11:06:00
##  6:                                     a 2018-08-07 11:06:00
##  7:                                 runif 2018-08-07 11:06:00
##  8:                                   952 2018-08-07 11:06:00
##  9:                   2018-08-07 11:06:00 2018-08-07 11:06:00
## 10:                          process_file 2018-08-07 11:06:00
## 11:                         process_group 2018-08-07 11:06:00
## 12:                   process_group.block 2018-08-07 11:06:00
## 13:                            call_block 2018-08-07 11:06:00
## 14:                            block_exec 2018-08-07 11:06:00
## 15:    n:969a49ec15bcd4323ff31538af321264 2018-08-07 11:06:00
## 16: .FUN:d2631d24c3b38b89c7bdd4ab7faaaac3 2018-08-07 11:06:00
## 17:                                   rda 2018-08-07 11:06:00
## 18:      fbc518cef93ac0f40d8c3a7eac57207c 2018-08-07 11:06:00
## 19:                               numeric 2018-08-07 11:06:00
## 20:                   2018-08-07 11:06:00 2018-08-07 11:06:00
## 21:      85874f26b2e0c1ef689a7d379d275ebf 2018-08-07 11:06:00
## 22:                                     b 2018-08-07 11:06:00
## 23:                                 rnorm 2018-08-07 11:06:00
## 24:                                   952 2018-08-07 11:06:00
## 25:                   2018-08-07 11:06:00 2018-08-07 11:06:00
## 26:                          process_file 2018-08-07 11:06:00
## 27:                         process_group 2018-08-07 11:06:00
## 28:                   process_group.block 2018-08-07 11:06:00
## 29:                            call_block 2018-08-07 11:06:00
## 30:                            block_exec 2018-08-07 11:06:00
## 31:    n:969a49ec15bcd4323ff31538af321264 2018-08-07 11:06:00
## 32: .FUN:7e9a928f110f80b3612e71883a6ec1f4 2018-08-07 11:06:00
##                                  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): 476 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): 476 bytes
##   Selected objects (not including Rasters): 476 bytes
##                             artifact         tagKey
##  1: a12547f9875d9c1eed262d32532d4e9e         format
##  2: a12547f9875d9c1eed262d32532d4e9e           name
##  3: a12547f9875d9c1eed262d32532d4e9e          class
##  4: a12547f9875d9c1eed262d32532d4e9e           date
##  5: a12547f9875d9c1eed262d32532d4e9e        cacheId
##  6: a12547f9875d9c1eed262d32532d4e9e     objectName
##  7: a12547f9875d9c1eed262d32532d4e9e       function
##  8: a12547f9875d9c1eed262d32532d4e9e    object.size
##  9: a12547f9875d9c1eed262d32532d4e9e       accessed
## 10: a12547f9875d9c1eed262d32532d4e9e otherFunctions
## 11: a12547f9875d9c1eed262d32532d4e9e otherFunctions
## 12: a12547f9875d9c1eed262d32532d4e9e otherFunctions
## 13: a12547f9875d9c1eed262d32532d4e9e otherFunctions
## 14: a12547f9875d9c1eed262d32532d4e9e otherFunctions
## 15: a12547f9875d9c1eed262d32532d4e9e      preDigest
## 16: a12547f9875d9c1eed262d32532d4e9e      preDigest
## 17: fbc518cef93ac0f40d8c3a7eac57207c         format
## 18: fbc518cef93ac0f40d8c3a7eac57207c           name
## 19: fbc518cef93ac0f40d8c3a7eac57207c          class
## 20: fbc518cef93ac0f40d8c3a7eac57207c           date
## 21: fbc518cef93ac0f40d8c3a7eac57207c        cacheId
## 22: fbc518cef93ac0f40d8c3a7eac57207c     objectName
## 23: fbc518cef93ac0f40d8c3a7eac57207c       function
## 24: fbc518cef93ac0f40d8c3a7eac57207c    object.size
## 25: fbc518cef93ac0f40d8c3a7eac57207c       accessed
## 26: fbc518cef93ac0f40d8c3a7eac57207c otherFunctions
## 27: fbc518cef93ac0f40d8c3a7eac57207c