Package: reproducible 3.1.1.9063

Eliot J B McIntire

reproducible: Enhance Reproducibility of R Code

A collection of high-level, machine- and OS-independent tools for making reproducible and reusable content in R. The two workhorse functions are 'Cache()' and 'prepInputs()'. 'Cache()' allows for nested caching, is robust to environments and objects with environments (like functions), and deals with some classes of file-backed R objects e.g., from 'terra' and 'raster' packages. Both functions have been developed to be foundational components of data retrieval and processing in continuous workflow situations. In both functions, efforts are made to make the first and subsequent calls of functions have the same result, but faster at subsequent times by way of checksums and digesting. Several features are still under development, including cloud storage of cached objects allowing for sharing between users. Several advanced options are available, see '?reproducibleOptions()'.

Authors:Eliot J B McIntire [aut, cre], Alex M Chubaty [aut], Tati Micheletti [ctb], Ceres Barros [ctb], Ian Eddy [ctb], His Majesty the King in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
reproducible/json (API)

# Install 'reproducible' in R:

install.packages('reproducible', repos = c('https://predictiveecology.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/predictiveecology/reproducible/issues

Pkgdown/docs site:https://reproducible.predictiveecology.org

On CRAN:

reproducibility reproducible-research

10.13 score 39 stars 14 packages 112 scripts 1.9k downloads 1 mentions 132 exports 11 dependencies

Last updated from:4248b74f72 (on development). Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	252
source / vignettes	OK	237
linux-release-x86_64	OK	241
macos-release-arm64	OK	145
macos-oldrel-arm64	OK	189
windows-devel	OK	200
windows-release	OK	200
windows-oldrel	OK	207
wasm-release	OK	123

Exports:.addChangedAttr .addTagsRepo .addTagsToOutput .cacheMessage .cacheMessageObjectToRetrieve .checkCacheRepo .file.move .formalsNotInCurrentDots .grepSysCalls .isCRSany .isGridded .isMemoised .isSF .isSpat .isSpatialAny .isVector .objSizeWithTry .orderDotsUnderscoreFirst .preDigestByClass .prefix .prepareOutput .requireNamespace .robustDigest .setSubAttrInList .sortDotsUnderscoreFirst .suffix .tagsByClass .unwrap .updateTagsRepo .whereInStack .wrap asPath assessDataType basename2 Cache CacheDBFile CacheDBTableName CacheDigest CacheGeo cacheId CacheIsACache CacheStorageDir CacheStoredFile CacheV2 cc checkAndMakeCloudFolderID checkPath Checksums clearCache clearUrlLog compareNA convertPaths convertRasterPaths Copy copyFile createCache cropInputs cropTo dataType2 detectActiveCores downloadFile extractFromCache Filenames fixErrors fixErrorsIn gdalMask gdalProject gdalResample getRelative internetExists isUpdated keepCache linkOrCopy listGoogleDriveFolder listNamed loadFile loadFromCache makeMemoisable makeRelative makeUrlRemap maskInputs maskTo maxFn mergeCache messageCache messageColoured messageDF messagePrepInputs messagePreProcess messageQuestion minFn movedCache nlayers2 normPath normPathRel numCoresToUse objSize objSizeSession paddedFloatToChar postProcess postProcessTerra postProcessTo prepInputs prepInputsCOG prepInputsLog prepInputsWithTiles prepopulateCacheAsync preProcess preProcessParams projectInputs projectTo purgeChecksums rasterRead remapFilenames reproducibleOptions retry rmFromCache searchFull searchFullEx set.randomseed showCache studyAreaName tempdir2 tempfile2 unmakeMemoisable updateFilenameSlots urlExists usesPointer values2 writeFuture writeOutputs writeTo

Dependencies:cli cpp11 crayon data.table digest filelock fpCompare fs lobstr prettyunits rlang

