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. 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] "C:/Users/emcintir.L-VIC-A023744/AppData/Local/Temp/RtmpwvOhxA/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 
##    1.93    0.14    2.08

# 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 
##    2.26    0.28    2.57

# vastly faster the second time
system.time(map2 <- Cache(projectRaster, ras, crs = newCRS, cacheRepo = tmpDir))

##   ...(Object to retrieve is large: 6.5 Mb)

##   loading cached result from previous projectRaster call, adding to memoised copy

##    user  system elapsed 
##    0.08    0.03    0.13

# even faster the third time
system.time(map3 <- Cache(projectRaster, ras, crs = newCRS, cacheRepo = tmpDir))

##   ...(Object to retrieve is large: 6.5 Mb)

##   loading memoised result from previous projectRaster call.

##    user  system elapsed 
##    0.01    0.06    0.08

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)
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

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): 1 Kb

##   Selected objects (not including Rasters): 504 bytes

##                             artifact         tagKey
##  1: 2d19b658e0a7ada02abe87f8ea5640f7         format
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##  5: 2d19b658e0a7ada02abe87f8ea5640f7        cacheId
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##  7: 2d19b658e0a7ada02abe87f8ea5640f7       function
##  8: 2d19b658e0a7ada02abe87f8ea5640f7    object.size
##  9: 2d19b658e0a7ada02abe87f8ea5640f7       accessed
## 10: 2d19b658e0a7ada02abe87f8ea5640f7 otherFunctions
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##                             tagValue         createdDate
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##                             tagValue         createdDate

showCache(tmpDir, userTags = c("^a$")) # regular expression ... "a" exactly

## Cache size:

##   Total (including Rasters): 1 Kb

##   Selected objects (not including Rasters): 252 bytes

##                             artifact         tagKey
##  1: c0c85ca54055013b9377ed859355928a         format
##  2: c0c85ca54055013b9377ed859355928a           name
##  3: c0c85ca54055013b9377ed859355928a          class
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showCache(tmpDir, userTags = c("runif")) # show only cached objects made during runif call

## Cache size:

##   Total (including Rasters): 1 Kb

##   Selected objects (not including Rasters): 252 bytes

##                             artifact         tagKey
##  1: 2d19b658e0a7ada02abe87f8ea5640f7         format
##  2: 2d19b658e0a7ada02abe87f8ea5640f7           name
##  3: 2d19b658e0a7ada02abe87f8ea5640f7          class
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##  8: 2d19b658e0a7ada02abe87f8ea5640f7    object.size
##  9: 2d19b658e0a7ada02abe87f8ea5640f7       accessed
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##                             tagValue         createdDate
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clearCache(tmpDir, userTags = c("runif"), ask = FALSE) # remove only cached objects made during runif call

