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rdtLite is an R package that collects provenance as an R script executes. The resulting provenance provides a detailed record of the execution of the script and includes information on the steps that were performed and the intermediate data values that were created. The resulting provenance can be used for a wide variety of applications that include debugging scripts, cleaning code, and reproducing results. rdtLite can also be used to collect provenance during console sessions.
The provenance is stored in PROV-JSON format (for details see JSON-format.md). For immediate use it maybe retrieved from memory using the prov.json function. For later use the provenance is also written to the file prov.json. This file and associated files are written by default to the R session temporary directory. The user may change this location by (1) using the optional parameter prov.dir in the prov.run or prov.init functions, or (2) setting the prov.dir option (e.g. by using the R options command or editing the Rprofile.site or .Rprofile file). If prov.dir is set to “.”, the current working directory is used.
rdtLite provides two modes of operation. In script mode, the prov.run function is used to execute a script and collect provenance as the script executes. In console mode, provenance is collected during a console session. Here the prov.init function is used to initiate provenance collection, prov.save is used to save provenance collected since the last time prov.save was used, and prov.quit is used to save and close the provenance file.
Simple data values are stored in the PROV-JSON file. “Snapshots” of complex data values (e.g. data frames) are optionally stored by adjusting the value of the parameter max.snapshot.size in prov.run or prov.init. To collect provenance for inputs/outputs only and not for individual statements, set the parameter details to FALSE in prov.run.
rdtLite belongs to a collection of R Tools developed as part of a larger project on End-to-end-provenance.
rdtLite currently requires R version 3.5.0 (or later) and the following R packages: curl, devtools, digest, ggplot2, grDevices, gtools, jsonlite, knitr, methods, stringr, tools, utils, XML.
rdtLite is easily installed from GitHub using devtools:
library(devtools)
install_github("End-to-end-provenance/rdtLite")Once installed, use the R library command to load rdtLite:
library(rdtLite)Note that all exported rdtLite functions begin with “prov.” to avoid confusion with variable or function names in the main script or other libraries.
To capture provenance for an R script, set the working directory, load the rdtLite package (as above), and enter the following:
prov.run("my-script.R")where “my-script.R” is an R script in the working directory. The prov.run command will execute the script and save the provenance in a subdirectory called “prov_my-script” under the current provenance directory (as above).
To capture provenance for a console session, enter the following:
prov.init()and enter commands at the R console. To save the provenance collected so far to a subdirectory called “prov_console” under the current provenance directory (as above), enter the following:
prov.save()To save the provenance and quit provenance collection, enter the following:
prov.quit()Note that various parameters of the prov.run and prov.init functions may be used to control where the provenance is stored and whether earlier provenance at the same location should be overwritten.
The source code for rdt and rdtLite is contained in the RDataTracker repository. A script is run nightly to create separate repos for each tool to facilitate GitHub installations. If you’d like to see the long history of code development and issues for rdt and rdtLite, or enter new issues, please see the RDataTracker repository.
The RDataTracker repository contains the necessary files to build and install rdt and rdtLite and to run extensive regression tests using Apache Ant. To do this, clone the RDataTracker repo and see the file README_Build_and_Test.md.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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