otherFunctions
## 28: fbc518cef93ac0f40d8c3a7eac57207c otherFunctions
## 29: fbc518cef93ac0f40d8c3a7eac57207c otherFunctions
## 30: fbc518cef93ac0f40d8c3a7eac57207c otherFunctions
## 31: fbc518cef93ac0f40d8c3a7eac57207c      preDigest
## 32: fbc518cef93ac0f40d8c3a7eac57207c      preDigest
##                             artifact         tagKey
##                                  tagValue         createdDate
##  1:                                   rda 2018-08-07 11:06:00
##  2:      a12547f9875d9c1eed262d32532d4e9e 2018-08-07 11:06:00
##  3:                               numeric 2018-08-07 11:06:00
##  4:                   2018-08-07 11:06:00 2018-08-07 11:06:00
##  5:      e37bb635c97bc2eeecab63816b881bbc 2018-08-07 11:06:00
##  6:                                     a 2018-08-07 11:06:00
##  7:                                 runif 2018-08-07 11:06:00
##  8:                                   952 2018-08-07 11:06:00
##  9:                   2018-08-07 11:06:00 2018-08-07 11:06:00
## 10:                          process_file 2018-08-07 11:06:00
## 11:                         process_group 2018-08-07 11:06:00
## 12:                   process_group.block 2018-08-07 11:06:00
## 13:                            call_block 2018-08-07 11:06:00
## 14:                            block_exec 2018-08-07 11:06:00
## 15:    n:969a49ec15bcd4323ff31538af321264 2018-08-07 11:06:00
## 16: .FUN:d2631d24c3b38b89c7bdd4ab7faaaac3 2018-08-07 11:06:00
## 17:                                   rda 2018-08-07 11:06:00
## 18:      fbc518cef93ac0f40d8c3a7eac57207c 2018-08-07 11:06:00
## 19:                               numeric 2018-08-07 11:06:00
## 20:                   2018-08-07 11:06:00 2018-08-07 11:06:00
## 21:      85874f26b2e0c1ef689a7d379d275ebf 2018-08-07 11:06:00
## 22:                                     b 2018-08-07 11:06:00
## 23:                                 rnorm 2018-08-07 11:06:00
## 24:                                   952 2018-08-07 11:06:00
## 25:                   2018-08-07 11:06:00 2018-08-07 11:06:00
## 26:                          process_file 2018-08-07 11:06:00
## 27:                         process_group 2018-08-07 11:06:00
## 28:                   process_group.block 2018-08-07 11:06:00
## 29:                            call_block 2018-08-07 11:06:00
## 30:                            block_exec 2018-08-07 11:06:00
## 31:    n:969a49ec15bcd4323ff31538af321264 2018-08-07 11:06:00
## 32: .FUN:7e9a928f110f80b3612e71883a6ec1f4 2018-08-07 11:06:00
##                                  tagValue         createdDate
# keep only objects that are either runif or rnorm ("or" search)
keepCache(tmpDir, userTags = "runif|rnorm")
## Cache size:
##   Total (including Rasters): 476 bytes
##   Selected objects (not including Rasters): 476 bytes
##                             artifact         tagKey
##  1: a12547f9875d9c1eed262d32532d4e9e         format
##  2: a12547f9875d9c1eed262d32532d4e9e           name
##  3: a12547f9875d9c1eed262d32532d4e9e          class
##  4: a12547f9875d9c1eed262d32532d4e9e           date
##  5: a12547f9875d9c1eed262d32532d4e9e        cacheId
##  6: a12547f9875d9c1eed262d32532d4e9e     objectName
##  7: a12547f9875d9c1eed262d32532d4e9e       function
##  8: a12547f9875d9c1eed262d32532d4e9e    object.size
##  9: a12547f9875d9c1eed262d32532d4e9e       accessed
## 10: a12547f9875d9c1eed262d32532d4e9e otherFunctions
## 11: a12547f9875d9c1eed262d32532d4e9e otherFunctions
## 12: a12547f9875d9c1eed262d32532d4e9e otherFunctions
