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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 utilites 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

0.2.5

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

November 16th, 2018

Functions in reproducible (0.2.5)

.checkForAuxiliaryFiles

Check a neededFile for commonly needed auxiliary files

Faster operations on rasters

determineFilename

Determine filename, either automatically or manually

Check directory path

Attach debug info to return for Cache

Try to pick a file to load

.checkGitConfig

Check global git config file

.objSizeInclEnviros

Determine object size of all objects inside environments

Internal function

Recursive object.size

.addTagsToOutput

Add tags to object

checkGDALVersion

Check whether the system has a minimum version of GDAL available

Do some minor error fixing

.listFilesInArchive

List files in either a zip or tar

makeMemoiseable

Generic method to make or unmake objects memoisable

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

Create a custom cache message by class

checkoutVersion

Clone, fetch, and checkout from GitHub.com repositories

Pipe that is Cache-aware, being deprecated

clearStubArtifacts

Clear erroneous archivist artifacts

Download file from Google Drive

getFunctionName

A set of helpers for Cache

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

Determine package dependencies, first looking at local filesystem

Hardlink, symlink, or copy a file

.checkCacheRepo

Check for cache repository info in ...

installedVersions

Determine versions all installed packages

.formalsNotInCurrentDots

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

Crop a Spatial* or Raster* object

Calculate the hashes of multiple files

fixErrors.SpatialPolygons

Fix rgeos::gIsValid failures in SpatialPolygons

Download, Checksum, Extract files

Download file from generic source url

Check the GDAL version in use

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

NA-aware comparison of two vectors

A wrapper around a set of downloading functions

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

Change the absolute path of a file

extractFromArchive

Extract files from archive

Take a snapshot of all the packages and version numbers

Normalize filepath

package_dependenciesMem

Memoised version of package_dependencies

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

Generic function to post process objects

.installPackages

Internal function to install packages

readLinesRcppInternal

Alternative to readLines that is faster

Deprecated functions

Make any modifications to object recovered from cacheRepo

reproducible-package

The reproducible package

installVersions

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

Project Raster* or Spatial* or sf objects

Create reproducible digests of objects in R

Purge individual line items from checksums file

Write to archivist repository, using future::future

Write module inputs on disk

Alternative to readLines that is faster

Mask module inputs

Merge two cache repositories together

Hierarchically get crs from Raster*, Spatial*

Download and optionally post process files

.preDigestByClass

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

.prepareFileBackedRaster

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

Search up the full scope for functions

.sortDotsUnderscoreFirst

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

Add extra tags to an archive based on class

Examining and modifying the cache

Assess the appropriate raster layer data type

.addChangedAttr

Add an attribute to an object indicating which named elements change

Coerce a character string to a class "Path"

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

Calculate checksum

assessDataTypeGDAL

Assess the appropriate raster layer data type for GDAL

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

Helper functions for assessDataType

available.packagesMem

Memoised version of available.packages