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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

0.1.4

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/PredictiveEcology/reproducible

Homepage

https://predictiveecology.github.io/reproducible/

Maintainer

Eliot J B

Last Published

January 25th, 2018

Functions in reproducible (0.1.4)

.checkCacheRepo

Check for cache repository info in ...

.checkGitConfig

Check global git config file

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

.addTagsToOutput

Add tags to object

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

Coerce a character string to a class "Path"

installedVersions

Determine versions all installed pacakges

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

package_dependenciesMem

Memoised version of package_dependencies

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

Create reproducible digests of objects in R

Search up the full scope for functions

Take a snapshot of all the packages and version numbers

.preDigestByClass

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

Examining and modifying the cache

checkoutVersion

Clone, fetch, and checkout from GitHub.com repositories

.prepareFileBackedRaster

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

Make any modifications to object recovered from cacheRepo

Deprecated functions

getFunctionName

A set of helpers for Cache

Create a custom cache message by class

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

Attach debug info to return for Cache

Normalize filepath

.objSizeInclEnviros

Determine object size of all objects inside environments

.sortDotsUnderscoreFirst

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

.installPackages

Internal function to install packages

installVersions

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

Pipe that is Cache-aware, being deprecated

Determine package dependencies, first looking at local filesystem

Add extra tags to an archive based on class

available.packagesMem

Memoised version of available.packages

Cache method that accommodates environments, S4 methods, Rasters

clearStubArtifacts

Clear erroneous archivist artifacts

NA-aware comparison of two vectors

Alternative to readLines that is faster

reproducible-package

The reproducible package

readLinesRcppInternal

Alternative to readLines that is faster