A Set of Tools that Enhance Reproducibility Beyond Package Management

Collection of high-level, robust, machine- and OS-independent tools for making deeply reproducible and reusable content in R. This includes light weight package management (similar to 'packrat' and 'checkpoint', but more flexible, lightweight, simpler and less tested than both), tools for caching, downloading and verifying or writing checksums, post-processing of common spatial datasets, and accessing GitHub repositories. Some features are still under active development.


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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)

Build Status Appveyor Build status Coverage Status

Install from CRAN:

install.packages("reproducible")

Install from GitHub:

#install.packages("devtools")
library("devtools")
install_github("PredictiveEcology/reproducible", dependencies = TRUE) 

Development version

Build Status Appveyor Build status Coverage Status

Install from GitHub:

#install.packages("devtools")
library("devtools")
install_github("PredictiveEcology/reproducible", ref = "development", dependencies = TRUE) 

News

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 0.2.7

New features

  • CHECKSUMS.txt should now be ordered consistently across operating systems (note: base::order will not succeed in doing this --> now using .orderDotsUnderscoreFirst)
  • cloudSyncCache has a new argument: cacheIds. Now user can control entries by cacheId, so can delete/upload individual objects by cacheId
  • Experimental support within the postProcess family for sf class objects

bug fixes

  • mostly minor
  • cloudCache bugfixes for more cases

version 0.2.6

Dependency changes

  • remove tibble from Imports as it's no longer being used

New features

  • remove %>% pipe that was long ago deprecated. User should use %C% if they want a pipe that is Cache-aware. See examples.
  • Full rewrite of all options descriptions now in reproducible, see ?reproducibleOptions
  • now cacheRepo and options("reproducible.cachePath") can take a vector of paths. Similar to how .libPaths() works for libraries, Cache will search first in the first entry in the cacheRepo, then the second etc. until it finds an entry. It will only write to the first entry.
  • new value for the option: options("reproducible.useCache" = "devMode"). The point of this mode is to facilitate using the Cache when functions and datasets are continually in flux, and old Cache entries are likely stale very often. In devMode, the cache mechanism will work as normal if the Cache call is the first time for a function OR if it successfully finds a copy in the cache based on the normal Cache mechanism. It differs from the normal Cache if the Cache call does not find a copy in the cacheRepo, but it does find an entry that matches based on userTags. In this case, it will delete the old entry in the cacheRepo (identified based on matching userTags), then continue with normal Cache. For this to work correctly, userTags must be unique for each function call. This should be used with caution as it is still experimental.
  • change to how hashes are calculated. This will cause existing caches to not work correctly. To allow a user to keep old behaviour (during a transition period), the "old" algorithm can be used, with options("reproducible.useNewDigestAlgorithm" = FALSE). There is a message of this change on package load.
  • add experimental cloud* functions, especially cloudCache which allows sharing of Cache among collaborators. Currently only works with googledrive
  • updated assessDataType to consolidate assessDataTypeGDAL and assessDataType into single function (#71, @ianmseddy)
  • cc: new function -- a shortcut for some commonly used options for clearCache()
  • added experimental capacity for prepInputs to handle .rar archives, on systems with correct binaries to deal with them (#86, @tati-micheletti)
  • remove fastdigest::fastdigest as it is not return the identical hash across operating systems

Bug fixes

  • prepInputs on GIS objects that don't use raster::raster to load object were skipping postProcess. Fixed.
  • under some circumstances, the prepInputs would cause virtually all entries in CHECKSUMS.txt to be deleted. 2 cases where this happened were identified and corrected.
  • data.table class objects would give an error sometimes due to use of attr(DT). Internally, attributes are now added with data.table::setattr to deal with this.
  • calling gdalwarp from prostProcess now correctly matches extent (#73, @tati-micheletti)
  • files from url that have unknown extension are now guessed with by preProcess (#92, @tati-micheletti)

version 0.2.5

Dependency changes

  • Added remotes to Imports and removed devtools

New features

  • New value possible for options(reproducible.useCache = 'overwrite'), which allows use of Cache in cases where the function call has an entry in the cacheRepo, will purge it and add the output of the current call instead.

  • New option reproducible.inputPaths (default NULL) and reproducible.inputPathsRecursive (default FALSE), which will be used in prepInputs as possible directory sources (searched recursively or not) for files being downloaded/extracted/prepared. This allows the using of local copies of files in (an)other location(s) instead of downloading them. If local location does not have the required files, it will proceed to download so there is little cost in setting this option. If files do exist on local system, the function will attempt to use a hardlink before making a copy.

  • dlGoogle() now sets options(httr_oob_default = TRUE) if using Rstudio Server.

  • Files in CHECKSUMS now sorted alphabetically.

