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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.

News

See updates from latest CRAN and development versions. Note that versions 1.0.0 and later are not compatible with previous versions "out of the box". However, setting the options("reproducible.useDBI" = FALSE) will return the behaviour to prior versions and so should be compatible. The new version is much faster and creates smaller repository files and allows for different (e.g., RPostgres backends for the database -- not the saved files, however; these are still saved locally).

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

1.0.0

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

February 20th, 2020

Functions in reproducible (1.0.0)

A version of base::basename that is NULL resistant

archiveExtractBinary

Tests if unrar or 7zip exist

.checkCacheRepo

Check for cache repository info in ...

getFunctionName

A set of helpers for Cache

checkAndMakeCloudFolderID

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

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

checkoutVersion

Clone, fetch, and checkout from GitHub.com repositories

Assess the appropriate raster layer data type

clearStubArtifacts

Clear erroneous archivist artifacts

Attach debug info to return for Cache

determineFilename

Determine filename, either automatically or manually

Return the filename(s) from a Raster* object

cloudSyncCacheOld

Sync cloud with local Cache

Faster operations on rasters

Try to pick a file to load

extractFromArchive

Extract files from archive

Grep system calls

assessDataTypeGDAL

Assess the appropriate raster layer data type for GDAL

checkGDALVersion

Check whether the system has a minimum version of GDAL available

available.packagesMem

Memoised version of available.packages

Create a custom cache message by class

Download from cloud, if necessary

Basic tool for using cloud-based caching

.checkForAuxiliaryFiles

Check a neededFile for commonly needed auxiliary files

A wrapper around a set of downloading functions

.removeCacheAtts

Remove attributes that are highly varying

installedVersions

Determine versions all installed packages

Upload to cloud, if necessary

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

cloudUploadFromCache

Upload a file to cloud directly from local cacheRepo

Mask module inputs

Merge two cache repositories together

.prepareFileBackedRaster

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

Alternative to interactive() for unit testing

.preDigestByClass

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

Download, Checksum, Extract files

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

Normalize filepath

Create a new cache

Make any modifications to object recovered from cacheRepo

Check directory path

Change the absolute path of a file

NA-aware comparison of two vectors

.checkGitConfig

Check global git config file

Crop a Spatial* or Raster* object

Basic tool for using cloud-based caching

Do some minor error fixing

A wrapper around try that retries on failure

Check the GDAL version in use

Generic method to make or unmake objects memoisable

Download file from Google Drive

Take a snapshot of all the packages and version numbers

Download file from generic source url

Generic function to post process objects

Calculate the hashes of multiple files

Create reproducible digests of objects in R

Search up the full scope for functions

.installPackages

Internal function to install packages

The reproducible package environment

.listFilesInArchive

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

.sortDotsUnderscoreFirst

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

Hardlink, symlink, or copy a file

Recursive object.size

Test whether system is Windows

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

installVersions

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

Determine package dependencies, first looking at local filesystem

.setSubAttrInList

Set subattributes within a list by reference

.formalsNotInCurrentDots

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

Hierarchically get crs from Raster*, Spatial*

Add extra tags to an archive based on class

The known path for unrar or 7z

Write to archivist repository, using future::future

Write module inputs on disk

Examining and modifying the cache

Project Raster* or Spatial* or sf objects

Purge individual line items from checksums file

reproducibleOptions

reproducible options

package_dependenciesMem

Memoised version of package_dependencies

reproducible-package

The reproducible package

Download and optionally post process files

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

Make a temporary sub-directory

testForArchiveExtract

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

.addChangedAttr

Add an attribute to an object indicating which named elements change

A collection of low level tools for Cache

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

.addTagsToOutput

Add tags to object

Coerce a character string to a class "Path"

Calculate checksum

The exact digest function that Cache uses

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