## Cache size:

##   Total (including Rasters): 1 Kb

##   Selected objects (not including Rasters): 252 bytes

showCache(tmpDir) # only those made during rnorm call

## Cache size:

##   Total (including Rasters): 804 bytes

##   Selected objects (not including Rasters): 804 bytes

##                             artifact         tagKey
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##                             artifact         tagKey
##                             tagValue         createdDate
##  1:                              rda 2019-11-18 06:58:20
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##  7:                             1104 2019-11-18 06:58:20
##  8:              2019-11-18 06:58:20 2019-11-18 06:58:20
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## 13:                       call_block 2019-11-18 06:58:20
## 14:                       block_exec 2019-11-18 06:58:20
## 15:                           in_dir 2019-11-18 06:58:20
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## 24:              2019-11-18 06:58:20 2019-11-18 06:58:20
## 25:                              rda 2019-11-18 06:58:20
## 26: 77359758c247829664ec20c0eecbf22e 2019-11-18 06:58:20
## 27:                          numeric 2019-11-18 06:58:20
## 28:              2019-11-18 06:58:20 2019-11-18 06:58:20
## 29:                 c16f0e2c57596069 2019-11-18 06:58:20
## 30:              rnorm pipe sequence 2019-11-18 06:58:20
## 31:                             1104 2019-11-18 06:58:20
## 32:              2019-11-18 06:58:20 2019-11-18 06:58:20
## 33:                 vweave_rmarkdown 2019-11-18 06:58:20
## 34:                     process_file 2019-11-18 06:58:20
## 35:                    process_group 2019-11-18 06:58:20
## 36:              process_group.block 2019-11-18 06:58:20
## 37:                       call_block 2019-11-18 06:58:20
## 38:                       block_exec 2019-11-18 06:58:20
## 39:                           in_dir 2019-11-18 06:58:20
## 40:                        timing_fn 2019-11-18 06:58:20
## 41:                           handle 2019-11-18 06:58:20
## 42:                      withVisible 2019-11-18 06:58:20
## 43:                              %C% 2019-11-18 06:58:20
## 44:                          do.call 2019-11-18 06:58:20
## 45:               n:c5775c3b366fb719 2019-11-18 06:58:20
## 46:            mean:152602b8ff81e5bb 2019-11-18 06:58:20
## 47:            .FUN:4f604aa46882b368 2019-11-18 06:58:20
## 48:                              rda 2019-11-18 06:58:20
## 49: c0c85ca54055013b9377ed859355928a 2019-11-18 06:58:20
## 50:                          numeric 2019-11-18 06:58:20
## 51:              2019-11-18 06:58:20 2019-11-18 06:58:20
## 52:                 f7bee22047b8d0c1 2019-11-18 06:58:20
## 53:                                a 2019-11-18 06:58:20
## 54:                            rnorm 2019-11-18 06:58:20
## 55:                             1008 2019-11-18 06:58:20
## 56:              2019-11-18 06:58:20 2019-11-18 06:58:20
## 57:                 vweave_rmarkdown 2019-11-18 06:58:20
## 58:                     process_file 2019-11-18 06:58:20
## 59:                    process_group 2019-11-18 06:58:20
## 60:              process_group.block 2019-11-18 06:58:20
## 61:                       call_block 2019-11-18 06:58:20
## 62:                       block_exec 2019-11-18 06:58:20
## 63:                           in_dir 2019-11-18 06:58:20
## 64:                        timing_fn 2019-11-18 06:58:21
## 65:                           handle 2019-11-18 06:58:21
## 66:                      withVisible 2019-11-18 06:58:21
## 67:               n:7eef4eae85fd9229 2019-11-18 06:58:21
## 68:            .FUN:4f604aa46882b368 2019-11-18 06:58:21
##                             tagValue         createdDate

clearCache(tmpDir, ask = FALSE)

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): 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 and 3 cols): md5hash,name,createdDate

clearCache(tmpDir, ask = FALSE)

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, ask = FALSE)

