The rOpenSci Team

Developing [dendroNetwork](https://docs.ropensci.org/dendroNetwork/) as
a package was not a goal from the beginning, but looking back, I think
that it should have been. I wish someone had suggested making a package
to me much earlier. Why? Because of many things, but mostly:
reproducibility and transparency. This enables others to also use the
method and software. In addition, I really enjoyed the open peer-review
process after submitting to rOpenSci, because the reviewers showed me
various improvements and how people from outside my discipline viewed
the software and documentation. Meeting new people is always nice and a
great bonus of the process.

A few years ago I published a method developed to explore patterns in
the similarity between tree-ring series using network
analysis.^[1](#fn:1){.footnote-ref role="doc-noteref"}^ In
dendrochronology the pair-wise comparison of tree-ring series is an
often used method to look for patterns in, for example, the provenance
of the wood, especially for archaeological wood, since we often know
where the wooden objects came from, but not where the trees were felled.
This type of study often results in a complex set of relations and I
think that network analysis is a great method for visualising and
analysing these relations without losing the complexity. I developed
this method and shared the code with my
publication.^[2](#fn:2){.footnote-ref role="doc-noteref"}^ Part of the
code had been written by others and adapted for the analyses. The fact
that Angelo Salatino (The Open University) shared his
[code](https://github.com/angelosalatino/CliquePercolationMethod-R)
openly and Andy Bunn (Western Washington University) did the
[same](https://github.com/AndyBunn/dplR/blob/master/R/rwi.stats.running.R),
shows how beneficial openly sharing code is to others and for the
progress of research. Further research was performed, refining the
method and exploring other avenues, such as looking at wood use within a
Roman ship and the provenance of wood used in these
ships.^[3](#fn:3){.footnote-ref role="doc-noteref"}^ Later, I read a
blog post about packaging and how easy it could be. Unfortunately, I do
not remember which blog it was, but it inspired me to convert my code
into a package, for the benefit of others, but also because I wanted to
learn how to do this.

For me, creating a package from my existing scripts started with these
three excellent resources (in random order):

- <https://devguide.ropensci.org/>

- <https://r-pkgs.org/>

- <https://carpentries-incubator.github.io/lesson-R-packaging/>

The easy bit was converting scripts into functions, since this is pretty
straight forward programming. However, I never realized how much work
writing (good) documentation is. This took me much longer than I
expected, also because I was (and am) doing this in my spare time.
However, it was also worthwhile to do this and explain what the
functions and variables are for. I also learned a lot about the
potential for continuous integration, automated testing and checking,
especially from the
[rOpenSci-documentation](https://devguide.ropensci.org/). A lot of
information can be found there, which is really helpful. It takes an
effort to read everything, but in the end it can save you a lot of time
if you read it *before* you start developing a package!

I really enjoyed the [open
peer-review](https://github.com/ropensci/software-review/issues/627)
process. After reading all the documentation and making sure that
dendroNetwork complied to the standards of rOpenSci, the process of
submission was very easy. I enjoyed the feedback I got from the
reviewers [Kaija Gahm](https://kaijagahm.netlify.app/) and [Zachary
Gajewski](https://github.com/gzach93) and their comments really improved
the software in a whole.

I would recommend any research who develops a new method with code to do
the following things:

- Be nice, and share and document your code!

- Develop functions not scripts.

- Develop a package from the start, especially when devising a new
  method(ology).

- Read the documentation (or: RTFM)

- Submit to rOpenSci and enjoy!

::: {.footnotes role="doc-endnotes"}

------------------------------------------------------------------------

1.  ::: {#fn:1}
    Visser, R. M. (2021). Dendrochronological Provenance Patterns.
    Network Analysis of Tree-Ring Material Reveals Spatial and Economic
    Relations of Roman Timber in the Continental North-Western
    Provinces. Journal of Computer Applications in Archaeology,
    4(1), 230.
    <https://doi.org/10.5334/jcaa.79> [↩︎](#fnref:1){.footnote-backref
    role="doc-backlink"}
    :::

2.  ::: {#fn:2}
    Visser, R. M. (2022). *Dendrochronological Provenance Patterns. Code
    and Data of Network Analysis of Tree-Ring Material* \[dataset\].
    <https://doi.org/10.5281/zenodo.10200361> [↩︎](#fnref:2){.footnote-backref
    role="doc-backlink"}
    :::

3.  ::: {#fn:3}
    Visser, R. M., & Vorst, Y. (2022). Connecting Ships: Using
    Dendrochronological Network Analysis to Determine the Wood
    Provenance of Roman-Period River Barges Found in the Lower Rhine
    Region and Visualise Wood Use Patterns. *International Journal of
    Wood Culture*, *3*(1-3), 123-151.
    <https://doi.org/10.1163/27723194-bja10014>

    Visser, R., & Vorst, Y. (2022). *Analyses, data and figures related
    to: 'Connecting ships: using dendrochronological network analysis to
    determine the wood provenance of Roman-period river barges found in
    the Lower Rhine region and to visualise patterns of wood use'*
    \[dataset\].
    <https://doi.org/10.5281/zenodo.7243539> [↩︎](#fnref:3){.footnote-backref
    role="doc-backlink"}
    :::
:::


Developing dendroNetwork as a package was not a goal from the beginning, but looking back, I think that it should have been. I wish someone had suggested making a package to me much earlier. Why? Because of many things, but mostly: reproducibility and transparency. This enables others to also use the method and software.

Messages de Rogue Scholar

From scripts to package. Developing dendroNetwork and learning with rOpenSci