## 13: a12547f9875d9c1eed262d32532d4e9e otherFunctions
## 14: a12547f9875d9c1eed262d32532d4e9e otherFunctions
## 15: a12547f9875d9c1eed262d32532d4e9e      preDigest
## 16: a12547f9875d9c1eed262d32532d4e9e      preDigest
## 17: fbc518cef93ac0f40d8c3a7eac57207c         format
## 18: fbc518cef93ac0f40d8c3a7eac57207c           name
## 19: fbc518cef93ac0f40d8c3a7eac57207c          class
## 20: fbc518cef93ac0f40d8c3a7eac57207c           date
## 21: fbc518cef93ac0f40d8c3a7eac57207c        cacheId
## 22: fbc518cef93ac0f40d8c3a7eac57207c     objectName
## 23: fbc518cef93ac0f40d8c3a7eac57207c       function
## 24: fbc518cef93ac0f40d8c3a7eac57207c    object.size
## 25: fbc518cef93ac0f40d8c3a7eac57207c       accessed
## 26: fbc518cef93ac0f40d8c3a7eac57207c otherFunctions
## 27: fbc518cef93ac0f40d8c3a7eac57207c otherFunctions
## 28: fbc518cef93ac0f40d8c3a7eac57207c otherFunctions
## 29: fbc518cef93ac0f40d8c3a7eac57207c otherFunctions
## 30: fbc518cef93ac0f40d8c3a7eac57207c otherFunctions
## 31: fbc518cef93ac0f40d8c3a7eac57207c      preDigest
## 32: fbc518cef93ac0f40d8c3a7eac57207c      preDigest
##                             artifact         tagKey
##                                  tagValue         createdDate
##  1:                                   rda 2018-08-07 11:06:00
##  2:      a12547f9875d9c1eed262d32532d4e9e 2018-08-07 11:06:00
##  3:                               numeric 2018-08-07 11:06:00
##  4:                   2018-08-07 11:06:00 2018-08-07 11:06:00
##  5:      e37bb635c97bc2eeecab63816b881bbc 2018-08-07 11:06:00
##  6:                                     a 2018-08-07 11:06:00
##  7:                                 runif 2018-08-07 11:06:00
##  8:                                   952 2018-08-07 11:06:00
##  9:                   2018-08-07 11:06:00 2018-08-07 11:06:00
## 10:                          process_file 2018-08-07 11:06:00
## 11:                         process_group 2018-08-07 11:06:00
## 12:                   process_group.block 2018-08-07 11:06:00
## 13:                            call_block 2018-08-07 11:06:00
## 14:                            block_exec 2018-08-07 11:06:00
## 15:    n:969a49ec15bcd4323ff31538af321264 2018-08-07 11:06:00
## 16: .FUN:d2631d24c3b38b89c7bdd4ab7faaaac3 2018-08-07 11:06:00
## 17:                                   rda 2018-08-07 11:06:00
## 18:      fbc518cef93ac0f40d8c3a7eac57207c 2018-08-07 11:06:00
## 19:                               numeric 2018-08-07 11:06:00
## 20:                   2018-08-07 11:06:00 2018-08-07 11:06:00
## 21:      85874f26b2e0c1ef689a7d379d275ebf 2018-08-07 11:06:00
## 22:                                     b 2018-08-07 11:06:00
## 23:                                 rnorm 2018-08-07 11:06:00
## 24:                                   952 2018-08-07 11:06:00
## 25:                   2018-08-07 11:06:00 2018-08-07 11:06:00
## 26:                          process_file 2018-08-07 11:06:00
## 27:                         process_group 2018-08-07 11:06:00
## 28:                   process_group.block 2018-08-07 11:06:00
## 29:                            call_block 2018-08-07 11:06:00
## 30:                            block_exec 2018-08-07 11:06:00
## 31:    n:969a49ec15bcd4323ff31538af321264 2018-08-07 11:06:00
## 32: .FUN:7e9a928f110f80b3612e71883a6ec1f4 2018-08-07 11:06:00
##                                  tagValue         createdDate
clearCache(tmpDir)
## Cache size:
##   Total (including Rasters): 476 bytes
##   Selected objects (not including Rasters): 476 bytes

