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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

0.2.7

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

March 7th, 2019

Functions in reproducible (0.2.7)

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

assessDataTypeGDAL

Assess the appropriate raster layer data type for GDAL

getFunctionName

A set of helpers for Cache

.checkCacheRepo

Check for cache repository info in ...

The exact digest function that Cache uses

.checkForAuxiliaryFiles

Check a neededFile for commonly needed auxiliary files

Create a custom cache message by class

Calculate checksum

Sync cloud with local Cache

Basic tool for using cloud-based caching

clearStubArtifacts

Clear erroneous archivist artifacts

NA-aware comparison of two vectors

available.packagesMem

Memoised version of available.packages

Experimental use of googledrive for Caching

Hardlink, symlink, or copy a file

Change the absolute path of a file

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

.listFilesInArchive

List files in either a zip or tar

.addChangedAttr

Add an attribute to an object indicating which named elements change

Take a snapshot of all the packages and version numbers

.addTagsToOutput

Add tags to object

Generic function to post process objects

Assess the appropriate raster layer data type

A wrapper around a set of downloading functions

Alternative to readLines that is faster

Purge individual line items from checksums file

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

A version of base::basename that is NULL resistant

Tests if unrar or 7zip exist

extractFromArchive

Extract files from archive

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

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

checkGDALVersion

Check whether the system has a minimum version of GDAL available

Crop a Spatial* or Raster* object

Check the GDAL version in use

.checkGitConfig

Check global git config file

Internal function

Check directory path

Merge two cache repositories together

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

Make any modifications to object recovered from cacheRepo

Faster operations on rasters

Attach debug info to return for Cache

checkoutVersion

Clone, fetch, and checkout from GitHub.com repositories

Project Raster* or Spatial* or sf objects

.sortDotsUnderscoreFirst

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

Basic tool for using cloud-based caching

Do some minor error fixing

determineFilename

Determine filename, either automatically or manually

Download file from Google Drive

installVersions

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

Add extra tags to an archive based on class

installedVersions

Determine versions all installed packages

.objSizeInclEnviros

Determine object size of all objects inside environments

cloudDownloadChecksums

.formalsNotInCurrentDots

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

package_dependenciesMem

Memoised version of package_dependencies

Hierarchically get crs from Raster*, Spatial*

.preDigestByClass

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

Search up the full scope for functions

Download and optionally post process files

Try to pick a file to load

.setSubAttrInList

Set subattributes within a list by reference

.installPackages

Internal function to install packages

Normalize filepath

Calculate the hashes of multiple files

Download file from generic source url

Recursive object.size

Generic method to make or unmake objects memoisable

.prepareFileBackedRaster

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

Write to archivist repository, using future::future

readLinesRcppInternal

Alternative to readLines that is faster

Write module inputs on disk

reproducible-package

The reproducible package

Mask module inputs

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

Determine package dependencies, first looking at local filesystem

Download, Checksum, Extract files

The known path for unrar or 7z

Examining and modifying the cache

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

reproducibleOptions

reproducible options

Create reproducible digests of objects in R

Coerce a character string to a class "Path"