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dendroNetwork · Issue #627 · ropensci/software-review · GitHub

Date accepted: 2024-04-25

Submitting Author Name: Ronald M. Visser
Submitting Author Github Handle: @RonaldVisser
Repository: https://github.com/RonaldVisser/dendroNetwork
Version submitted: 0.5.0
Submission type: Standard
Editor: @ldecicco-USGS
Reviewers: @kaijagahm, @gzach93

Archive: TBD
Version accepted: TBD
Language: en

• Paste the full DESCRIPTION file inside a code block below:

Package: dendroNetwork
Type: Package
Title: Create networks of dendrochronological series using pairwise similarity
Version: 0.5.0
Authors@R: 
    c(person(given ="Ronald", 
            family = "Visser", 
            email = "r.m.visser@saxion.nl", 
            role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-6966-1729")),
    person(given = "Angelino", 
            family ="Salentino",
            role = "ctb",
            comment = c(ORCID = "0000-0002-4763-3943")),
   person(given = "Andy", 
            family ="Bunn",
            role = "ctb",
            comment = c(ORCID = "0000-0001-9027-2162")))
Maintainer: Ronald Visser <r.m.visser@saxion.nl>
Depends: R (>= 3.5.0)
Imports: 
    dplR (>= 1.7.2),
    igraph,
    stringr,
    reshape2,
    RCy3,
    dplyr,
    RColorBrewer,
    tidyr,
    foreach,
    magrittr,
    doParallel,
    lifecycle, 
    stats,
    grDevices
Description: This package makes it easy to create dendrochronological networks based on the similarity between tree-ring series or chronologies. It includes various functions to compare tree-ring curves building upon dplR. The networks can be used to visualise and understand the relations between tree-ring curves. These networks are also very useful to estimate the provenance or wood-use within a structure/context/site.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.1
Suggests: 
    testthat (>= 3.0.0)
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)

• 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.):

  • data retrieval
  • data extraction
  • data munging
  • data deposition
  • data validation and testing
  • workflow automation
  • version control
  • citation management and bibliometrics
  • scientific software wrappers
  • field and lab reproducibility tools
  • database software bindings
  • geospatial data
  • text analysis

• Explain how and why the package falls under these categories (briefly, 1-2 sentences):
  The software deals with the analysis of dendrochronological data and aims the help to study, understand and visualize patterns in the data using network analyses. The software combines R with Cytoscape.

• Who is the target audience and what are scientific applications of this package?
  Dendrochronologist. The scientific application lies in the analyses and visualization of large datasets using networks. The method has been applied before to determine the provenance of wood from archaeological contexts, but can also be used to determine other patterns based on the similarity between tree-ring series or even other time series.

• 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, none as far as I know.

• (If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?
  NA

• If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

• Explain reasons for any pkgcheck items which your package is unable to pass.

I tried to run pkgcheck, but it failed with the following feedback:

Error in vapply(tag_data, function(i) i$keyword, character(1L)) :
values must be length 1,
but FUN(X[[12]]) result is length 2

I have absolutely no idea why....

The same error occurs locally and using github action.

Confirm each of the following by checking the box.

• I have read the rOpenSci packaging guide.
• I have read the author guide and I expect to maintain this package for at least 2 years or to find a replacement.

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, created with roxygen2.
• contains a vignette with examples of its essential functions and uses.
• has a test suite.
• has continuous integration, including reporting of test coverage.

• Do you intend for this package to go on CRAN?

• Do you intend for this package to go on Bioconductor?

• 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 guarantee that your manuscript will 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)

• I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

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