1.8 Example 5: using caching to speed up rerunning expensive computations

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

1.9 Nested Caching

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] 0.2417744 0.8798532 1.8686174
## attr(,"tags")
## [1] "cacheId:e09bf93970f9e94d5c639cfa8ca722f0"
## attr(,".Cache")
## attr(,".Cache")$newCache
## [1] TRUE
## 
## attr(,"call")
## [1] ""
showCache(tmpdir1) # 2 function calls
## Cache size:
##   Total (including Rasters): 476 bytes
##   Selected objects (not including Rasters): 476 bytes
##                             artifact         tagKey
##  1: 21b0fbddb437e25f2ff1cf6f84e03804         format
##  2: 21b0fbddb437e25f2ff1cf6f84e03804           name
##  3: 21b0fbddb437e25f2ff1cf6f84e03804          class
##  4: 21b0fbddb437e25f2ff1cf6f84e03804           date
##  5: 21b0fbddb437e25f2ff1cf6f84e03804        cacheId
##  6: 21b0fbddb437e25f2ff1cf6f84e03804       function
##  7: 21b0fbddb437e25f2ff1cf6f84e03804    object.size
##  8: 21b0fbddb437e25f2ff1cf6f84e03804       accessed
##  9: 21b0fbddb437e25f2ff1cf6f84e03804 otherFunctions
## 10: 21b0fbddb437e25f2ff1cf6f84e03804 otherFunctions
## 11: 21b0fbddb437e25f2ff1cf6f84e03804 otherFunctions
## 12: 21b0fbddb437e25f2ff1cf6f84e03804 otherFunctions
## 13: 21b0fbddb437e25f2ff1cf6f84e03804 otherFunctions
## 14: 21b0fbddb437e25f2ff1cf6f84e03804      preDigest
## 15: 21b0fbddb437e25f2ff1cf6f84e03804      preDigest
## 16: d9dd71da44acdefc43bd8f7db9d308cd         format
## 17: d9dd71da44acdefc43bd8f7db9d308cd           name
## 18: d9dd71da44acdefc43bd8f7db9d308cd          class
## 19: d9dd71da44acdefc43bd8f7db9d308cd           date
## 20: d9dd71da44acdefc43bd8f7db9d308cd        cacheId
## 21: d9dd71da44acdefc43bd8f7db9d308cd       function
## 22: d9dd71da44acdefc43bd8f7db9d308cd    object.size
## 23: d9dd71da44acdefc43bd8f7db9d308cd       accessed
## 24: d9dd71da44acdefc43bd8f7db9d308cd otherFunctions
## 25: d9dd71da44acdefc43bd8f7db9d308cd otherFunctions
## 26: d9dd71da44acdefc43bd8f7db9d308cd otherFunctions
## 27: d9dd71da44acdefc43bd8f7db9d308cd otherFunctions
## 28: d9dd71da44acdefc43bd8f7db9d308cd otherFunctions
## 29: d9dd71da44acdefc43bd8f7db9d308cd      preDigest
## 30: d9dd71da44acdefc43bd8f7db9d308cd      preDigest
## 31: d9dd71da44acdefc43bd8f7db9d308cd      preDigest
##                             artifact         tagKey
##                                  tagValue         createdDate
##  1:                                   rda 2018-08-07 11:06:00
##  2:      21b0fbddb437e25f2ff1cf6f84e03804 2018-08-07 11:06:00
##  3:                               numeric 2018-08-07 11:06:00
##  4:                   2018-08-07 11:06:00 2018-08-07 11:06:00
##  5:      e09bf93970f9e94d5c639cfa8ca722f0 2018-08-07 11:06:00
##  6:                                 outer 2018-08-07 11:06:00
##  7:                                   952 2018-08-07 11:06:00
##  8:                   2018-08-07 11:06:00 2018-08-07 11:06:00
##  9:                          process_file 2018-08-07 11:06:00
## 10:                         process_group 2018-08-07 11:06:00
## 11:                   process_group.block 2018-08-07 11:06:00
## 12:                            call_block 2018-08-07 11:06:00
## 13:                            block_exec 2018-08-07 11:06:00
## 14:    n:8128a6180a705341ab7c05cfa945edfb 2018-08-07 11:06:00
## 15: .FUN:b5f6bcbdd9f23e39c2c5d4020e73a6ff 2018-08-07 11:06:00
## 16:                                   rda 2018-08-07 11:06:00
## 17:      d9dd71da44acdefc43bd8f7db9d308cd 2018-08-07 11:06:00
## 18:                               numeric 2018-08-07 11:06:00
## 19:                   2018-08-07 11:06:00 2018-08-07 11:06:00
## 20:      cec73d63ad3864af8bcd7efc5fae864d 2018-08-07 11:06:00
## 21:                                 rnorm 2018-08-07 11:06:00
## 22:                                   952 2018-08-07 11:06:00
## 23:                   2018-08-07 11:06:00 2018-08-07 11:06:00
## 24:                          process_file 2018-08-07 11:06:00
## 25:                         process_group 2018-08-07 11:06:00
## 26:                   process_group.block 2018-08-07 11:06:00
## 27:                            call_block 2018-08-07 11:06:00
## 28:                            block_exec 2018-08-07 11:06:00
## 29:    n:4ae3e6b6364de42fdc243469d73448cc 2018-08-07 11:06:00
## 30: mean:c28b87a0be6a99966bdaa5e556974b43 2018-08-07 11:06:00
## 31: .FUN:7e9a928f110f80b3612e71883a6ec1f4 2018-08-07 11:06:00
##                                  tagValue         createdDate
showCache(tmpdir2) # 1 function call