## Cache size:

##   Total (including Rasters): 504 bytes

##   Selected objects (not including Rasters): 504 bytes

##                             artifact         tagKey
##  1: 0b0c4f2cad84630f12497c0d05c107a9         format
##  2: 0b0c4f2cad84630f12497c0d05c107a9           name
##  3: 0b0c4f2cad84630f12497c0d05c107a9          class
##  4: 0b0c4f2cad84630f12497c0d05c107a9           date
##  5: 0b0c4f2cad84630f12497c0d05c107a9        cacheId
##  6: 0b0c4f2cad84630f12497c0d05c107a9     objectName
##  7: 0b0c4f2cad84630f12497c0d05c107a9       function
##  8: 0b0c4f2cad84630f12497c0d05c107a9    object.size
##  9: 0b0c4f2cad84630f12497c0d05c107a9       accessed
## 10: 0b0c4f2cad84630f12497c0d05c107a9 otherFunctions
## 11: 0b0c4f2cad84630f12497c0d05c107a9 otherFunctions
## 12: 0b0c4f2cad84630f12497c0d05c107a9 otherFunctions
## 13: 0b0c4f2cad84630f12497c0d05c107a9 otherFunctions
## 14: 0b0c4f2cad84630f12497c0d05c107a9 otherFunctions
## 15: 0b0c4f2cad84630f12497c0d05c107a9 otherFunctions
## 16: 0b0c4f2cad84630f12497c0d05c107a9 otherFunctions
## 17: 0b0c4f2cad84630f12497c0d05c107a9 otherFunctions
## 18: 0b0c4f2cad84630f12497c0d05c107a9 otherFunctions
## 19: 0b0c4f2cad84630f12497c0d05c107a9 otherFunctions
## 20: 0b0c4f2cad84630f12497c0d05c107a9      preDigest
## 21: 0b0c4f2cad84630f12497c0d05c107a9      preDigest
## 22: 623adedd3ce9c482c1ba68613776e7ba         format
## 23: 623adedd3ce9c482c1ba68613776e7ba           name
## 24: 623adedd3ce9c482c1ba68613776e7ba          class
## 25: 623adedd3ce9c482c1ba68613776e7ba           date
## 26: 623adedd3ce9c482c1ba68613776e7ba        cacheId
## 27: 623adedd3ce9c482c1ba68613776e7ba     objectName
## 28: 623adedd3ce9c482c1ba68613776e7ba       function
## 29: 623adedd3ce9c482c1ba68613776e7ba    object.size
## 30: 623adedd3ce9c482c1ba68613776e7ba       accessed
## 31: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 32: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 33: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 34: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 35: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 36: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 37: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 38: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 39: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 40: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 41: 623adedd3ce9c482c1ba68613776e7ba      preDigest
## 42: 623adedd3ce9c482c1ba68613776e7ba      preDigest
##                             artifact         tagKey
##                             tagValue         createdDate
##  1:                              rda 2019-11-18 06:58:22
##  2: 0b0c4f2cad84630f12497c0d05c107a9 2019-11-18 06:58:22
##  3:                          numeric 2019-11-18 06:58:22
##  4:              2019-11-18 06:58:22 2019-11-18 06:58:22
##  5:                 3aef38d1fc02aee5 2019-11-18 06:58:22
##  6:                                b 2019-11-18 06:58:22
##  7:                            runif 2019-11-18 06:58:22
##  8:                             1008 2019-11-18 06:58:22
##  9:              2019-11-18 06:58:22 2019-11-18 06:58:22
## 10:                 vweave_rmarkdown 2019-11-18 06:58:22
## 11:                     process_file 2019-11-18 06:58:22
## 12:                    process_group 2019-11-18 06:58:22
## 13:              process_group.block 2019-11-18 06:58:22
## 14:                       call_block 2019-11-18 06:58:22
## 15:                       block_exec 2019-11-18 06:58:22
## 16:                           in_dir 2019-11-18 06:58:22
## 17:                        timing_fn 2019-11-18 06:58:22
## 18:                           handle 2019-11-18 06:58:22
## 19:                      withVisible 2019-11-18 06:58:22
## 20:               n:7eef4eae85fd9229 2019-11-18 06:58:22
## 21:            .FUN:881ec847b7161f3c 2019-11-18 06:58:22
## 22:                              rda 2019-11-18 06:58:22
## 23: 