  • Checksums can now have a CHECKSUMS.txt file located in a different place than the destinationPath

  • Attempt to select raster resampling method based on raster type if no method supplied (#63, @ianmseddy)

  • projectInputs

  • new function assessDataTypeGDAL, used in postProcess, to identify smallest datatype for large Raster* objects passed to GDAL system call

    • when masking and reprojecting large Raster objects, enact gdalwarp system call if raster::canProcessInMemory(x,4) = FALSE for faster and memory-safe processing
    • better handling of various data types in Raster objects, including factor rasters

Bug fixes

  • Work around internally inside extractFromArchive for large (>2GB) zip files. In the R help manual, unzip fails for zip files >2GB. This uses a system call if the zip file is too large and fails using base::unzip.
  • Work around for raster::getData issues.
  • Speed up of Cache() when deeply nested, due to grep(sys.calls(), ...) that would take long and hang.
  • Bugfix for preProcess(url = NULL) (#65, @tati-micheletti)
  • Improved memory performance of clearCache (#67), especially for large Raster objects that are stored as binary R files (i.e., .rda)
  • Other minor bugfixes

Other changes

  • Deal with new raster package changes in development version of raster package
  • Added checks for float point number issues in raster resolutions produced by raster::projectRaster
  • .robustDigest now does not include Cache-added attributes
  • Additional tests for preProcess() (#68, @tati-micheletti)
  • Many new unit tests written, which caught several minor bugs

version 0.2.3

  • fix and skip downloading test on CRAN

version 0.2.2

Dependency changes

  • Add future to Suggests.

New features

  • new option on non-Windows OSs to use future for Cache saving to SQLite database, via options("reproducible.futurePlan"), if the future package is installed. This is FALSE by default.
  • If a do.call function is Cached, previously, it would be labelled in the database as do.call. Now it attempts to extract the actual function being called by the do.call. Messaging is similarly changed.
  • new option reproducible.ask, logical, indicating whether clearCache should ask for deletions when in an interactive session
  • prepInputs, preProcess and downloadFile now have dlFun, to pass a custom function for downloading (e.g., "raster::getData")
  • prepInputs will automatically use readRDS if the file is a .rds.
  • prepInputs will return a list if fun = "base::load", with a message; can still pass an envir to obtain standard behaviour of base::load.
  • clearCache - new argument ask.
  • new function assessDataType, used in postProcess, to identify smallest datatype for Raster* objects, if user does not pass an explicit datatype in prepInputs or postProcess (#39, @CeresBarros).

Bug fixes

  • fix problems with tests introduced by recent git2r update (@stewid, #36).
  • .prepareRasterBackedFile -- now will postpend an incremented numeric to a cached copy of a file-backed Raster object, if it already exists. This mirrors the behaviour of the .rda file. Previously, if two Cache events returned the same file name backing a Raster object, even if the content was different, it would allow the same file name. If either cached object was deleted, therefore, it would cause the other one to break as its file-backing would be missing.
  • options were wrongly pointing to spades.XXX and should have been reproducible.XXX.
  • copyFile did not perform correctly under all cases; now better handling of these cases, often sending to file.copy (slower, but more reliable)
  • extractFromArchive needed a new Checksum function call under some circumstances
  • several other minor bug fixes.
  • extractFromArchive -- when dealing with nested zips, not all args were passed in recursively (#37, @CeresBarros)
  • prepInputs -- arguments that were same as Cache were not being correctly passed internally to Cache, and if wrapped in Cache, it was not passed into prepInputs. Fixed.
  • .prepareFileBackedRaster was failing in some cases (specifically if it was inside a do.call) (#40, @CeresBarros).
  • Cache was failing under some cases of Cache(do.call, ...). Fixed.
  • Cache -- when arguments to Cache were the same as the arguments in FUN, Cache would "take" them. Now, they are correctly passed to the FUN.
  • preProcess -- writing to checksums may have produced a warning if CHECKSUMS.txt was not present. Now it does not.
  • numerous other minor bugfixes

Other changes

  • most tests now use a standardized approach to attaching libraries, creating objects, paths, enabling easier, error resistant test building

version 0.2.1

New features

  • new functions:

    • convertPaths and convertRasterPaths to assist with renaming moved files.
  • prepInputs -- new features

    • alsoExtract now has more options (NULL, NA, "similar") and defaults to extracting all files in an archive (NULL).
    • skips postProcess altogether if no studyArea or rasterToMatch. Previously, this would invoke Cache even if there was nothing to postProcess.

Bug fixes

  • copyFile correctly handles directory names containing spaces.
  • makeMemoisable fixed to handle additional edge cases.
  • other minor bug fixes.

version 0.2.0

New features

  • new functions:

    • prepInputs to aid in data downloading and preparation problems, solved in a reproducible, Cache-aware way.
    • postProcess which is a wrapper for sequences of several other new functions (cropInputs, fixErrors, projectInputs, maskInputs, writeOutputs, and determineFilename)
    • downloadFile can handle Google Drive and ftp/http(s) files
    • zipCache and mergeCache
    • compareNA does comparisons with NA as a possible value e.g., compareNA(c(1,NA), c(2, NA)) returns FALSE, TRUE
  • Cache -- new features:

    • new arguments showSimilar, verbose which can help with debugging
    • new argument useCache which allows turning caching on and off at a high level (e.g., options("useCache"))
    • new argument cacheId which allows user to hard code a result from a Cache
    • deprecated arguments: digestPathContent --> quick, compareRasterFileLength --> length
    • Cache arguments now propagate inward to nested Cache function calls, unless explicitly set on the inner functions
    • more precise messages provided upon each use
    • many more userTags added automatically to cache entries so much more powerful searching via showCache(userTags="something")
  • checksums now returns a data.table with the same columns whether write = TRUE or write = FALSE.