## Cache size:
##   Total (including Rasters): 238 bytes
##   Selected objects (not including Rasters): 238 bytes
##                             artifact         tagKey
##  1: a0b80588bbabc414a4469941351d0579         format
##  2: a0b80588bbabc414a4469941351d0579           name
##  3: a0b80588bbabc414a4469941351d0579          class
##  4: a0b80588bbabc414a4469941351d0579           date
##  5: a0b80588bbabc414a4469941351d0579        cacheId
##  6: a0b80588bbabc414a4469941351d0579       function
##  7: a0b80588bbabc414a4469941351d0579    object.size
##  8: a0b80588bbabc414a4469941351d0579       accessed
##  9: a0b80588bbabc414a4469941351d0579 otherFunctions
## 10: a0b80588bbabc414a4469941351d0579 otherFunctions
## 11: a0b80588bbabc414a4469941351d0579 otherFunctions
## 12: a0b80588bbabc414a4469941351d0579 otherFunctions
## 13: a0b80588bbabc414a4469941351d0579 otherFunctions
## 14: a0b80588bbabc414a4469941351d0579      preDigest
## 15: a0b80588bbabc414a4469941351d0579      preDigest
##                                  tagValue         createdDate
##  1:                                   rda 2018-08-07 11:06:00
##  2:      a0b80588bbabc414a4469941351d0579 2018-08-07 11:06:00
##  3:                               numeric 2018-08-07 11:06:00
##  4:                   2018-08-07 11:06:00 2018-08-07 11:06:00
##  5:      19b808ac6871e0184e63c421a116cb61 2018-08-07 11:06:00
##  6:                                 inner 2018-08-07 11:06:00
##  7:                                   952 2018-08-07 11:06:00
##  8:                   2018-08-07 11:06:00 2018-08-07 11:06:00
##  9:                          process_file 2018-08-07 11:06:00
## 10:                         process_group 2018-08-07 11:06:00
## 11:                   process_group.block 2018-08-07 11:06:00
## 12:                            call_block 2018-08-07 11:06:00
## 13:                            block_exec 2018-08-07 11:06:00
## 14: mean:c28b87a0be6a99966bdaa5e556974b43 2018-08-07 11:06:00
## 15: .FUN:56a1302d7ef43383766d7af6ca072c4e 2018-08-07 11:06:00
# userTags get appended
# all items have the outer tag propagate, plus inner ones only have inner ones
clearCache(tmpdir1)
## Cache size:
##   Total (including Rasters): 476 bytes
##   Selected objects (not including Rasters): 476 bytes
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): 714 bytes
##   Selected objects (not including Rasters): 714 bytes
##                             artifact         tagKey
##  1: 5cdf5467f1160de931286a18c96d669a         format
##  2: 5cdf5467f1160de931286a18c96d669a           name
##  3: 5cdf5467f1160de931286a18c96d669a          class
##  4: 5cdf5467f1160de931286a18c96d669a           date
##  5: 5cdf5467f1160de931286a18c96d669a        cacheId
##  6: 5cdf5467f1160de931286a18c96d669a       innerTag
##  7: 5cdf5467f1160de931286a18c96d669a       outerTag
##  8: 5cdf5467f1160de931286a18c96d669a       function
##  9: 5cdf5467f1160de931286a18c96d669a    object.size
## 10: 5cdf5467f1160de931286a18c96d669a       accessed
## 11: 5cdf5467f1160de931286a18c96d669a otherFunctions
## 12: 5cdf5467f1160de931286a18c96d669a otherFunctions
## 13: 5cdf5467f1160de931286a18c96d669a otherFunctions
## 14: 5cdf5467f1160de931286a18c96d669a otherFunctions
## 15: 5cdf5467f1160de931286a18c96d669a otherFunctions
## 16: 5cdf5467f1160de931286a18c96d669a      preDigest
## 17: 5cdf5467f1160de931286a18c96d669a      preDigest
## 18: 5cdf5467f1160de931286a18c96d669a      preDigest
## 19: dd943b69f9017b3af1a0f6da95936123         format
## 20: dd943b69f9017b3af1a0f6da95936123           name
## 21: dd943b69f9017b3af1a0f6da95936123          class
## 22: dd943b69f9017b3af1a0f6da95936123           date
## 23: dd943b69f9017b3af1a0f6da95936123        cacheId
## 24: dd943b69f9017b3af1a0f6da95936123       outerTag
## 25: dd943b69f9017b3af1a0f6da95936123       function
## 26: dd943b69f9017b3af1a0f6da95936123    object.size
## 27: dd943b69f9017b3af1a0f6da95936123       accessed
## 28: dd943b69f9017b3af1a0f6da95936123 otherFunctions
## 29: dd943b69f9017b3af1a0f6da95936123 otherFunctions
## 30: dd943b69f9017b3af1a0f6da95936123 otherFunctions
## 31: dd943b69f9017b3af1a0f6da95936123 otherFunctions
## 32: dd943b69f9017b3af1a0f6da95936123 otherFunctions
## 33: dd943b69f9017b3af1a0f6da95936123      