submission: babette

[richelbilderbeek]

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 <richel@richelbilderbeek.nl>
Maintainer: Richel J.C. Bilderbeek <richel@richelbilderbeek.nl>
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.md matching JOSS's requirements with a high-level description in the package root or in inst/.
  • 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 (or devtools::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

[richelbilderbeek]

This submission is a continuation of #208

[noamross]

Editor checks:

• Fit: The package meets criteria for fit and overlap
• Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
• License: The package has a CRAN or OSI accepted license
• Repository: The repository link resolves correctly
• Archive (JOSS only, may be post-review): The repository DOI resolves correctly
• Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?

---

Editor comments

Thanks for this (continued) submission, @richelbilderbeek! I have two initial pieces of feedback, neither of which preclude moving forward, so I'll go ahead and look for reviewers.

• First, BEAST2 is platform-agnostic, but as it is often easy to run into platform-specific issues while making system calls, please set up Windows CI via Appveyor.

• Second, this came up as I was doing local testing and figuring out paths: I suggest you use the rappdirs to set a platform-agnostic default path for the BEAST2 .jar and have install_beast2() place it there by default. The recently accepted rtika does this. For users who already have BEAST2 installed, let them set an environment variable in .Renviron such as BEAST2_PATH. This way users can 'set it and forget it' once on package setup, no matter what platform they are on. You can either implement this now or wait until reviews are in.

• I won't include goodpractice::gp() checks as they are all clean! Nice work including these in your CI setup.

---

Reviewers:
Due date:

[richelbilderbeek]

Thanks for the great feedback! Will do so at latest at 2018-04-16:

• Add AppVeyor
• Use rappdir

[GuangchuangYu]

The example on tracerer README is broken since the function get_path was renamed to get_tracerer_path. Please update documentations accordingly.

The parse_beast_trees internally uses rBEAST::beast2out.read.trees, which output multiPhylo object without any BEAST inferences. I think you need to describe this in vignette and a link to treeio is helpful, see also #179. treeio is able to parse BEAST tree with corresponding statistics.

The output of the example is 10 phylogenetic trees:

trees <- parse_beast_trees(
  get_tracerer_path("beast2_example_output.trees")
)

while treeio outputs 11 trees.

After looking at the source code, there is an option:

opt.burnin: how many phylogenies to discard,

which by default is setting to 0, in the function rBEAST::beast2out.read.trees.

Although by default it is expected to discard 0 tree, it actually discard the first one. Is this a bug or intended for some reasons?

---

> rBEAST::beast2out.read.trees
function (file, opt.rescale.edge.length = 1, opt.burnin = 0)
{
    tmp <- readLines(file, n = 2000, warn = FALSE)
    tmp <- which(grepl("#NEXUS", tmp))
    if (length(tmp) > 1) {
        cat(paste("\nFound #NEXUS headers, n=", length(tmp),
            ".\nDiscard all lines before last entry on line",
            tail(tmp, 1)))
        cmd <- paste("sed -i\".bak\" 1,", tail(tmp, 1) - 1, "d ",
            file, sep = "")
        system(cmd)
        cmd <- paste("sed -i\".bak2\" 1s/\\;// ", file, sep = "")
        system(cmd)
        cmd <- list.files(paste(rev(rev(strsplit(file, "/")[[1]])[-1]),
            collapse = "/"), pattern = "*bak*", full.names = TRUE)
        cat(paste("\nrm files\n", paste(cmd, collapse = "\n")))
        file.remove(cmd)
    }
    mph <- ape::read.nexus(file)
    tmp <- regexpr("[0-9]+", names(mph))
    if (any(tmp < 0))
        stop("unexpected nexus file without STATE iteration numbers")
    mph.it <- as.numeric(regmatches(names(mph), tmp))
    mph <- lapply(which(mph.it > opt.burnin), function(j) mph[[j]])
    mph.it <- mph.it[mph.it > opt.burnin]
    names(mph) <- paste("STATE_", mph.it, sep = "")
    if (opt.rescale.edge.length != 1)
        for (j in seq_along(mph)) mph[[j]]$edge.length <- mph[[j]]$edge.length *
            opt.rescale.edge.length
    mph
}

The implementation of rBEAST::beast2out.read.trees is not robust.

• It only read first 2000 lines.
• use system command (i.e. sed, which may not be available for Windows and may have different behaviors in Unix-like system for there are different implementations of sed, e.g. GNU or BSD implementations).

### something like this in pure R is more favorable.

    con <- readLines(file, n = 2000, warn = FALSE)
    tmp <- which(grepl("#NEXUS", con))
    if (length(tmp) > 1) {
        cat(paste("\nFound #NEXUS headers, n=", length(tmp),
            ".\nDiscard all lines before last entry on line",
            tail(tmp, 1)))
########
        con <- con[tmp[length(tmp)]:length(con)]
  }
  mph <- ape::read.nexus(textConnection(con))
########
  ...

[noamross]

Thanks @GuangchuangYu! @richelbilderbeek, for clarification, Guangchuang wasn't able to do a full review, but posted this contribution anyway - the benefit of open review is that anyone from the community can contribute! I'm still hunting for full reviewers.

[richelbilderbeek]

Thanks for your review @GuangchuangYu!

• Update doc in README
• Fix rBEAST::beast2out.read.trees

EDIT: I use ape::read.nexus instead of rBEAST::beast2out.read.trees, which is cleaner, simpler, etc.
EDIT: Removed earlier (imperfect) ideas about treeio

BEAST .trees file

From the treeio test file:

#NEXUS

Begin taxa;
	Dimensions ntax=15;
	Taxlabels
		A_1995
    [some more]
		O_1998
		;
End;

Begin trees;
	Translate
		1 A_1995,
    [some more]
		15 O_1998
		;
tree TREE1 = [&R] 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End;

BEAST2 .trees file

From here:

#NEXUS

Begin taxa;
	Dimensions ntax=5;
		Taxlabels
			t1 
      [some more]
			t2
			;
End;
Begin trees;
	Translate
		   1 t1,
       [some more]
		   5 t2
;
tree STATE_0 = ((1:0.4796940031825733,4:0.4796940031825733):0.15868524443147886,(2:0.47305110906182046,(3:0.43063449002200127,5:0.43063449002200127):0.04241661903981919):0.16532813855223172):0.0;
[some more]
tree STATE_10000 = (1:0.7693617408342179,(2:0.6138287429830985,((3:0.11136214949831788,4:0.11136214949831788):0.22798021162858859,5:0.33934236112690647):0.27448638185619206):0.1555329978511194):0.0;
End;