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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 utilities of packrat and checkpoint by including tools for caching and accessing GitHub repositories.

Installation

Current release (on CRAN)

Install from CRAN:

install.packages("reproducible")

Install from GitHub:

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

Development version

Install from GitHub:

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

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Version

Install

install.packages('reproducible')

Monthly Downloads

1,072

Version

0.2.9

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/PredictiveEcology/reproducible

Homepage

http://reproducible.predictiveecology.org

Maintainer

Eliot J B

Last Published

July 9th, 2019

Functions in reproducible (0.2.9)

The exact digest function that Cache uses

Calculate checksum

.addChangedAttr

Add an attribute to an object indicating which named elements change

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

Return the filename or filenames from a Raster* object

assessDataTypeGDAL

Assess the appropriate raster layer data type for GDAL

Coerce a character string to a class "Path"

available.packagesMem

Memoised version of available.packages

.checkCacheRepo

Check for cache repository info in ...

.checkForAuxiliaryFiles

Check a neededFile for commonly needed auxiliary files

cloudDownloadChecksumsOld

checkAndMakeCloudFolderID

Check for presence of checkFolderID (for Cache(useCloud))

Create a custom cache message by class

Download from cloud, if necessary

A version of base::basename that is NULL resistant

Upload to cloud, if necessary

cloudSyncCacheOld

Sync cloud with local Cache

Calculate the hashes of multiple files

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

checkGDALVersion

Check whether the system has a minimum version of GDAL available

determineFilename

Determine filename, either automatically or manually

Attach debug info to return for Cache

extractFromArchive

Extract files from archive

Download file from generic source url

.checkGitConfig

Check global git config file

checkoutVersion

Clone, fetch, and checkout from GitHub.com repositories

getFunctionName

A set of helpers for Cache

Check directory path

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

.removeCacheAtts

Remove attributes that are highly varying

clearStubArtifacts

Clear erroneous archivist artifacts

Check the GDAL version in use

A shortcut to create a .libPaths() with only two directories

Do some minor error fixing

Crop a Spatial* or Raster* object

cloudUploadFromCache

Upload a file to cloud directly from local cacheRepo

Normalize filepath

Basic tool for using cloud-based caching

Generic function to post process objects

Hierarchically get crs from Raster*, Spatial*

reproducibleOptions

reproducible options

reproducible-package

The reproducible package

Generic method to make or unmake objects memoisable

Faster operations on rasters

.listFilesInArchive

List files in either a zip or tar

The known path for unrar or 7z

A wrapper around a set of downloading functions

Hardlink, symlink, or copy a file

installedVersions

Determine versions all installed packages

.prepareFileBackedRaster

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

package_dependenciesMem

Memoised version of package_dependencies

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

Take a snapshot of all the packages and version numbers

Purge individual line items from checksums file

Project Raster* or Spatial* or sf objects

Determine package dependencies, first looking at local filesystem

Download file from Google Drive

.formalsNotInCurrentDots

Identify which formals to a function are not in the current ...

Search up the full scope for functions

.setSubAttrInList

Set subattributes within a list by reference

Make any modifications to object recovered from cacheRepo

Examining and modifying the cache

Write module inputs on disk

Write to archivist repository, using future::future

Basic tool for using cloud-based caching

Change the absolute path of a file

Internal function

Try to pick a file to load

NA-aware comparison of two vectors

Mask module inputs

Recursive object.size

Merge two cache repositories together

.objSizeInclEnviros

Determine object size of all objects inside environments

.installPackages

Internal function to install packages

installVersions

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

Download, Checksum, Extract files

Download and optionally post process files

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

.sortDotsUnderscoreFirst

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

Add extra tags to an archive based on class

.preDigestByClass

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

Create reproducible digests of objects in R

Returns unrar path and creates a shortcut as .unrarPath Was not incorporated in previous function so it can be used in the tests

A wrapper around try that retries on failure

Tests if unrar or 7zip exist

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

Assess the appropriate raster layer data type

.addTagsToOutput

Add tags to object