preDigest
## 34: dd943b69f9017b3af1a0f6da95936123      preDigest
## 35: dfe9fa463103a9de94aaabf0b9bdc8f3         format
## 36: dfe9fa463103a9de94aaabf0b9bdc8f3           name
## 37: dfe9fa463103a9de94aaabf0b9bdc8f3          class
## 38: dfe9fa463103a9de94aaabf0b9bdc8f3           date
## 39: dfe9fa463103a9de94aaabf0b9bdc8f3        cacheId
## 40: dfe9fa463103a9de94aaabf0b9bdc8f3       outerTag
## 41: dfe9fa463103a9de94aaabf0b9bdc8f3       function
## 42: dfe9fa463103a9de94aaabf0b9bdc8f3    object.size
## 43: dfe9fa463103a9de94aaabf0b9bdc8f3       accessed
## 44: dfe9fa463103a9de94aaabf0b9bdc8f3 otherFunctions
## 45: dfe9fa463103a9de94aaabf0b9bdc8f3 otherFunctions
## 46: dfe9fa463103a9de94aaabf0b9bdc8f3 otherFunctions
## 47: dfe9fa463103a9de94aaabf0b9bdc8f3 otherFunctions
## 48: dfe9fa463103a9de94aaabf0b9bdc8f3 otherFunctions
## 49: dfe9fa463103a9de94aaabf0b9bdc8f3      preDigest
## 50: dfe9fa463103a9de94aaabf0b9bdc8f3      preDigest
##                             artifact         tagKey
##                                  tagValue         createdDate
##  1:                                   rda 2018-08-07 11:06:00
##  2:      5cdf5467f1160de931286a18c96d669a 2018-08-07 11:06:00
##  3:                               numeric 2018-08-07 11:06:00
##  4:                   2018-08-07 11:06:00 2018-08-07 11:06:00
##  5:      cec73d63ad3864af8bcd7efc5fae864d 2018-08-07 11:06:00
##  6:                              innerTag 2018-08-07 11:06:00
##  7:                              outerTag 2018-08-07 11:06:00
##  8:                                 rnorm 2018-08-07 11:06:00
##  9:                                   952 2018-08-07 11:06:00
## 10:                   2018-08-07 11:06:00 2018-08-07 11:06:00
## 11:                          process_file 2018-08-07 11:06:00
## 12:                         process_group 2018-08-07 11:06:00
## 13:                   process_group.block 2018-08-07 11:06:00
## 14:                            call_block 2018-08-07 11:06:00
## 15:                            block_exec 2018-08-07 11:06:00
## 16:    n:4ae3e6b6364de42fdc243469d73448cc 2018-08-07 11:06:00
## 17: mean:c28b87a0be6a99966bdaa5e556974b43 2018-08-07 11:06:00
## 18: .FUN:7e9a928f110f80b3612e71883a6ec1f4 2018-08-07 11:06:00
## 19:                                   rda 2018-08-07 11:06:00
## 20:      dd943b69f9017b3af1a0f6da95936123 2018-08-07 11:06:00
## 21:                               numeric 2018-08-07 11:06:00
## 22:                   2018-08-07 11:06:00 2018-08-07 11:06:00
## 23:      44f57deb36c53cd9c395e04c51fea77a 2018-08-07 11:06:00
## 24:                              outerTag 2018-08-07 11:06:00
## 25:                                 outer 2018-08-07 11:06:00
## 26:                                   952 2018-08-07 11:06:00
## 27:                   2018-08-07 11:06:00 2018-08-07 11:06:00
## 28:                          process_file 2018-08-07 11:06:00
## 29:                         process_group 2018-08-07 11:06:00
## 30:                   process_group.block 2018-08-07 11:06:00
## 31:                            call_block 2018-08-07 11:06:00
## 32:                            block_exec 2018-08-07 11:06:00
## 33:    n:8128a6180a705341ab7c05cfa945edfb 2018-08-07 11:06:00
## 34: .FUN:62302feda89e19149a56ca40fde725e1 2018-08-07 11:06:00
## 35:                                   rda 2018-08-07 11:06:00
## 36:      dfe9fa463103a9de94aaabf0b9bdc8f3 2018-08-07 11:06:00
## 37:                               numeric 2018-08-07 11:06:00
## 38:                   2018-08-07 11:06:00 2018-08-07 11:06:00
## 39:      994d1330fbd961f795ab0dc508271963 2018-08-07 11:06:00
## 40:                              outerTag 2018-08-07 11:06:00
## 41:                                 inner 2018-08-07 11:06:00
## 42:                                   952 2018-08-07 11:06:00
## 43:                   2018-08-07 11:06:00 2018-08-07 11:06:00
## 44:                          process_file 2018-08-07 11:06:00
## 45:                         process_group 2018-08-07 11:06:00
## 46:                   process_group.block 2018-08-07 11:06:00
## 47:                            call_block 2018-08-07 11:06:00
## 48:                            block_exec 2018-08-07 11:06:00
## 49: mean:c28b87a0be6a99966bdaa5e556974b43 2018-08-07 11:06:00
## 50: .FUN:b910401646b09073940de757678db03d 2018-08-07 11:06:00
##                                  tagValue         createdDate

