Package‘rdtLite’
October14,2022
Title Provenance Collector
Version1.4
Date2022-08-06
Copyright President and Fellows of Harvard College,Trustees of Mount Holyoke College
Depends R(>=3.6.0)
Description Defines functions that can be used to collect provenance as an'R'script executes or during a console session.The output is a text
file in'PROV-JSON'format.
License GPL-3
URL github/End-to-end-provenance/rdtLite
BugReports github/End-to-end-provenance/rdtLite/issues Imports curl,digest,grDevices,gtools,jsonlite,knitr,methods,
provViz(>=1.0.6),rlang,rmarkdown,sessioninfo,stringi,
tools,utils,XML
Suggests ggplot2,provSummarizeR,roxygen2,testthat,vroom VignetteBuilder knitr
RoxygenNote7.2.0
Encoding UTF-8
NeedsCompilation no
Author Barbara Lerner[aut,cre],
Emery Boose[aut],
Elizabeth Fong[aut],
Luis Perez[aut],
Thomas Pasquier[ctb],
Matthew Lau[ctb],
Yada Pruksachatkun[ctb],
Alex Liu[ctb],
Moe Pwint Phyu[ctb],
Connor Gregorich-Trevor[ctb],
Aaron Ellison[res],
1
Margo Seltzer[res],
Joe Wonsil[res],
Orenna Brand[res]
Maintainer Barbara Lerner<*********************>
Repository CRAN
Date/Publication2022-08-0810:50:02UTC
R topics documented:
prov.init (2)
prov.json (5)
Index7 prov.init Provenance Collection Functions
Description
prov.init intializes a new provenance graph.This function can be executed in the console or placed inside an R script.
prov.save saves the current provenance graph to a prov-jsonfile.If more R statements are executed, the provenance for these statements is added to the graph.The graph isfinalized with prov.quit.
This function can be executed in the console or placed inside an R script.
prov.quit saves and closes the current provenance graph.This function can be executed in the console or placed inside an R script.
prov.run initiates execution of a script and collects provenance as the script executes.This function should be used if you want to collect provenance for a script that is in an Rfile and you do not want to modify the R script directly to include calls to prov.init,prov.save and prov.quit.It essentially wraps the execution of the script with calls to prov.init and prov.quit.
prov.source loads an R script and executes it,collecting provenance as it does so.It assumes that provenance has already been initialized,either via a call to prov.init,or because the R script was executed using prov.run.If you want to collect provenance inside scripts that are loaded with R’s source function,you should replace calls to source with calls to prov.source.
Usage
prov.init(
prov.dir=NULL,
overwrite=TRUE,
snapshot.size=0,
hash.algorithm="md5",
save.debug=FALSE
)
prov.save(save.debug=FALSE)
prov.quit(save.debug=FALSE)
prov.run(
r.script.path,
prov.dir=NULL,
overwrite=TRUE,
details=TRUE,
snapshot.size=0,
hash.algorithm="md5",
save.debug=FALSE,
exprs,
...
)
prov.source(file,exprs,...)
Arguments
prov.dir the directory where the provenance graph will be saved.If not provided,the directory specified by the prov.dir option is used.Otherwise the R session tem-
porary directory is used.
overwrite if FALSE,includes a time stamp in the provenance graph directory name.
snapshot.size the maximum size for snapshotfiles.If0,no snapshots are saved.If Inf,the complete state of an object is stored in the snapshotfile.For other values,the
head of the object,truncated to a size near the specified limit,is saved.The size
is in kilobytes.
hash.algorithm the hash algorithm to use forfiles.Choices are md5(default),sha1,crc32, sha256,sha512,xxhash32,xxhash64and murmur32.This feature uses the di-
gest function from the digest package.
save.debug If TRUE,debugfiles are saved to the debug directory.This is intended for developers of the rdt/rdtLite package.
r.script.path the full path to the R scriptfile that is being executed.A copy of the script will be saved with the provenance graph.
details if FALSE,provenance is not collected for top-level statements.
truncated zip file怎么解决
exprs Instead of specifyingfile,an expression,call,or list of call’s,can be passed in to be executed.
...parameters passed on to the source function.See documentation of source for details.
file the name of the R scriptfile to source.
Details
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 repro-ducing results.
There are two ways in which a user can collect provenance.To collect provenance from commands stored in a scriptfile,use prov.run.This will execute the commands that are in the script,collecting provenance as it does so.
The user can also collect provenance while executing commands in the console.To do this,first execut
e prov.init.Then enter console commands as normal.When done with the commands for which you want provenance,use prov.quit.If you want to save the current provenance without turn-ing off provenance collection,call prov.save instead of prov.quit.You can call prov.save multiple times before calling prov.quit.Each call will append to the same provenancefile.
The provenance is stored in PROV-JSON format.For immediate use it may be retrieved from mem-ory using the prov.json function.For later use the provenance is also written to thefile prov.json.
Thisfile and associatedfiles are written by default to the R session temporary directory.The user can 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 by using the R options command or editing the Rprofile.site or.Rprofilefile).If prov.dir is set to".",the current working directory is used.
If prov.source is called when provenance is not initialized,it will just source thefile.No provenance will be collected.
Value
prov.init initializes the provenance collector.The prov.init function does not return a value.
prov.save writes the current provenance to afile but does not return a value.
prov.quit writes the current provenance to afile but does not return a value.
prov.run runs a script,collecting provenance as it does so.It does not return a value.
The prov.source function does not return a value.
See Also
prov.json for access to the JSON text of the provenance,
Examples
##Not run:prov.run("script.R")
##Not run:prov.source("script.R")
prov.init()
a<-1
b<-2
prov.save()
ab<-a+b
prov.quit()
prov.json5 prov.json Provenance Access Functions
Description
prov.json returns the current provenance graph as a prov-json string.
prov.dir returns the current provenance directory.
prov.visualize displays the current provenance as a graph.
prov.summarize outputs a text summary to the R console
Usage
prov.json()
prov.dir()
prov.visualize()
prov.summarize(
save=FALSE,
create.zip=FALSE,
details=FALSE,
check=TRUE,
console=TRUE,
notes=TRUE
)
Arguments
save if true saves the summary to thefi in the provenance direc-tory
create.zip if true all of the provenance data will be packaged up into a zipfile stored in the current working directory.
details if true,a more detailed summary is provided
check if true,the user’sfile system is checked to see if inputfiles,outputfiles,and scripts(in their original locations)are unchanged,changed,or missing.
console if true,the summary is displayed in the console
notes if true,notes are included to explain how to interpret the summary
Details
rdtLite collects provenance as a script executes.Once collected,prov.json can be called to access the provenance as a JSON string.This is useful for applications that operate on the provenance.
The JSON is consistent with the PROV-JSON standard.

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