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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

1,334

Version

1.1.0

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

May 15th, 2020

Functions in reproducible (1.1.0)

Coerce a character string to a class "Path"

Calculate checksum

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

A collection of low level tools for Cache

.addChangedAttr

Add an attribute to an object indicating which named elements change

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

The exact digest function that Cache uses

Return the filename(s) from a Raster* object

.addTagsToOutput

Add tags to object

assessDataTypeGDAL

Assess the appropriate raster layer data type for GDAL

A version of base::basename that is NULL resistant

Download from cloud, if necessary

Basic tool for using cloud-based caching

checkoutVersion

Clone, fetch, and checkout from GitHub.com repositories

Create a new cache

Create a custom cache message by class

clearStubArtifacts

Clear erroneous archivist artifacts

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

Attach debug info to return for Cache

archiveExtractBinary

Tests if unrar or 7zip exist

NA-aware comparison of two vectors

getFunctionName

A set of helpers for Cache

Assess the appropriate raster layer data type

Download file from generic source url

Generic method to make or unmake objects memoisable

Hardlink, symlink, or copy a file

Change the absolute path of a file

checkAndMakeCloudFolderID

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

.listFilesInArchive

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

Check directory path

Mask module inputs

.checkGitConfig

Check global git config file

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

Calculate the hashes of multiple files

.checkCacheRepo

Check for cache repository info in ...

Basic tool for using cloud-based caching

.formalsNotInCurrentDots

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

Take a snapshot of all the packages and version numbers

Merge two cache repositories together

Faster operations on rasters

determineFilename

Determine filename, either automatically or manually

.installPackages

Internal function to install packages

cloudUploadFromCache

Upload a file to cloud directly from local cacheRepo

Try to pick a file to load

Download file from Google Drive

Generic function to post process objects

Deal with moved cache issues

Hierarchically get crs from Raster*, Spatial*

Write module inputs on disk

Write to cache repository, using future::future

reproducible-package

The reproducible package

.preDigestByClass

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

Purge individual line items from checksums file

Do some minor error fixing

Search up the full scope for functions

Crop a Spatial* or Raster* object

Create reproducible digests of objects in R

available.packagesMem

Memoised version of available.packages

installVersions

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

.setSubAttrInList

Set subattributes within a list by reference

Determine package dependencies, first looking at local filesystem

.prepareFileBackedRaster

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

Download and optionally post-process files

installedVersions

Determine versions all installed packages

The reproducible package environment

A wrapper around a set of downloading functions

checkGDALVersion

Check whether the system has a minimum version of GDAL available

cloudSyncCacheOld

Sync cloud with local Cache

.checkForAuxiliaryFiles

Check a neededFile for commonly needed auxiliary files

extractFromArchive

Extract files from archive

Check the GDAL version in use

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

.sortDotsUnderscoreFirst

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

Make a temporary sub-directory or file in that subdirectory

testForArchiveExtract

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

Grep system calls

Normalize filepath

Upload to cloud, if necessary

.removeCacheAtts

Remove attributes that are highly varying

Download, Checksum, Extract files

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

reproducibleOptions

reproducible options

A wrapper around try that retries on failure

The known path for unrar or 7z

Examining and modifying the cache

Alternative to interactive() for unit testing

.requireNamespace

Provide standard messaging for missing package dependencies

Recursive object.size

Test whether system is Windows

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

Make any modifications to object recovered from cacheRepo

Project Raster* or Spatial* or sf objects

Get a unique name for a given study area

Add extra tags to an archive based on class