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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

2,317

Version

0.2.8

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 18th, 2019

Functions in reproducible (0.2.8)

Coerce a character string to a class "Path"

checkGDALVersion

Check whether the system has a minimum version of GDAL available

A version of base::basename that is NULL resistant

Download file from generic source url

.installPackages

Internal function to install packages

installVersions

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

Download file from Google Drive

Create a custom cache message by class

.addChangedAttr

Add an attribute to an object indicating which named elements change

checkoutVersion

Clone, fetch, and checkout from GitHub.com repositories

clearStubArtifacts

Clear erroneous archivist artifacts

.checkCacheRepo

Check for cache repository info in ...

.checkGitConfig

Check global git config file

determineFilename

Determine filename, either automatically or manually

Calculate the hashes of multiple files

Do some minor error fixing

Check the GDAL version in use

Change the absolute path of a file

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

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

Check directory path

getFunctionName

A set of helpers for Cache

Normalize filepath

Experimental use of googledrive for Caching

Basic tool for using cloud-based caching

Basic tool for using cloud-based caching

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

Determine package dependencies, first looking at local filesystem

Take a snapshot of all the packages and version numbers

NA-aware comparison of two vectors

cloudDownloadChecksums

Crop a Spatial* or Raster* object

Sync cloud with local Cache

Attach debug info to return for Cache

extractFromArchive

Extract files from archive

.formalsNotInCurrentDots

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

A wrapper around a set of downloading functions

Generic function to post process objects

Faster operations on rasters

installedVersions

Determine versions all installed packages

Hierarchically get crs from Raster*, Spatial*

Add extra tags to an archive based on class

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

.listFilesInArchive

List files in either a zip or tar

Hardlink, symlink, or copy a file

Generic method to make or unmake objects memoisable

Recursive object.size

.objSizeInclEnviros

Determine object size of all objects inside environments

package_dependenciesMem

Memoised version of package_dependencies

Internal function

Try to pick a file to load

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

Project Raster* or Spatial* or sf objects

Mask module inputs

Merge two cache repositories together

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

Purge individual line items from checksums file

Alternative to readLines that is faster

Download and optionally post process files

readLinesRcppInternal

Alternative to readLines that is faster

Search up the full scope for functions

Create reproducible digests of objects in R

Tests if unrar or 7zip exist

.preDigestByClass

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

The known path for unrar or 7z

.prepareFileBackedRaster

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

Examining and modifying the cache

Make any modifications to object recovered from cacheRepo

Write to archivist repository, using future::future

.setSubAttrInList

Set subattributes within a list by reference

.sortDotsUnderscoreFirst

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

Download, Checksum, Extract files

reproducible-package

The reproducible package

reproducibleOptions

reproducible options

Write module inputs on disk

The exact digest function that Cache uses

Calculate checksum

.checkForAuxiliaryFiles

Check a neededFile for commonly needed auxiliary files

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

.addTagsToOutput

Add tags to object

Assess the appropriate raster layer data type

assessDataTypeGDAL

Assess the appropriate raster layer data type for GDAL

available.packagesMem

Memoised version of available.packages

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