623adedd3ce9c482c1ba68613776e7ba 2019-11-18 06:58:22
## 24:                          numeric 2019-11-18 06:58:22
## 25:              2019-11-18 06:58:22 2019-11-18 06:58:22
## 26:                 f7bee22047b8d0c1 2019-11-18 06:58:22
## 27:                                a 2019-11-18 06:58:22
## 28:                            rnorm 2019-11-18 06:58:22
## 29:                             1008 2019-11-18 06:58:22
## 30:              2019-11-18 06:58:21 2019-11-18 06:58:22
## 31:                 vweave_rmarkdown 2019-11-18 06:58:22
## 32:                     process_file 2019-11-18 06:58:22
## 33:                    process_group 2019-11-18 06:58:22
## 34:              process_group.block 2019-11-18 06:58:22
## 35:                       call_block 2019-11-18 06:58:22
## 36:                       block_exec 2019-11-18 06:58:22
## 37:                           in_dir 2019-11-18 06:58:22
## 38:                        timing_fn 2019-11-18 06:58:22
## 39:                           handle 2019-11-18 06:58:22
## 40:                      withVisible 2019-11-18 06:58:22
## 41:               n:7eef4eae85fd9229 2019-11-18 06:58:22
## 42:            .FUN:4f604aa46882b368 2019-11-18 06:58:22
##                             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: 623adedd3ce9c482c1ba68613776e7ba         format
##  2: 623adedd3ce9c482c1ba68613776e7ba           name
##  3: 623adedd3ce9c482c1ba68613776e7ba          class
##  4: 623adedd3ce9c482c1ba68613776e7ba           date
##  5: 623adedd3ce9c482c1ba68613776e7ba        cacheId
##  6: 623adedd3ce9c482c1ba68613776e7ba     objectName
##  7: 623adedd3ce9c482c1ba68613776e7ba       function
##  8: 623adedd3ce9c482c1ba68613776e7ba    object.size
##  9: 623adedd3ce9c482c1ba68613776e7ba       accessed
## 10: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 11: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 12: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 13: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 14: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 15: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 16: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 17: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 18: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 19: 623adedd3ce9c482c1ba68613776e7ba otherFunctions
## 20: 623adedd3ce9c482c1ba68613776e7ba      preDigest
## 21: 623adedd3ce9c482c1ba68613776e7ba      preDigest
##                             artifact         tagKey
##                             tagValue         createdDate
##  1:                              rda 2019-11-18 06:58:22
##  2: 623adedd3ce9c482c1ba68613776e7ba 2019-11-18 06:58:22
##  3:                          numeric 2019-11-18 06:58:22
##  4:              2019-11-18 06:58:22 2019-11-18 06:58:22
##  5:                 f7bee22047b8d0c1 2019-11-18 06:58:22
##  6:                                a 2019-11-18 06:58:22
##  7:                            rnorm 2019-11-18 06:58:22
##  8:                             1008 2019-11-18 06:58:22
##  9:              2019-11-18 06:58:21 2019-11-18 06:58:22
## 10:                 vweave_rmarkdown 2019-11-18 06:58:22
## 11:                     process_file 2019-11-18 06:58:22
## 12:                    process_group 2019-11-18 06:58:22
## 13:              process_group.block 2019-11-18 06:58:22
## 14:                       call_block 2019-11-18 06:58:22
## 15:                       block_exec 2019-11-18 06:58:22
## 16:                           in_dir 2019-11-18 06:58:22
## 17:                        timing_fn 2019-11-18 06:58:22
## 18:                           handle 2019-11-18 06:58:22
## 19:                      withVisible 2019-11-18 06:58:22
## 20:               n:7eef4eae85fd9229 2019-11-18 06:58:22
## 21:            .FUN:4f604aa46882b368 2019-11-18 06:58:22
##                             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 and 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): 504 bytes

