In franapoli/repo: A Data-Centered Data Flow Manager

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^{_{Master: Dev:}}

Repo

Repo is a data-centered data flow manager. It allows to store R data files in a central local repository, together with tags, annotations, provenance and dependence information. Any saved object can then be easily located and loaded through the repo interface.

A paper about Repo has been published in BMC Bioinformatics.

Latest news are found in the NEWS.md file of the "Untested" branch.

Minimal example

Creating a dummy repository under the R temporary folder (skipping confirmation):

library(repo)
rp <- repo_open(tempdir(), force=T)

Storing data. In this case, just item values and names are specified:

God <- Inf
rp$put(God)          ## item name inferred from variable name
rp$put(0, "user")    ## item name specified

More data with specified dependencies:

rp$put(pi, "The Pi costant", depends="God")
rp$put(1:10, "r", depends="user")

Loading items from the repository on the fly using names:

diam <- 2 * rp$get("r")
circum <- 2 * rp$get("The Pi costant") * rp$get("r")
area <- rp$get("The Pi costant") * rp$get("r") ^ 2

Storing more data with verbose descriptions:

rp$put(diam, "diameters", "These are the diameters", depends = "r")
rp$put(circum, "circumferences", "These are the circumferences",
       depends = c("The Pi costant", "r"))
rp$put(area, "areas", "These are the areas",
       depends = c("The Pi costant", "r"))

Showing repository contents:

print(rp)

rp$info()

rp$info("areas")

Visualizing dependencies:

rp$dependencies()

Manual acces to stored data:

fpath <- rp$attr("r", "path")
readRDS(fpath)

Development branches

• Master: stable major releases, usually in sync with lastest CRAN version.

• Dev: minor releases passing automatic checks.

• Untested: in progress versions and prototype code, not necessarily working.

Manuals

Besides inline help, two documents are available as introductory material:

• A paper published on BMC Bioinformatics

• An introductory vignette.

Download and Installation

Repo is on CRAN and can be installed from within R as follows:

install.packages("repo")

Latest stable release can be downloaded from Github at https://github.com/franapoli/repo. Repo can then be installed from the downloaded sources as follows:

install.packages("path-to-downloaded-source", repos=NULL)

devtools users can install Repo directly from github as follows:

install_github("franapoli/repo", ref="dev")

franapoli/repo documentation built on May 17, 2021, 7:24 p.m.