# Enhance Reproducibility of R Code

## Documentation for package ‘reproducible’ version 3.1.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I K L M N O P R S T U V W misc

reproducible-package | The 'reproducible' package

## -- A --

asPath | Coerce a character string to a class "Path"
asPath.character | Coerce a character string to a class "Path"
asPath.null | Coerce a character string to a class "Path"
assessDataType | Assess the appropriate raster layer data type
assessDataType.default | Assess the appropriate raster layer data type

## -- B --

basename2 | A version of 'base::basename' that is 'NULL' resistant

## -- C --

Cache | Saves a wide variety function call outputs to disk and optionally RAM, for recovery later
cache2 | Saves a wide variety function call outputs to disk and optionally RAM, for recovery later
CacheDBFile | Low-level functions to create and work with a cache
CacheDBTableName | Low-level functions to create and work with a cache
CacheDigest | The exact digest function that 'Cache' uses
CacheGeo | Cache-like function for spatial domains
cacheId | Extract the cache id of an object
CacheIsACache | Low-level functions to create and work with a cache
CacheStorageDir | Low-level functions to create and work with a cache
CacheStoredFile | Low-level functions to create and work with a cache
CacheV2 | Saves a wide variety function call outputs to disk and optionally RAM, for recovery later
cc | Examining and modifying the cache
checkAndMakeCloudFolderID | Check for presence of 'checkFolderID' (for 'Cache(useCloud)')
checkPath | Check directory path
checkPath-method | Check directory path
checkRelative | An alternative to 'basename' and 'dirname' when there are sub-folders
Checksums | Calculate checksum
Checksums-method | Calculate checksum
clearCache | Examining and modifying the cache
clearCache-method | Examining and modifying the cache
cloudDownload | Download from cloud, if necessary
compareNA | 'NA'-aware comparison of two vectors
convertCallToCommonFormat | Convert all ways of calling a function into canonical form, including defaults
convertPaths | Change the absolute path of a file
convertRasterPaths | Change the absolute path of a file
Copy | Recursive copying of nested environments, and other "hard to copy" objects
Copy-method | Recursive copying of nested environments, and other "hard to copy" objects
copyFile | Copy a file using 'robocopy' on Windows and 'rsync' on Linux/macOS
copySingleFile | Copy a file using 'robocopy' on Windows and 'rsync' on Linux/macOS
createCache | Low-level functions to create and work with a cache
cropTo | Transform a GIS dataset so it has the properties (extent, projection, mask) of another

## -- D --

dataType2 | Get min or maximum value of a (Spat)Raster
detectActiveCores | Count Active Threads Based on CPU Usage
determineFilename | Determine filename, either automatically or manually
downloadFile | A wrapper around a set of downloading functions
downloadRemote | Download a remote file

## -- E --

extractFromArchive | Extract files from archive
extractFromCache | Low-level functions to create and work with a cache

## -- F --

Filenames | Return the filename(s) from a Raster* object
Filenames-method | Return the filename(s) from a Raster* object
fixErrorsIn | Fix common errors in GIS layers, using 'terra'

## -- G --

gdalMask | 3-Step postProcess sequence for SpatRasters using 'gdalwarp'
gdalProject | 3-Step postProcess sequence for SpatRasters using 'gdalwarp'
gdalResample | 3-Step postProcess sequence for SpatRasters using 'gdalwarp'
getRelative | Relative paths

## -- H --

harmonizeCall | Harmonize all forms of call

## -- I --

internetExists | Checks for existed of a url or the internet using <https://CRAN.R-project.org>
isSpatial | Some spatial helper functions
isUpdated | Has a cached object has been updated?

## -- K --

keepCache | Examining and modifying the cache
keepCache-method | Examining and modifying the cache
keepOrigGeom | Keep original geometries of 'sf' objects

## -- L --

linkOrCopy | Hardlink, symlink, or copy a file
listNamed | Create a list with names from object names
loadFile | Load a file from the cache
loadFromCache | Low-level functions to create and work with a cache

## -- M --

makeRelative | Relative paths
maskTo | Transform a GIS dataset so it has the properties (extent, projection, mask) of another
matchCall2 | Remove 'quote' and determine if call uses '...'
maxFn | Get min or maximum value of a (Spat)Raster
mergeCache | Merge two cache repositories together
mergeCache-method | Merge two cache repositories together
messageCache | Use 'message' with a consistent use of 'verbose'
messageColoured | Use 'message' with a consistent use of 'verbose'
messageDF | Use 'message' with a consistent use of 'verbose'
messagePrepInputs | Use 'message' with a consistent use of 'verbose'
messagePreProcess | Use 'message' with a consistent use of 'verbose'
messageQuestion | Use 'message' with a consistent use of 'verbose'
minFn | Get min or maximum value of a (Spat)Raster
movedCache | Deal with moved cache issues

