Description
Summary
- What does this package do? (explain in 50 words or less):
babette provides for a full workflow alternative of four different
GUI and command-line tools.
- Paste the full DESCRIPTION file inside a code block below:
Package: babette
Title: Control BEAST2 from R
Version: 1.2.2
Author: Richel J.C. Bilderbeek <[email protected]>
Maintainer: Richel J.C. Bilderbeek <[email protected]>
Description: 'BEAST2' (<http://www.beast2.org>) is a widely used
Bayesian phylogenetic tool, that uses DNA/RNA/protein data
and many model priors to create a posterior of jointly estimated
phylogenies and parameters.
'BEAST2' is commonly accompanied by 'BEAUti 2' (<http://www.beast2.org>),
'Tracer' <http://tree.bio.ed.ac.uk/software/tracer/>
and Densitree (<http://www.beast2.org>).
'babette' provides for an alternative workflow of using
all these tools seperately. This allows doing complex Bayesian
phylogenetics easily and reproducibly from R.
License: GPL-3 | file LICENSE
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
URL: https://github.com/richelbilderbeek/babette
BugReports: https://github.com/richelbilderbeek/babette/issues
Imports:
beautier,
beastier,
phangorn,
tracerer,
testit,
xml2
Suggests:
devtools,
ggplot2,
knitr,
lintr,
nLTT,
rmarkdown,
testthat
Remotes:
jimhester/covr,
jimhester/lintr,
richelbilderbeek/beautier,
richelbilderbeek/beastier,
richelbilderbeek/nLTT,
richelbilderbeek/tracerer,
MangoTheCat/goodpractice,
KlausVigo/phangorn
- URL for the package (the development repository, not a stylized html page):
https://github.com/richelbilderbeek/babette
- Please indicate which category or categories from our package fit policies this package falls under *and why(? (e.g., data retrieval, reproducibility. If you are unsure, we suggest you make a pre-submission inquiry.):
[e.g., "data extraction, because the package parses a scientific data file format"]
reproducibility, as it provides a way to script three error-prone (and tedius) GUI
and one command-line tool.
- Who is the target audience and what are scientific applications of this package?
Scientists that use the tool 'BEAST2' to do a Bayesian phylogenetic inference on DNA data.
- Are there other R packages that accomplish the same thing? If so, how does
yours differ or meet our criteria for best-in-category?
No
- If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.
Requirements
Confirm each of the following by checking the box. This package:
- does not violate the Terms of Service of any service it interacts with.
- has a CRAN and OSI accepted license.
- contains a README with instructions for installing the development version.
- includes documentation with examples for all functions.
- contains a vignette with examples of its essential functions and uses.
- has a test suite.
- has continuous integration, including reporting of test coverage, using services such as Travis CI, Coveralls and/or CodeCov.
- I agree to abide by ROpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.
Publication options
- Do you intend for this package to go on CRAN?
- Do you wish to automatically submit to the Journal of Open Source Software? If so:
- The package has an obvious research application according to JOSS's definition.
- The package contains a
paper.mdmatching JOSS's requirements with a high-level description in the package root or ininst/. - The package is deposited in a long-term repository with the DOI:
- (Do not submit your package separately to JOSS)
- Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:
- The package is novel and will be of interest to the broad readership of the journal.
- The manuscript describing the package is no longer than 3000 words.
- You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see MEE's Policy on Publishing Code)
- (Scope: Do consider MEE's Aims and Scope for your manuscript. We make no gaurantee that your manuscript willl be within MEE scope.)
- (Although not required, we strongly recommend having a full manuscript prepared when you submit here.)
- (Please do not submit your package separately to Methods in Ecology and Evolution)
Detail
-
Does
R CMD check(ordevtools::check()) succeed? Paste and describe any errors or warnings: -
Does the package conform to rOpenSci packaging guidelines? Please describe any exceptions:
Deviation from this guideline
There is one point I deviate from this guideline:
When using roxygen2, add #' @noRd to internal functions.
There are two functions beautier::default_params_doc and beastier::default_params_doc
that are empty internal function. Their purpose is to have their parameters inherited.
Adding #' @noRd stops internal and exported functions to inherit these parameters.
If there is alternative, I'd be happy to hear it.
Deviate from goodpractice::gp()
There is one goodpractice::gp() warning I ignore. About the 'Date' field in
the DESCRIPTION file. goodpractice suggest to remove it, R CMD check --as-cran
forces to add it. I followed the CRAN standards,
If there is way to satisfy both checks, I'd love to hear it.
-
If this is a resubmission following rejection, please explain the change in circumstances:
-
If possible, please provide recommendations of reviewers - those with experience with similar packages and/or likely users of your package - and their GitHub user names:
Klaus Schliep, KlausVigo
Luke Harmon, lukejharmon
Jonathan Eastman, eastman
Joseph W. Brown, josephwb