# R Consortium volcalc proposal

### Editing notes

- In proposal, should "Detail" includes documentation, testing, etc. details?
- 4 weeks of Eric's time and 2 weeks of mine = 260 hours

### RFP proposal sections

We should make sure these are all addressed somewhere in the proposal

The Problem:
- What problem do you want to solve?
- Why is it a problem?
- Who does it affect?
- What will solving the problem enable?
- This section should include a brief summary of existing work, such as R packages that may be relevant.

The Plan:
- How are you going to solve the problem?
- Include the concrete actions you will take and an estimated timeline.
- What are likely failure modes and how will you recover from them?

The Team:
- Who will work on the project? Briefly describe all participants, and the skills they will bring to the project.

Project Milestones:
- Outline the milestones for development and how much funding will be required for each stage (as payments will be tied to project milestone completion). Each milestone should specify the work to be done and the expected outcomes, providing enough detail for the ISC to understand the scope of the project work and assess the likelihood of success.

How Can The ISC Help:
- Detailed itemized budget and spending plan for labor costs.

Dissemination:
- How will you ensure that your work is available to the widest number of people?
- Please specify the open source or creative commons license(s) you will use, how you will host your code so that others can contribute, and how you will publicize your work. We encourage you to plan content to be shared quarterly on the R Consortium blog.

### Sponsored projects

**Title**

Automating compound volatility with volcalc

**Scope of work**

Objective

To make the R package `volcalc` more usable to domain scientists who are interested in compound volatility, including the ability to input compounds from more diverse sources. Additionally, to improve the quality, longevity, and availability of the package for the benefit of the scientific community.

Deliverables:
1. Improve automated test coverage of code (target date July 1, 2023)
2. Enable direct input of any mol file (target date September 1, 2023)
3. Improve documentation of code (target date November 1, 2023)
4. Enable inputs in addition to mol files (target January 31, 2024)

**Budget justification**

Budget will support the time of two scientific programmers which necessary to complete the proposed work improving this software. They have the required expertise in R code development, software dissemination, and scientific domain knowledge.

(note of due date)

### Notes

- Immediate TODOs
- Ask Laura about being "project team" vs "contributors"
- Ask Laura about how to use Biocyc
- Make repo public
- Set up meeting with Laura, Meredith, Kristina, Eric to discuss proposal; include brief demo on why generalizing inputs to package will help solve problems
- Run proposal timelines by Chris
- Kristina revise proposal section
- Immediate TODOs
- Discuss with Matt
- He thinks it's a great idea
- Send along the repo link when public
- Discuss with Anna Bounds
- No indirect costs
- They need info to put together a budget
- Discuss with Laura & Marshall
- Make repo public and share with other possible users for feedback
- Improvement ideas
- Expand to include more compounds
- Which additional databases have mol files for compounds?
- Eric: Instead of expanding to include more databases, I'd prefer to focus on splitting the current main function so that there is an exported function that can be used on *any* .mol file on disk. Then, you can use packages like `webchem` to download the .mol files, get a vector of file paths, and pass it to `volcalc`
- What compound files can we get from Biocyc, and can they be converted to mol if they aren't already?
- Improve usability
- Add to CRAN and/or r-universe
- More documentation (vignettes)
- Easier installation of dependencies?
- Eric: It might be possible to include the relevant C++ files *in* the R package, but that's all new to me, so might want to do a little preliminary investigation into whether this is an option.
- Improve quality
- Spot-checking more compounds?
- Add CI (GH actions)
- Check test coverage with codecov
- Submit to rOpenSci for review??
- Budget
- 2 weeks of my time + 3 weeks of Eric = $12K?
- Anything else besides our time?
- Timeline