Creates an HTML-based visualization of provenance
How scientific results come to be is the product of various domain-specifc, economic, historical, social, and technical factors. As a consequence, information about how these factors shaped and produced these results is essential to both artistic trade and scientific reproducibility. Whether these results are material or digital, provenance provides the historical accounts of objects: paintings, bones, essays, scientific tables, and plots.
Using the idea of provenance and associated End-to-end-provenance tools that collect provenance, we develop an R package that presents visualizations of provenance for R scripts. This tool is called provBookR, and it allows users to get and visualize the history of single R data objects (e.g., plots, scientific tables, variables).
Install from GitHub:
# install.packages("devtools")
devtools::install_github("End-to-end-provenance/provBookR")
Once installed, load the package:
library(provBookR)The provBookR package uses a browser interface for the generation of provbooks and specification of provenance operations. The browser has two interface modes: lite and full. The lite mode is intended for quick generation of provbooks, while the full mode is intended to support the exploration of the collected provenance.
- To quickly generate a provebook from the already collected provenance:
# Run provBookR with lite option specified
> provBookR("prov.json", mode="lite")variable name?:
provBookR.lite> f
Running provBookR lite for "f" from prov.json...
[1] "f <- function(x) {\ty <- x^2\treturn(y)}"
[2] "f"
Generate a provbook for this object history? (Y/N):
provBookR> Y
Done!
provbook for variable "f" is stored in /path/to/current/working/directory
- To record the provenance from a recently created R script:
# Run provBookR with lite option specified
> provBookR("myscript.R", mode="full")provBookR browser initializing...
Checking file extension...
Collecting provenance...
Provenance collected!
- To explore the different object lineages or use the core E2E provenance processing tools:
# Run provBookR with lite option specified
> provBookR("prov.json", mode="full")provBookR browser initialized!
provBookR browser running, type "help" for more information or Q to quit
prov.json
provBookR> help
provBookR(operations)> [command][space][variable.name]:
Quit provBookR : "q"
provBookR operations : "help"
List R objects : "ls"
Show me how R object was created : "BO"
Show me what this R object was used to create : "AO"
Summarize provenance : "S"
Debug script : "DB"
Clean script : "C"