Submitting Author: Name (@wlandau)
Repository:
targets: https://github.com/wlandau/targetstarchetypes: https://github.com/wlandau/tarchetypes. (tarchetypes is a small companion package that only serves to extend targets, so thought it appropriate to submit it for review along with targets.)Version submitted:
targets)tarchetypes and the manual)Editor: @maurolepore
Reviewer 1: @limnoliver
Reviewer 2: @tjmahr
Archive: TBD
Version accepted: TBD
targetsPackage: targets
Title: Dynamic Function-Oriented Make-Like Declarative Pipelines for R
Description: The targets package is a pipeline toolkit that brings together
function-oriented programming and Make-like declarative workflows for
Statistics and data science in R. It implements a workflow as collection of
interconnected tasks, analyzes the dependency relationships among these
tasks, skips steps that are already up to date, runs the necessary
computations with optional parallel workers, abstracts files as
R objects, and provides tangible evidence that the results match
the underlying code and data. The methodology in this package
borrows from GNU Make by Richard Stallman (2015, ISBN:978-9881443519)
and drake by Will Landau (2018) <doi:10.21105/joss.00550>.
Version: 0.0.0.9001
License: MIT + file LICENSE
URL: https://wlandau.github.io/targets/, https://github.com/wlandau/targets
BugReports: https://github.com/wlandau/targets/issues
Authors@R: c(
person(
given = c("William", "Michael"),
family = "Landau",
role = c("aut", "cre"),
email = "will.landau@gmail.com",
comment = c(ORCID = "0000-0003-1878-3253")
),
person(
family = "Eli Lilly and Company",
role = "cph"
),
person(
given = c("Matthew", "T."),
family = "Warkentin",
role = "ctb"
))
Depends:
R (>= 3.5.0)
Imports:
callr (>= 3.4.3),
cli (>= 2.0.2),
codetools (>= 0.2.16),
data.table (>= 1.12.8),
digest (>= 0.6.25),
igraph (>= 1.2.5),
R6 (>= 2.4.1),
rlang (>= 0.4.5),
tibble (>= 3.0.1),
tidyselect (>= 1.1.0),
utils,
vctrs (>= 0.2.4),
withr (>= 2.1.2)
Suggests:
aws.s3 (>= 0.3.21),
clustermq (>= 0.8.9),
curl (>= 4.3),
dplyr (>= 1.0.0),
fst (>= 0.9.2),
future (>= 1.17.0),
keras (>= 2.2.5.0),
knitr (>= 1.30),
rmarkdown (>= 2.4),
qs (>= 0.23.2),
rstudioapi (>= 0.11),
testthat (>= 2.3.2),
torch (>= 0.1.0),
usethis (>= 1.6.3),
visNetwork (>= 2.0.9)
Encoding: UTF-8
Language: en-US
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1.9000
VignetteBuilder: knitr
tarchetypesPackage: tarchetypes
Title: Archetypes for Targets
Description: The targets package is a pipeline toolkit that brings together
function-oriented programming and Make-like declarative workflows for
Statistics and data science in R. The tarchetypes package provides
convenient user-side functions to create specialized targets,
making pipelines easier to create and read. The methods in this package
were influenced by the drake R package by Will Landau (2018)
<doi:10.21105/joss.00550>.
Version: 0.0.0.9000
License: MIT + file LICENSE
URL: https://wlandau.github.io/tarchetypes/, https://github.com/wlandau/tarchetypes
BugReports: https://github.com/wlandau/tarchetypes/issues
Authors@R: c(
person(
given = c("William", "Michael"),
family = "Landau",
role = c("aut", "cre"),
email = "will.landau@gmail.com",
comment = c(ORCID = "0000-0003-1878-3253")
),
person(
family = "Eli Lilly and Company",
role = "cph"
))
Depends:
R (>= 3.5.0)
Imports:
fs (>= 1.4.2),
rlang (>= 0.4.7),
targets,
tidyselect (>= 1.1.0),
utils,
vctrs (>= 0.3.4),
withr (>= 2.1.2)
Suggests:
digest (>= 0.6.25),
knitr (>= 1.28),
rmarkdown (>= 2.1),
testthat (>= 2.3.2)
Remotes:
wlandau/targets
Encoding: UTF-8
Language: en-US
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1.9000
Package: targets.manual
Title: Targets R Package User Manual
Description: This repository contains the source files of the targets R
package user manual.
Version: 0.0.0.9000
License: MIT + file LICENSE
URL: https://wlandau.github.io/targets-manual,
https://github.com/wlandau/targets-manual
BugReports: https://github.com/wlandau/targets-manual/issues
Authors@R: c(
person(
given = c("William", "Michael"),
family = "Landau",
role = c("aut", "cre"),
email = "will.landau@gmail.com",
comment = c(ORCID = "0000-0003-1878-3253")
),
person(
family = "Eli Lilly and Company",
role = "cph"
))
Depends:
R (>= 3.5.0)
Imports:
biglm (>= 0.9.2),
bookdown (>= 0.19),
fs (>= 1.4.1),
purrr (>= 0.3.4),
tarchetypes,
targets,
tidyverse (>= 1.3.0),
visNetwork (>= 2.0.9),
withr (>= 2.2.0)
Remotes:
wlandau/tarchetypes,
wlandau/targets
Encoding: UTF-8
Language: en-US
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.0
VignetteBuilder: knitr
Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):
Explain how and why the package falls under these categories (briefly, 1-2 sentences):
targets is an R-focused pipeline toolkit for Make-like declarative workflows. It resolves the dependency relationships among steps of a data analysis workflow and skips steps that are already up to date.
targets is for R users who maintain computationally intense function-oriented data analysis projects (with large codebases and/or long runtimes). Such projects may include but are not limited to Bayesian statistics, simulation, machine learning, PK/PD, and spatial statistics.
targets is the long-term successor to drake. After four years of development, drake has improved so much that its insurmountable problems have become its most pressing ones. A new package is necessary to advance the capability further. So while I still believe drake is thriving, and even though I will continue to maintain drake indefinitely, I created targets to try to break new ground. At https://wlandau.github.io/targets/articles/need.html#drake, I take a detailed dive into the ways that targets surpasses drake's permanent limitations.
N/A
N/A
Technical checksConfirm each of the following by checking the box.
This package:
targets and to avoid maintaining duplicated documentation, the vignettes of the actual package only include the statement of need and design documents. The README is deliberately short and links to all this existing documentation.targets can be automated, especially when it comes to visualization and profiling, so many of the tests live in non-testthat folders in https://github.com/wlandau/targets/tree/master/tests. Whenever I use a #nocov block, I always include a comment with a justification and/or a reference to one of these semi-automated tests.paper.md matching JOSS's requirements with a high-level description in the package root or in inst/. I have written a paper.md, but I need to run it through my company's scientific disclosure process before I share it. That could take a few weeks.paper.md and paper.bib now disclosed and included inside inst/.RetroSearch is an open source project built by @garambo | Open a GitHub Issue
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