Merge pull request #6 from cct-datascience/reports

Final Report

.gitignore

@@ -2,18 +2,12 @@
 .Rhistory
 .Rapp.history
 
-# Example code in package build process
-*-Ex.R
-
 # RStudio files
 .Rproj.user/
 
-# produced vignettes
-vignettes/*.html
-vignettes/*.pdf
-.Rproj.user
-
 # File gen artefacts
 *.html
 *.pdf
 *.docx
+!report_volcalc_milestone2.pdf
+!final_report.pdf

final_report.qmd

@@ -0,0 +1,86 @@
+---
+title: "R Consortium Report"
+subtitle: "volcalc: Calculate Volatility of Chemical Compounds"
+date: today
+author: 
+  - name: Kristina Riemer
+    orcid: 0000-0003-3802-3331
+    affiliations:
+      - ref: cct
+  - name: Eric R. Scott
+    orcid: 0000-0002-7430-7879
+    affiliations:
+      - ref: cct
+  - name: Laura Meredith
+    orcid: 0000-0003-4244-4366
+    affiliations:
+      - ref: snre
+  - name: S. Marshall Ledford
+    affiliations:
+      - ref: snre
+
+affiliations:
+  - id: cct
+    name: "Communications & Cyber Technologies, University of Arizona"
+  - id: snre
+    name: "School of Natural Resources and the Environment, University of Arizona"
+format: 
+  hikmah-pdf: default
+  # typst: default
+  # pdf: default
+editor: visual
+bibliography: references.bib
+---
+
+## Summary
+
+This is the final report on the ISC-funded work on the `volcalc` package.
+The GitHub repository for the current version of `volcacl` can be found at: <https://github.com/Meredith-Lab/volcalc>.
+We have completed the proposed milestones 3 and 4 as well as a modified version of our proposed dissemination plan.
+
+## Milestone 3
+
+`volcalc` now includes two vignettes—one demonstrating downloading .mol files from KEGG, and another showing general usage for calculating estimated volatility.
+A `pkgdown` website including these vignettes is available here: <https://meredith-lab.github.io/volcalc/>.
+The code for `volcalc` has been archived on Zenodo [@riemer2023] and a methods paper has been published in *Frontiers in Microbiology* [@meredith2023].
+We've submitted `volcalc` to CRAN and it was rejected due to issues that are unfortunately out of our hands—the "License" field in the DESCRIPTION file of a Bioconductor dependency was not CRAN compliant.
+As of today, this issue appears to have been fixed, but now automated checks on Windows are failing because of [issues with the `RCurl` package](https://cran.r-project.org/web/checks/check_results_RCurl.html) and on macOS because of issues [building `ChemmineOB`](https://github.com/girke-lab/ChemmineOB/issues/35).
+When these problems in dependencies are fixed, we may attempt another CRAN submission.
+In the meantime, `volcalc` can be installed from GitHub or [r-universe](https://cct-datascience.r-universe.dev/volcalc).
+
+## Milestone 4
+
+We added functionality to supply chemical representations as SMILES strings in addition to paths to .mol files.
+We have not (yet) added a vignette about integrating `webchem` and `volcalc` because few `webchem` functions provide results with SMILES strings.
+`ChemmineOB` is able to translate from more commonly returned formats such as InChI, however that feature is not available on Windows, so we are questioning the value of adding this feature to `volcalc`.
+
+## Other improvements
+
+We also added some validation abilities to `volcalc` that are important due to the way `ChemmineOB` and `ChemmineR` interact with the command line program Open Babel.
+When Open Babel encounters errors parsing a .mol file or SMILES string, error messages are displayed on the R console, but cannot be captured and acted on (see discussion in issue [#56](https://github.com/Meredith-Lab/volcalc/issues/56)).
+The workaround we implemented was to include code to look for the "symptoms" of parsing errors—namely a missing value for `InChI` returned by `ChemmineR::propOB()`.
+Unfortunately, this strategy doesn't work on Windows because InChI generation is not available on that OS.
+We implemented this as a `validate` argument to `calc_vol()` and `get_fx_groups()` which defaults to `TRUE` and prints an warning when set to `TRUE` and run on Windows.
+
+## Dissemination
+
+In addition to the *Frontiers in Microbiology* publication, we have shared `volcalc` on social media (Mastodon), in blog posts, in the rOpenSci Slack group, and in talks.
+The package authors have also reached out personally to researchers who may be interested in these calculations.
+
+## Future opportunities
+
+Besides continuing to try to get `volcalc` on CRAN, we have a few open issues that we see as potential improvements to `volcalc` that could be part of future work.
+Because of various difficulties encountered with `ChemmineOB` and `ChemmineR`, we are considering dropping these Bioconductor dependencies and implementing interactions with Open Babel directly in `volcalc`.
+This would potentially lead to a more stable and self-contained package, however it would be a substantial amount of work.
+Similarly, we may consider dropping the `KEGGREST` dependency as it is only used for one function to access the KEGG API, and we've already created other functions in `volcalc` that access different KEGG API endpoints.
+
+In the original SIMPOL.1 method, equations are provided to calculate group contribution coefficients at any temperature [@pankowSIMPOLSimpleGroup2008].
+As it is implemented currently in `volcalc`, however, volatility is only estimated at a fixed temperature of 20ºC.
+Implementing a variable temperature would not be trivial, but would add a great deal of flexibility for estimating relative volatility at a range of environmental conditions.
+
+We have opened GitHub issues for all of these future improvements and will consider pursuing additional funding for another round of `volcalc` development as the user base grows.
+
+## References
+
+::: refs
+:::

references.bib

@@ -82,3 +82,27 @@ @article{meredith
 	author = {Meredith, L.K. and Riemer, K. and Geffre, P. and Honeker, L. and Krechmer, J. and Graves, K. and Tfaily, M. and Ledford, S.K.},
 	year = {\emph{in prep}}
 }
+
+@book{riemer2023,
+	title = {{volcalc}: Calculate Volatility of Chemical Compounds},
+	author = {Riemer, Kristina and Scott, Eric R. and Meredith, Laura K.},
+	year = {2023},
+	month = {12},
+	date = {2023-12-15},
+	publisher = {Zenodo},
+	doi = {10.5281/ZENODO.8015154},
+	url = {https://zenodo.org/doi/10.5281/zenodo.8015154}
+}
+
+@article{meredith2023,
+	title = {Automating methods for estimating metabolite volatility},
+	author = {Meredith, Laura K. and Ledford, S. Marshall and Riemer, Kristina and Geffre, Parker and Graves, Kelsey and Honeker, Linnea K. and LeBauer, David and Tfaily, Malak M. and Krechmer, Jordan},
+	year = {2023},
+	month = {12},
+	date = {2023-12-14},
+	journal = {Frontiers in Microbiology},
+	volume = {14},
+	doi = {10.3389/fmicb.2023.1267234},
+	url = {http://dx.doi.org/10.3389/fmicb.2023.1267234}
+}
+