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reproducible

A set of tools for R that enhance reproducibility beyond package management. Built on top of git2r and archivist, this package aims at making high-level, robust, machine and OS independent tools for making deeply reproducible and reusable content in R. This extends beyond the package management utilites of packrat and checkpoint by including tools for caching and accessing GitHub repositories.

Installation

Current stable release

Install from CRAN:

install.packages("reproducible")

Install from GitHub:

#install.packages("devtools")
library("devtools")
install_github("PredictiveEcology/reproducible", dependencies = TRUE) # stable

Development version (unstable)

Install from GitHub:

#install.packages("devtools")
library("devtools")
install_github("PredictiveEcology/reproducible", ref = "development", dependencies = TRUE) # unstable

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Version

Install

install.packages('reproducible')

Monthly Downloads

988

Version

0.2.3

License

GPL-3

Issues

Pull Requests

Stars

Forks

Maintainer

Eliot J B

Last Published

August 7th, 2018

Functions in reproducible (0.2.3)

Checksums

Calculate checksum
.cacheMessage

Create a custom cache message by class
.checkCacheRepo

Check for cache repository info in ...
assessDataType

Assess the appropriate raster layer data type
dlGoogle

Download file from Google Drive
available.packagesMem

Memoised version of available.packages
Cache

Cache method that accommodates environments, S4 methods, Rasters, & nested caching
getFunctionName

A set of helpers for Cache
downloadFile

A wrapper around a set of downloading functions
.checkGitConfig

Check global git config file
.installPackages

Internal function to install packages
checkoutVersion

Clone, fetch, and checkout from GitHub.com repositories
checkPath

Check filepath
Require

Repeatability-safe install and load packages, optionally with specific versions
convertPaths

Change the absolute path of a file
compareNA

NA-aware comparison of two vectors
.checkForAuxiliaryFiles

Check a neededFile for commonly needed auxiliary files
extractFromArchive

Extract files from archive
checkGDALVersion

Check whether the system has a minimum version of GDAL available
.debugCache

Attach debug info to return for Cache
installVersions

Install exact package versions from a package version text file & GitHub
determineFilename

Determine filename, either automatically or manually
installedVersions

Determine versions all installed packages
.listFilesInArchive

List files in either a zip or tar
cropInputs

Crop a Spatial* or Raster* object
copyFile

Copy a file using robocopy on Windows and rsync on Linux/macOS
.addChangedAttr

Add an attribute to an object indicating which named elements change
.addTagsToOutput

Add tags to object
clearStubArtifacts

Clear erroneous archivist artifacts
.objSizeInclEnviros

Determine object size of all objects inside environments
pkgDep

Determine package dependencies, first looking at local filesystem
fastMask

Faster operations on rasters
normPath

Normalize filepath
pkgSnapshot

Take a snapshot of all the packages and version numbers
postProcess

Generic function to post process objects
makeMemoiseable

Generic method to make or unmake objects memoisable
getGDALVersion

Check the GDAL version in use
objSize

Recursive object.size
package_dependenciesMem

Memoised version of package_dependencies
maskInputs

Mask module inputs
mergeCache

Merge two cache repositories together
.prefix

Add a prefix or suffix to the basename part of a file path
.digest

Calculate the hashes of multiple files
guessAtTarget

Try to pick a file to load
clearCache

Examining and modifying the cache
.getTargetCRS

Hierarchically get crs from Raster*, Spatial*
.prepareOutput

Make any modifications to object recovered from cacheRepo
.prepareFileBackedRaster

Copy the file-backing of a file-backed Raster* object
writeFuture

Write to archivist repository, using future::future
prepInputs

Download and optionally post process files
.preDigestByClass

Any miscellaneous things to do before .robustDigest and after FUN call
readLinesRcpp

Alternative to readLines that is faster
.sortDotsUnderscoreFirst

Sort or order any named object with dotted names and underscores first
dlGeneric

Download file from generic source url
.tagsByClass

Add extra tags to an archive based on class
preProcess

Download, Checksum, Extract files
cache

Deprecated functions
reproducible-package

The reproducible package
writeOutputs

Write module inputs on disk
readLinesRcppInternal

Alternative to readLines that is faster
fixErrors

Do some minor error fixing
newLibPaths

A shortcut to create a .libPaths() with only 2 folders
fixErrors.SpatialPolygons

Fix rgeos::gIsValid failures in SpatialPolygons
pipe

A cache-aware pipe that does not mask with %>%
pipe2

Pipe that is Cache-aware, being deprecated
projectInputs

Project Raster* or Spatial* or sf objects
.purge

Purge individual line items from checksums file
searchFull

Search up the full scope for functions
.robustDigest

Create reproducible digests of objects in R
Path-class

Coerce a character string to a class "Path"
Copy

Recursive copying of nested environments, and other "hard to copy" objects