## -- N --

nlayers2 | Get min or maximum value of a (Spat)Raster
normPath | Normalize file paths
normPath-method | Normalize file paths
normPathRel | Normalize file paths
numCoresToUse | Estimate Number of CPU Cores to Use for Parallel Processing

## -- O --

objSize | Wrapper around 'lobstr::obj_size'
objSizeSession | Wrapper around 'lobstr::obj_size'

## -- P --

paddedFloatToChar | Convert numeric to character with padding
Path-class | Coerce a character string to a class "Path"
postProcess | Generic function to post process objects
postProcess.default | Generic function to post process objects
postProcess.list | Generic function to post process objects
postProcessTerra | Transform a GIS dataset so it has the properties (extent, projection, mask) of another
postProcessTo | Transform a GIS dataset so it has the properties (extent, projection, mask) of another
prepInputs | Download and optionally post-process files
prepInputsCOG | Fast spatial subsetting of Cloud Optimized GeoTiff (COG) files
prepInputsWithTiles | Alternative to 'prepInputs' that can use Spatial Tiles stored locally or on Google Drive
prepopulateCacheAsync | Pre-populate the in-memory 'showCache' cache for a given 'cachePath'
preProcess | Download, checksum, extract files
preProcessParams | Download, checksum, extract files
projectTo | Transform a GIS dataset so it has the properties (extent, projection, mask) of another
purgeChecksums | Purge the checksums of a single file

## -- R --

rasterRead | A helper to 'getOption("reproducible.rasterRead")'
remapFilenames | Remap file names
reproducible | The 'reproducible' package
reproducibleOptions | 'reproducible' options
retry | A wrapper around 'try' that retries on failure
rmFromCache | Low-level functions to create and work with a cache

## -- S --

saveToCache | Save an object to Cache
searchFull | Search up the full scope for functions
searchFullEx | Search up the full scope for functions
set.randomseed | Set seed with a random value using Sys.time()
showCache | Examining and modifying the cache
showCache-method | Examining and modifying the cache
studyAreaName | Get a unique name for a given study area
studyAreaName-method | Get a unique name for a given study area
suffix | Add a prefix or suffix to the basename part of a file path

## -- T --

tempdir2 | Make a temporary (sub-)directory
tempfile2 | Make a temporary file in a temporary (sub-)directory

## -- U --

unrarPath | The known path for unrar or 7z
urlExists | Checks for existed of a url or the internet using <https://CRAN.R-project.org>
usesPointer | Does an object use a pointer?

## -- V --

values2 | Get min or maximum value of a (Spat)Raster

## -- W --

writeFuture | Write to cache repository, using 'future::future'
writeTo | Transform a GIS dataset so it has the properties (extent, projection, mask) of another

## -- misc --

.addTagsRepo | Add a Tag to a Cached Object in the Repository
.debugCache | Attach debug info to return for Cache
.file.move | Move a file to a new location - Defunct - use 'hardLinkOrCopy'
.isCRSany | Some spatial helper functions
.isGridded | Some spatial helper functions
.isMemoised | Evaluate whether a cacheId is memoised
.isSF | Some spatial helper functions
.isSpat | Some spatial helper functions
.isSpatialAny | Some spatial helper functions
.isVector | Some spatial helper functions
.messageFunctionFn | Use 'message' with a consistent use of 'verbose'
.objSizeWithTry | 'lobstr::obj_size' with a 'try' to address issue #72
.prefix | Add a prefix or suffix to the basename part of a file path
.prepareFileBackedRaster | Copy the file-backing of a file-backed Raster* object
.removeCacheAtts | Remove attributes that are highly varying
.requireNamespace | Provide standard messaging for missing package dependencies
.setSubAttrInList | Set subattributes within a list by reference
.suffix | Add a prefix or suffix to the basename part of a file path
.systemArchivePath | The known path for unrar or 7z
.unwrap | Deal with class for saving to and loading from Cache or Disk
.unwrap.data.table | Deal with class for saving to and loading from Cache or Disk
.unwrap.default | Deal with class for saving to and loading from Cache or Disk
.unwrap.environment | Deal with class for saving to and loading from Cache or Disk
.unwrap.list | Deal with class for saving to and loading from Cache or Disk
.unwrap.PackedSpatExtent2 | Deal with class for saving to and loading from Cache or Disk
.unwrap.PackedSpatVector | Deal with class for saving to and loading from Cache or Disk
.unwrap.PackedSpatVector2 | Deal with class for saving to and loading from Cache or Disk
.updateTagsRepo | Add a Tag to a Cached Object in the Repository
.whereInStack | Search for objects in the call stack
.wrap | Deal with class for saving to and loading from Cache or Disk
.wrap.default | Deal with class for saving to and loading from Cache or Disk
.wrap.environment | Deal with class for saving to and loading from Cache or Disk
.wrap.list | Deal with class for saving to and loading from Cache or Disk