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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)

Contributions

Please see CONTRIBUTING.md for information on how to contribute to this project.

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Version

Install

install.packages('reproducible')

Monthly Downloads

2,317

Version

0.2.11

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/PredictiveEcology/reproducible

Homepage

https://reproducible.predictiveecology.org

Maintainer

Eliot J B

Last Published

November 19th, 2019

Functions in reproducible (0.2.11)

Do some minor error fixing

Test whether system is Windows

available.packagesMem

Memoised version of available.packages

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

.checkForAuxiliaryFiles

Check a neededFile for commonly needed auxiliary files

Check the GDAL version in use

A version of base::basename that is NULL resistant

Hardlink, symlink, or copy a file

Crop a Spatial* or Raster* object

checkGDALVersion

Check whether the system has a minimum version of GDAL available

getFunctionName

A set of helpers for Cache

A wrapper around try that retries on failure

Generic function to post process objects

Take a snapshot of all the packages and version numbers

reproducible-package

The reproducible package

Upload to cloud, if necessary

Create a custom cache message by class

reproducibleOptions

reproducible options

Purge individual line items from checksums file

cloudSyncCacheOld

Sync cloud with local Cache

checkAndMakeCloudFolderID

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

Attach debug info to return for Cache

Calculate checksum

Assess the appropriate raster layer data type

checkoutVersion

Clone, fetch, and checkout from GitHub.com repositories

.checkCacheRepo

Check for cache repository info in ...

Calculate the hashes of multiple files

clearStubArtifacts

Clear erroneous archivist artifacts

Download file from generic source url

NA-aware comparison of two vectors

Basic tool for using cloud-based caching

Grep system calls

Mask module inputs

assessDataTypeGDAL

Assess the appropriate raster layer data type for GDAL

Download from cloud, if necessary

Try to pick a file to load

Merge two cache repositories together

determineFilename

Determine filename, either automatically or manually

Change the absolute path of a file

Download file from Google Drive

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

.checkGitConfig

Check global git config file

Faster operations on rasters

extractFromArchive

Extract files from archive

installedVersions

Determine versions all installed packages

Check directory path

Alternative to interactive() for unit testing

cloudUploadFromCache

Upload a file to cloud directly from local cacheRepo

Determine package dependencies, first looking at local filesystem

.formalsNotInCurrentDots

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

.objSizeInclEnviros

Determine object size of all objects inside environments

Recursive object.size

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

Download and optionally post process files

Basic tool for using cloud-based caching

.listFilesInArchive

List files in either a .zip or or .tar file

Generic method to make or unmake objects memoisable

.removeCacheAtts

Remove attributes that are highly varying

A wrapper around a set of downloading functions

Normalize filepath

Write module inputs on disk

.sortDotsUnderscoreFirst

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

.setSubAttrInList

Set subattributes within a list by reference

.prepareFileBackedRaster

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

.installPackages

Internal function to install packages

package_dependenciesMem

Memoised version of package_dependencies

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

installVersions

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

Make any modifications to object recovered from cacheRepo

Project Raster* or Spatial* or sf objects

Create reproducible digests of objects in R

Search up the full scope for functions

The reproducible package environment

Write to archivist repository, using future::future

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

Examining and modifying the cache

testForArchiveExtract

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

Download, Checksum, Extract files

The known path for unrar or 7z

Hierarchically get crs from Raster*, Spatial*

.preDigestByClass

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

Add extra tags to an archive based on class

Make a temporary sub-directory

The exact digest function that Cache uses

Return the filename(s) from a Raster* object

Coerce a character string to a class "Path"

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

.addChangedAttr

Add an attribute to an object indicating which named elements change

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

.addTagsToOutput

Add tags to object

archiveExtractBinary

Tests if unrar or 7zip exist