1.10 cacheId

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(,"tags")
## [1] "cacheId:23dc247384c1b270f0d36de4bca1b138"
## attr(,".Cache")
## attr(,".Cache")$newCache
## [1] TRUE
## 
## attr(,"call")
## [1] ""
# manually look at output attribute which shows cacheId: ad184ce64541972b50afd8e7b75f821b
Cache(rnorm, 1, cacheRepo = tmpdir1, cacheId = "ad184ce64541972b50afd8e7b75f821b") # same value
## cacheId is not same as calculated hash. Manually searching for cacheId:ad184ce64541972b50afd8e7b75f821b
## [1] 0.1836433
## attr(,"tags")
## [1] "cacheId:ad184ce64541972b50afd8e7b75f821b"
## attr(,".Cache")
## attr(,".Cache")$newCache
## [1] TRUE
## 
## 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(,"tags")
## [1] "cacheId:ad184ce64541972b50afd8e7b75f821b"
## attr(,".Cache")
## attr(,".Cache")$newCache
## [1] FALSE
## 
## attr(,"call")
## [1] ""
## cleanup
unlink(c("filename.rda", "filename1.rda"))

1.11 Working with the Cache manually

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): 3.1 Kb
##   Selected objects (not including Rasters): 3.1 Kb

## cleanup
unlink(dirname(tmpDir), recursive = TRUE)

2 Reproducible Workflow

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.

2.1 Nested Caching

2.1.0.1 Cache individual functions

Cache(<functionName>, <other arguments>)

This will allow fine scale control of individual function calls.