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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

2,317

Version

0.2.0

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

June 17th, 2018

Functions in reproducible (0.2.0)

.checkGitConfig

Check global git config file

.sortDotsUnderscoreFirst

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

NA-aware comparison of two vectors

Pipe that is Cache-aware, being deprecated

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

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

Try to pick a file to load

Make any modifications to object recovered from cacheRepo

Merge two cache repositories together

Recursive object.size

determineFilename

Determine filename, either automatically or manually

checkGDALVersion

Check whether the system has a minimum version of GDAL available

fixErrors.SpatialPolygons

Fix rgeos::gIsValid failures in SpatialPolygons

Create a custom cache message by class

checkoutVersion

Clone, fetch, and checkout from GitHub.com repositories

Coerce a character string to a class "Path"

.checkForAuxiliaryFiles

Check a neededFile for commonly needed auxiliary files

.checkCacheRepo

Check for cache repository info in ...

Purge individual line items from checksums file

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

Search up the full scope for functions

Calculate the hashes of multiple files

.addTagsToOutput

Add tags to object

A wrapper around a set of downloading functions

extractFromArchive

Extract files from archive

Determine package dependencies, first looking at local filesystem

Hierarchically get crs from Raster*, Spatial*

.installPackages

Internal function to install packages

clearStubArtifacts

Clear erroneous archivist artifacts

Create reproducible digests of objects in R

available.packagesMem

Memoised version of available.packages

Faster operations on rasters

Download file from generic source url

Add extra tags to an archive based on class

Deprecated functions

.objSizeInclEnviros

Determine object size of all objects inside environments

.preDigestByClass

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

getFunctionName

A set of helpers for Cache

Check the GDAL version in use

package_dependenciesMem

Memoised version of package_dependencies

Project Raster* or Spatial* or sf objects

Attach debug info to return for Cache

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

Do some minor error fixing

Calculate checksum

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

installVersions

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

Crop a Spatial* or Raster* object

Mask module inputs

Normalize filepath

reproducible-package

The reproducible package

installedVersions

Determine versions all installed packages

readLinesRcppInternal

Alternative to readLines that is faster

Download, Checksum, Extract files

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

Download file from Google Drive

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

Alternative to readLines that is faster

Take a snapshot of all the packages and version numbers

Generic function to post process objects

.prepareFileBackedRaster

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

Download and optionally post process files

Examining and modifying the cache

Write module inputs on disk