##   Selected objects (not including Rasters): 504 bytes

##                             artifact         tagKey
##  1: 106559c99d270496c331b4e50a597135         format
##  2: 106559c99d270496c331b4e50a597135           name
##  3: 106559c99d270496c331b4e50a597135          class
##  4: 106559c99d270496c331b4e50a597135           date
##  5: 106559c99d270496c331b4e50a597135        cacheId
##  6: 106559c99d270496c331b4e50a597135     objectName
##  7: 106559c99d270496c331b4e50a597135       function
##  8: 106559c99d270496c331b4e50a597135    object.size
##  9: 106559c99d270496c331b4e50a597135       accessed
## 10: 106559c99d270496c331b4e50a597135 otherFunctions
## 11: 106559c99d270496c331b4e50a597135 otherFunctions
## 12: 106559c99d270496c331b4e50a597135 otherFunctions
## 13: 106559c99d270496c331b4e50a597135 otherFunctions
## 14: 106559c99d270496c331b4e50a597135 otherFunctions
## 15: 106559c99d270496c331b4e50a597135 otherFunctions
## 16: 106559c99d270496c331b4e50a597135 otherFunctions
## 17: 106559c99d270496c331b4e50a597135 otherFunctions
## 18: 106559c99d270496c331b4e50a597135 otherFunctions
## 19: 106559c99d270496c331b4e50a597135 otherFunctions
## 20: 106559c99d270496c331b4e50a597135      preDigest
## 21: 106559c99d270496c331b4e50a597135      preDigest
## 22: 95eb7b563db3ed7ccbdcb4bae23f00f7         format
## 23: 95eb7b563db3ed7ccbdcb4bae23f00f7           name
## 24: 95eb7b563db3ed7ccbdcb4bae23f00f7          class
## 25: 95eb7b563db3ed7ccbdcb4bae23f00f7           date
## 26: 95eb7b563db3ed7ccbdcb4bae23f00f7        cacheId
## 27: 95eb7b563db3ed7ccbdcb4bae23f00f7     objectName
## 28: 95eb7b563db3ed7ccbdcb4bae23f00f7       function
## 29: 95eb7b563db3ed7ccbdcb4bae23f00f7    object.size
## 30: 95eb7b563db3ed7ccbdcb4bae23f00f7       accessed
## 31: 95eb7b563db3ed7ccbdcb4bae23f00f7 otherFunctions
## 32: 95eb7b563db3ed7ccbdcb4bae23f00f7 otherFunctions
## 33: 95eb7b563db3ed7ccbdcb4bae23f00f7 otherFunctions
## 34: 95eb7b563db3ed7ccbdcb4bae23f00f7 otherFunctions
## 35: 95eb7b563db3ed7ccbdcb4bae23f00f7 otherFunctions
## 36: 95eb7b563db3ed7ccbdcb4bae23f00f7 otherFunctions
## 37: 95eb7b563db3ed7ccbdcb4bae23f00f7 otherFunctions
## 38: 95eb7b563db3ed7ccbdcb4bae23f00f7 otherFunctions
## 39: 95eb7b563db3ed7ccbdcb4bae23f00f7 otherFunctions
## 40: 95eb7b563db3ed7ccbdcb4bae23f00f7 otherFunctions
## 41: 95eb7b563db3ed7ccbdcb4bae23f00f7      preDigest
## 42: 95eb7b563db3ed7ccbdcb4bae23f00f7      preDigest
##                             artifact         tagKey
##                             tagValue         createdDate
##  1:                              rda 2019-11-18 06:58:22
##  2: 106559c99d270496c331b4e50a597135 2019-11-18 06:58:22
##  3:                          numeric 2019-11-18 06:58:22
##  4:              2019-11-18 06:58:22 2019-11-18 06:58:22
##  5:                 f7bee22047b8d0c1 2019-11-18 06:58:22
##  6:                                b 2019-11-18 06:58:22
##  7:                            rnorm 2019-11-18 06:58:22
##  8:                             1008 2019-11-18 06:58:22
##  9:              2019-11-18 06:58:22 2019-11-18 06:58:22
## 10:                 vweave_rmarkdown 2019-11-18 06:58:22
## 11:                     process_file 2019-11-18 06:58:22
## 12:                    process_group 2019-11-18 06:58:22
## 13:              process_group.block 2019-11-18 06:58:22
## 14:                       call_block 2019-11-18 06:58:22
## 15:                       block_exec 2019-11-18 06:58:22
## 16:                           in_dir 2019-11-18 06:58:22
## 17:                        timing_fn 2019-11-18 06:58:22
## 18:                           handle 2019-11-18 06:58:22
## 19:                      withVisible 2019-11-18 06:58:22
## 20:               n:7eef4eae85fd9229 2019-11-18 06:58:22
## 21:            .FUN:4f604aa46882b368 2019-11-18 06:58:22
## 22:                              rda 2019-11-18 06:58:22
## 23: 95eb7b563db3ed7ccbdcb4bae23f00f7 2019-11-18 06:58:22
## 24:                          numeric 2019-11-18 06:58:22
## 25:              2019-11-18 06:58:22 2019-11-18 06:58:22
## 26:                 3aef38d1fc02aee5 2019-11-18 06:58:22
## 27:                                a 2019-11-18 06:58:22
## 28:                            runif 2019-11-18 06:58:22
## 29:                             1008 2019-11-18 06:58:22
## 30:              2019-11-18 06:58:22 2019-11-18 06:58:22
## 31:                 vweave_rmarkdown 2019-11-18 06:58:22
## 32:                     process_file 2019-11-18 06:58:22
## 33:                    process_group 2019-11-18 06:58:22
## 34:              process_group.block 2019-11-18 06:58:22
## 35:                       call_block 2019-11-18 06:58:22
## 36:                       block_exec 2019-11-18 06:58:22
## 37:                           in_dir 2019-11-18 06:58:22
## 38:                        timing_fn 2019-11-18 06:58:22
## 39:                           handle 2019-11-18 06:58:22
## 40:                      withVisible 2019-11-18 06:58:22
## 41:               n:7eef4eae85fd9229 2019-11-18 06:58:22
## 42:            .FUN:881ec847b7161f3c 2019-11-18 06:58:22
##                             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 and 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: 106559c99d270496c331b4e50a597135         format
##  2: 