Introduction to Cache

Rendered fromIntro-to-Cache.Rmdusingknitr::rmarkdown

Last update: 2026-05-15
Started: 2018-06-14

Help page	Topics
The 'reproducible' package	reproducible-package reproducible
Add a Tag to a Cached Object in the Repository	.addTagsRepo .updateTagsRepo
Attach debug info to return for Cache	.debugCache
Move a file to a new location - Defunct - use 'hardLinkOrCopy'	.file.move
Some spatial helper functions	.isCRSany .isGridded .isSF .isSpat .isSpatialAny .isVector isSpatial
Evaluate whether a cacheId is memoised	.isMemoised
'lobstr::obj_size' with a 'try' to address issue #72	.objSizeWithTry
Add a prefix or suffix to the basename part of a file path	.prefix .suffix suffix
Copy the file-backing of a file-backed Raster* object	.prepareFileBackedRaster
Remove attributes that are highly varying	.removeCacheAtts
Provide standard messaging for missing package dependencies	.requireNamespace
Set subattributes within a list by reference	.setSubAttrInList
Search for objects in the call stack	.whereInStack
Deal with class for saving to and loading from Cache or Disk	.unwrap .unwrap.data.table .unwrap.default .unwrap.environment .unwrap.list .unwrap.PackedSpatExtent2 .unwrap.PackedSpatVector .unwrap.PackedSpatVector2 .wrap .wrap.default .wrap.environment .wrap.list
Assess the appropriate raster layer data type	assessDataType assessDataType.default
A version of 'base::basename' that is 'NULL' resistant	basename2
Saves a wide variety function call outputs to disk and optionally RAM, for recovery later	Cache cache2 CacheV2
The exact digest function that 'Cache' uses	CacheDigest
Cache-like function for spatial domains	CacheGeo
Extract the cache id of an object	cacheId
Check for presence of 'checkFolderID' (for 'Cache(useCloud)')	checkAndMakeCloudFolderID
Check directory path	checkPath checkPath,character,logical-method checkPath,character,missing-method checkPath,missing,ANY-method checkPath,NULL,ANY-method
An alternative to 'basename' and 'dirname' when there are sub-folders	checkRelative
Calculate checksum	Checksums Checksums,character,logical-method Checksums,character,missing-method
Download from cloud, if necessary	cloudDownload
'NA'-aware comparison of two vectors	compareNA
Convert all ways of calling a function into canonical form, including defaults	convertCallToCommonFormat
Change the absolute path of a file	convertPaths convertRasterPaths
Recursive copying of nested environments, and other "hard to copy" objects	Copy Copy,ANY-method Copy,data.frame-method Copy,data.table-method Copy,list-method Copy,refClass-method
Copy a file using 'robocopy' on Windows and 'rsync' on Linux/macOS	copyFile copySingleFile
Low-level functions to create and work with a cache	CacheDBFile CacheDBTableName CacheIsACache CacheStorageDir CacheStoredFile createCache extractFromCache loadFromCache rmFromCache
Count Active Threads Based on CPU Usage	detectActiveCores
Determine filename, either automatically or manually	determineFilename
A wrapper around a set of downloading functions	downloadFile
Download a remote file	downloadRemote
Extract files from archive	extractFromArchive
Return the filename(s) from a Raster* object	Filenames Filenames,ANY-method Filenames,data.table-method Filenames,environment-method Filenames,list-method Filenames,Path-method
Fix common errors in GIS layers, using 'terra'	fixErrorsIn
3-Step postProcess sequence for SpatRasters using 'gdalwarp'	gdalMask gdalProject gdalResample
Relative paths	getRelative makeRelative
Harmonize all forms of call	harmonizeCall
Checks for existed of a url or the internet using <https://CRAN.R-project.org>	internetExists urlExists
Has a cached object has been updated?	isUpdated
Keep original geometries of 'sf' objects	keepOrigGeom
Hardlink, symlink, or copy a file	linkOrCopy
List a Google Drive folder, using a mirror listing when remapped	listGoogleDriveFolder
Create a list with names from object names	listNamed
Load a file from the cache	loadFile
Build a URL remap function from a manifest	makeUrlRemap
Remove 'quote' and determine if call uses '...'	matchCall2
Merge two cache repositories together	mergeCache mergeCache,ANY-method
Use 'message' with a consistent use of 'verbose'	.messageFunctionFn messageCache messageColoured messageDF messagePrepInputs messagePreProcess messageQuestion
Get min or maximum value of a (Spat)Raster	dataType2 maxFn minFn nlayers2 values2
Deal with moved cache issues	movedCache
Normalize file paths	normPath normPath,character-method normPath,list-method normPath,logical-method normPath,missing-method normPath,NULL-method normPathRel
Estimate Number of CPU Cores to Use for Parallel Processing	numCoresToUse
Wrapper around 'lobstr::obj_size'	objSize objSizeSession
Convert numeric to character with padding	paddedFloatToChar
Coerce a character string to a class "Path"	asPath asPath.character asPath.null Path-class
Generic function to post process objects	postProcess postProcess.default postProcess.list
Transform a GIS dataset so it has the properties (extent, projection, mask) of another	cropTo maskTo postProcessTerra postProcessTo projectTo writeTo
Download and optionally post-process files	prepInputs
Fast spatial subsetting of Cloud Optimized GeoTiff (COG) files	prepInputsCOG
URL access log for 'prepInputs' / 'preProcess'	clearUrlLog prepInputsLog
Alternative to 'prepInputs' that can use Spatial Tiles stored locally or on Google Drive	prepInputsWithTiles
Pre-populate the in-memory 'showCache' cache for a given 'cachePath'	prepopulateCacheAsync
Download, checksum, extract files	preProcess preProcessParams
Purge the checksums of a single file	purgeChecksums
A helper to 'getOption("reproducible.rasterRead")'	rasterRead
Remap file names	remapFilenames
'reproducible' options	reproducibleOptions
A wrapper around 'try' that retries on failure	retry
Save an object to Cache	saveToCache
Search up the full scope for functions	searchFull searchFullEx
Set seed with a random value using Sys.time()	set.randomseed
Examining and modifying the cache	cc clearCache clearCache,ANY-method keepCache keepCache,ANY-method showCache showCache,ANY-method
Get a unique name for a given study area	studyAreaName studyAreaName,ANY-method studyAreaName,character-method
Make a temporary (sub-)directory	tempdir2
Make a temporary file in a temporary (sub-)directory	tempfile2
The known path for unrar or 7z	.systemArchivePath unrarPath
Does an object use a pointer?	usesPointer
Write to cache repository, using 'future::future'	writeFuture

Package: reproducible 3.1.1.9063

reproducible: Enhance Reproducibility of R Code

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