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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

1,998

Version

1.1.1

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 20th, 2020

Functions in reproducible (1.1.1)

The exact digest function that Cache uses

Calculate checksum

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

.addChangedAttr

Add an attribute to an object indicating which named elements change

A collection of low level tools for Cache

Return the filename(s) from a Raster* object

Coerce a character string to a class "Path"

.addTagsToOutput

Add tags to object

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

A version of base::basename that is NULL resistant

checkoutVersion

Clone, fetch, and checkout from GitHub.com repositories

clearStubArtifacts

Clear erroneous archivist artifacts

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

Assess the appropriate raster layer data type

Download from cloud, if necessary

NA-aware comparison of two vectors

Basic tool for using cloud-based caching

archiveExtractBinary

Tests if unrar or 7zip exist

Change the absolute path of a file

cloudSyncCacheOld

Sync cloud with local Cache

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

assessDataTypeGDAL

Assess the appropriate raster layer data type for GDAL

available.packagesMem

Memoised version of available.packages

Crop a Spatial* or Raster* object

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

Try to pick a file to load

.installPackages

Internal function to install packages

Upload to cloud, if necessary

Normalize filepath

Project Raster* or Spatial* or sf objects

Make any modifications to object recovered from cacheRepo

Download file from Google Drive

Get a unique name for a given study area

Calculate the hashes of multiple files

Download file from generic source url

.removeCacheAtts

Remove attributes that are highly varying

Add extra tags to an archive based on class

Create a new cache

Check directory path

Create a custom cache message by class

cloudUploadFromCache

Upload a file to cloud directly from local cacheRepo

.requireNamespace

Provide standard messaging for missing package dependencies

.checkGitConfig

Check global git config file

checkAndMakeCloudFolderID

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

.checkCacheRepo

Check for cache repository info in ...

.formalsNotInCurrentDots

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

Attach debug info to return for Cache

Basic tool for using cloud-based caching

Hardlink, symlink, or copy a file

Generic method to make or unmake objects memoisable

Mask module inputs

Download, Checksum, Extract files

.listFilesInArchive

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

determineFilename

Determine filename, either automatically or manually

Check the GDAL version in use

A wrapper around a set of downloading functions

getFunctionName

A set of helpers for Cache

extractFromArchive

Extract files from archive

Take a snapshot of all the packages and version numbers

Grep system calls

Faster operations on rasters

checkGDALVersion

Check whether the system has a minimum version of GDAL available

installVersions

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

installedVersions

Determine versions all installed packages

.checkForAuxiliaryFiles

Check a neededFile for commonly needed auxiliary files

Alternative to interactive() for unit testing

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

Search up the full scope for functions

Do some minor error fixing

Recursive object.size

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

Create reproducible digests of objects in R

.sortDotsUnderscoreFirst

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

.setSubAttrInList

Set subattributes within a list by reference

Deal with moved cache issues

Merge two cache repositories together

Generic function to post process objects

Make a temporary sub-directory or file in that subdirectory

Test whether system is Windows

Download and optionally post-process files

.prepareFileBackedRaster

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

Determine package dependencies, first looking at local filesystem

reproducible-package

The reproducible package

The known path for unrar or 7z

Purge individual line items from checksums file

.preDigestByClass

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

The reproducible package environment

Examining and modifying the cache

reproducibleOptions

reproducible options

Write to cache repository, using future::future

A wrapper around try that retries on failure

testForArchiveExtract

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

Write module inputs on disk

Hierarchically get crs from Raster*, Spatial*