106559c99d270496c331b4e50a597135           name
##  3: 106559c99d270496c331b4e50a597135          class
##  4: 106559c99d270496c331b4e50a597135           date
##  5: 106559c99d270496c331b4e50a597135        cacheId
##  6: 106559c99d270496c331b4e50a597135     objectName
##  7: 106559c99d270496c331b4e50a597135       function
##  8: 106559c99d270496c331b4e50a597135    object.size
##  9: 106559c99d270496c331b4e50a597135       accessed
## 10: 106559c99d270496c331b4e50a597135 otherFunctions
## 11: 106559c99d270496c331b4e50a597135 otherFunctions
## 12: 106559c99d270496c331b4e50a597135 otherFunctions
## 13: 106559c99d270496c331b4e50a597135 otherFunctions
## 14: 106559c99d270496c331b4e50a597135 otherFunctions
## 15: 106559c99d270496c331b4e50a597135 otherFunctions
## 16: 106559c99d270496c331b4e50a597135 otherFunctions
## 17: 106559c99d270496c331b4e50a597135 otherFunctions
## 18: 106559c99d270496c331b4e50a597135 otherFunctions
## 19: 106559c99d270496c331b4e50a597135 otherFunctions
## 20: 106559c99d270496c331b4e50a597135      preDigest
## 21: 106559c99d270496c331b4e50a597135      preDigest
## 22: 95eb7b563db3ed7ccbdcb4bae23f00f7         format
## 23: 95eb7b563db3ed7ccbdcb4bae23f00f7           name
## 24: 95eb7b563db3ed7ccbdcb4bae23f00f7          class
## 25: 95eb7b563db3ed7ccbdcb4bae23f00f7           date
## 26: 95eb7b563db3ed7ccbdcb4bae23f00f7        cacheId
## 27: 95eb7b563db3ed7ccbdcb4bae23f00f7     objectName
## 28: 95eb7b563db3ed7ccbdcb4bae23f00f7       function
## 29: 95eb7b563db3ed7ccbdcb4bae23f00f7    object.size
## 30: 95eb7b563db3ed7ccbdcb4bae23f00f7       accessed
## 31: 95eb7b563db3ed7ccbdcb4bae23f00f7 otherFunctions
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##                             tagValue         createdDate
##  1:                              rda 2019-11-18 06:58:22
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## 16:                           in_dir 2019-11-18 06:58:22
## 17:                        timing_fn 2019-11-18 06:58:22
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## 19:                      withVisible 2019-11-18 06:58:22
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## 28:                            runif 2019-11-18 06:58:22
## 29:                             1008 2019-11-18 06:58:22
## 30:              2019-11-18 06:58:22 2019-11-18 06:58:22
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## 33:                    process_group 2019-11-18 06:58:22
## 34:              process_group.block 2019-11-18 06:58:22
## 35:                       call_block 2019-11-18 06:58:22
## 36:                       block_exec 2019-11-18 06:58:22
## 37:                           in_dir 2019-11-18 06:58:22
## 38:                        timing_fn 2019-11-18 06:58:22
## 39:                           handle 2019-11-18 06:58:22
## 40:                      withVisible 2019-11-18 06:58:22
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##                             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: 106559c99d270496c331b4e50a597135         format
##  2: 106559c99d270496c331b4e50a597135           name
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##  5: 106559c99d270496c331b4e50a597135        cacheId
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##                             tagValue         createdDate
##  1:                              rda 2019-11-18 06:58:22
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##  5:                 f7bee22047b8d0c1 2019-11-18 06:58:22
##  6:                                b 2019-11-18 06:58:22
##  7:                            rnorm 2019-11-18 06:58:22
##  8:                             1008 2019-11-18 06:58:22
##  9:              2019-11-18 06:58:22 2019-11-18 06:58:22
## 10:                 vweave_rmarkdown 2019-11-18 06:58:22
## 11:                     process_file 2019-11-18 06:58:22
## 12:                    process_group 2019-11-18 06:58:22
## 13:              process_group.block 2019-11-18 06:58:22
## 14:                       call_block 2019-11-18 06:58:22
## 15:                       block_exec 2019-11-18 06:58:22
## 16:                           in_dir 2019-11-18 06:58:22
## 17:                        timing_fn 2019-11-18 06:58:22
## 18:                           handle 2019-11-18 06:58:22
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## 28:                            runif 2019-11-18 06:58:22
## 29:                             1008 2019-11-18 06:58:22
## 30:              2019-11-18 06:58:22 2019-11-18 06:58:22
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## 32:                     process_file 2019-11-18 06:58:22
## 33:                    process_group 2019-11-18 06:58:22
## 34:              process_group.block 2019-11-18 06:58:22
## 35:                       call_block 2019-11-18 06:58:22
## 36:                       block_exec 2019-11-18 06:58:22
## 37:                           in_dir 2019-11-18 06:58:22
## 38:                        timing_fn 2019-11-18 06:58:22
## 39:                           handle 2019-11-18 06:58:22
## 40:                      withVisible 2019-11-18 06:58:22
## 41:               n:7eef4eae85fd9229 2019-11-18 06:58:22
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##                             tagValue         createdDate