  • clearCache and showCache now give messages and require user intervention if request to clearCache would be large quantities of data deleted

  • memoise::memoise now used on 3rd run through an identical Cache call, dramatically speeding up in most cases

  • new options: reproducible.cachePath, reproducible.quick, reproducible.useMemoise, reproducible.useCache, reproducible.useragent, reproducible.verbose

  • asPath has a new argument indicating how deep should the path be considered when included in caching (only relevant when quick = TRUE)

  • New vignette on using Cache

  • Cache is parallel-safe, meaning there are tryCatch around every attempt at writing to SQLite database so it can be used safely on multi-threaded machines

  • bug fixes, unit tests, more imports for packages e.g., stats

  • updates for R 3.6.0 compact storage of sequence vectors

  • experimental pipes (%>%, %C%) and assign %<%

  • several performance enhancements

version 0.1.4

  • mergeCache: a new function to merge two different Cache repositories

  • memoise::memoise is now used on loadFromLocalRepo, meaning that the 3rd time Cache() is run on the same arguments (and the 2nd time in a session), the returned Cache will be from a RAM object via memoise. To stop this behaviour and use only disk-based Caching, set options(reproducible.useMemoise = FALSE) .

  • Cache assign -- %<% can be used instead of normal assign, equivalent to lhs <- Cache(rhs).

  • new option: reproducible.verbose, set to FALSE by default, but if set to true may help understand caching behaviour, especially for complex highly nested code.

  • all options now described in ?reproducible.

  • All Cache arguments other than FUN and ... will now propagate to internal, nested Cache calls, if they are not specified explicitly in each of the inner Cache calls.

  • Cached pipe operator %C% -- use to begin a pipe sequence, e.g., Cache() %C% ...

  • Cache arg sideEffect can now be a path

  • Cache arg digestPathContent default changed from FALSE (was for speed) to TRUE (for content accuracy)

  • New function, searchFull, which shows the full search path, known alternatively as "scope", or "binding environments". It is where R will search for a function when requested by a user.

  • Uses memoise::memoise for several functions (loadFromLocalRepo, pkgDep, package_dependencies, available.packages) for speed -- will impact memory at the expense of speed.

  • New Require function

    • attempts to create a lighter weight package reproducibility chain. This function is usable in a reproducible workflow: it includes both installing and loading of packages, it can maintain version numbers, and uses smart caching for speed. In tests, it can evaluate whether 20 packages and their dependencies (~130 packages) are installed and loaded quickly (i.e., if all TRUE, ~0.1 seconds). This is much slower than running require on those 20 packages, but require does not check for dependencies and deal with them if missing: it just errors. This speed should be fast enough for many purposes.
    • can accept uncommented name, if length 1.
  • remove dplyr from Imports

  • Add RCurl to Imports

  • change name of digestRaster to .digestRaster

version 0.1.3

  • fix R CMD check errors on Solaris that were not previously resolved

version 0.1.2

  • fix R CMD check errors on Solaris
  • fix bug in digestRaster affecting in-memory rasters
  • move rgdal to Suggests

version 0.1.1

  • cleanup examples and do run them (per CRAN)
  • add tests to ensure all exported (non-dot) functions have examples

version 0.1.0

  • A new package, which takes all caching utilities out of the SpaDES package.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("reproducible")

0.2.9 by Eliot J B McIntire, 9 days ago


http://reproducible.predictiveecology.org, https://github.com/PredictiveEcology/reproducible


Report a bug at https://github.com/PredictiveEcology/reproducible/issues


Browse source code at https://github.com/cran/reproducible


Authors: Eliot J B McIntire [aut, cre] , Alex M Chubaty [aut] , Tati Micheletti [ctb] , Ceres Barros [ctb] , Ian Eddy [ctb] , Her Majesty the Queen in Right of Canada , as represented by the Minister of Natural Resources Canada [cph]


Documentation:   PDF Manual  


GPL-3 license


Imports archivist, backports, crayon, data.table, digest, dplyr, fastdigest, fasterize, fpCompare, gdalUtils, git2r, googledrive, httr, magrittr, memoise, methods, parallel, quickPlot, R.utils, raster, RCurl, remotes, rgdal, rgeos, rlang, sf, sp, testthat, tools, utils, versions

Suggests covr, future, knitr, rmarkdown, TimeWarp

System requirements: 'unrar' (Linux/macOS) or '7-Zip' (Windows) to work with '.rar' files.


Imported by SpaDES, SpaDES.addins, SpaDES.tools.

Depended on by SpaDES.core.


See at CRAN