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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

0.2.10

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

September 11th, 2019

Functions in reproducible (0.2.10)

Assess the appropriate raster layer data type

Calculate checksum

The exact digest function that Cache uses

.addTagsToOutput

Add tags to object

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

Coerce a character string to a class "Path"

Return the filename(s) from a Raster* object

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

.addChangedAttr

Add an attribute to an object indicating which named elements change

Create a custom cache message by class

available.packagesMem

Memoised version of available.packages

assessDataTypeGDAL

Assess the appropriate raster layer data type for GDAL

checkAndMakeCloudFolderID

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

A version of base::basename that is NULL resistant

Check directory path

checkoutVersion

Clone, fetch, and checkout from GitHub.com repositories

clearStubArtifacts

Clear erroneous archivist artifacts

.checkForAuxiliaryFiles

Check a neededFile for commonly needed auxiliary files

.checkCacheRepo

Check for cache repository info in ...

determineFilename

Determine filename, either automatically or manually

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

Basic tool for using cloud-based caching

Download file from generic source url

cloudSyncCacheOld

Sync cloud with local Cache

NA-aware comparison of two vectors

cloudDownloadChecksumsOld

Download from cloud, if necessary

Change the absolute path of a file

Upload to cloud, if necessary

Attach debug info to return for Cache

Basic tool for using cloud-based caching

cloudUploadFromCache

Upload a file to cloud directly from local cacheRepo

Download, Checksum, Extract files

.removeCacheAtts

Remove attributes that are highly varying

Generic method to make or unmake objects memoisable

A wrapper around a set of downloading functions

.preDigestByClass

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

Download and optionally post process files

.formalsNotInCurrentDots

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

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

Download file from Google Drive

Normalize filepath

.listFilesInArchive

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

checkGDALVersion

Check whether the system has a minimum version of GDAL available

Mask module inputs

Merge two cache repositories together

Calculate the hashes of multiple files

Make any modifications to object recovered from cacheRepo

Write to archivist repository, using future::future

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

getFunctionName

A set of helpers for Cache

Hierarchically get crs from Raster*, Spatial*

.installPackages

Internal function to install packages

Try to pick a file to load

installVersions

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

Grep system calls

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

Examining and modifying the cache

Generic function to post process objects

.checkGitConfig

Check global git config file

Take a snapshot of all the packages and version numbers

Determine package dependencies, first looking at local filesystem

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

Add extra tags to an archive based on class

.prepareFileBackedRaster

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

The reproducible package environment

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

Crop a Spatial* or Raster* object

reproducible-package

The reproducible package

Create reproducible digests of objects in R

.setSubAttrInList

Set subattributes within a list by reference

Do some minor error fixing

installedVersions

Determine versions all installed packages

Check the GDAL version in use

Project Raster* or Spatial* or sf objects

Search up the full scope for functions

extractFromArchive

Extract files from archive

Faster operations on rasters

package_dependenciesMem

Memoised version of package_dependencies

Purge individual line items from checksums file

Hardlink, symlink, or copy a file

Tests if unrar or 7zip exist

.objSizeInclEnviros

Determine object size of all objects inside environments

The known path for unrar or 7z

Write module inputs on disk

reproducibleOptions

reproducible options

Recursive object.size

A wrapper around try that retries on failure

.sortDotsUnderscoreFirst

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