clearCache(tmpDir, ask = FALSE)

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] -0.7060652 -1.3127788 -0.3790895
## 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: 168921ebe4d5ca61a7210618a190e512         format
##  2: 168921ebe4d5ca61a7210618a190e512           name
##  3: 168921ebe4d5ca61a7210618a190e512          class
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## 38: a441ef97515c69501a6c23e15d93d169 otherFunctions
## 39: a441ef97515c69501a6c23e15d93d169 otherFunctions
## 40: a441ef97515c69501a6c23e15d93d169      preDigest
## 41: a441ef97515c69501a6c23e15d93d169      preDigest
##                             artifact         tagKey
##                             tagValue         createdDate
##  1:                              rda 2019-11-18 06:58:23
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##  3:                          numeric 2019-11-18 06:58:23
##  4:              2019-11-18 06:58:23 2019-11-18 06:58:23
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##  7:                             1008 2019-11-18 06:58:23
##  8:              2019-11-18 06:58:23 2019-11-18 06:58:23
##  9:                 vweave_rmarkdown 2019-11-18 06:58:23
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## 12:              process_group.block 2019-11-18 06:58:23
## 13:                       call_block 2019-11-18 06:58:23
## 14:                       block_exec 2019-11-18 06:58:23
## 15:                           in_dir 2019-11-18 06:58:23
## 16:                        timing_fn 2019-11-18 06:58:23
## 17:                           handle 2019-11-18 06:58:23
## 18:                      withVisible 2019-11-18 06:58:23
## 19:               n:7f12988bd88a0fb8 2019-11-18 06:58:23
## 20:            mean:22413394efd9f6a3 2019-11-18 06:58:23
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## 25:              2019-11-18 06:58:23 2019-11-18 06:58:23
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## 34:                       call_block 2019-11-18 06:58:23
## 35:                       block_exec 2019-11-18 06:58:23
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## 39:                      withVisible 2019-11-18 06:58:23
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##                             tagValue         createdDate

showCache(tmpdir2) # 1 function call

## Cache size:

##   Total (including Rasters): 252 bytes

##   Selected objects (not including Rasters): 252 bytes

##                             artifact         tagKey
##  1: 8e37b3bffeb6257415bf3c921e05c54d         format
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##  8: 8e37b3bffeb6257415bf3c921e05c54d       accessed
##  9: 8e37b3bffeb6257415bf3c921e05c54d otherFunctions
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##                             tagValue         createdDate
##  1:                              rda 2019-11-18 06:58:23
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##  3:                          numeric 2019-11-18 06:58:23
##  4:              2019-11-18 06:58:23 2019-11-18 06:58:23
##  5:                 33ceb4fb525fd08f 2019-11-18 06:58:23
##  6:                            inner 2019-11-18 06:58:23
##  7:                             1008 2019-11-18 06:58:23
##  8:              2019-11-18 06:58:23 2019-11-18 06:58:23
##  9:                 vweave_rmarkdown 2019-11-18 06:58:23
## 10:                     process_file 2019-11-18 06:58:23
## 11:                    process_group 2019-11-18 06:58:23
## 12:              process_group.block 2019-11-18 06:58:23
## 13:                       call_block 2019-11-18 06:58:23
## 14:                       block_exec 2019-11-18 06:58:23
## 15:                           in_dir 2019-11-18 06:58:23
## 16:                        timing_fn 2019-11-18 06:58:23
## 17:                           handle 2019-11-18 06:58:23
## 18:                      withVisible 2019-11-18 06:58:23
## 19:            mean:22413394efd9f6a3 2019-11-18 06:58:23
## 20:            .FUN:87e2c30917a34d25 2019-11-18 06:58:23

# 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: 1abdd84da8f62e178e8301d3170254ec         format
##  2: 1abdd84da8f62e178e8301d3170254ec           name
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##                             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(,".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"))

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): 3.3 Kb

##   Selected objects (not including Rasters): 3.3 Kb

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

Introduction to Cache

Eliot J. B. McIntire

November 18 2019