Skip to content

Minutes

Jump to bottom
Kelli Johnson edited this page Aug 11, 2020 · 8 revisions

Table of contents

2019-10-16

Attendees - Kelli Johnson, Chantel Wetzel

Goals

Create a template that is user friendly such that it is actually used and continually developed. Complicated code is not as likely to be used and will be a waste of time.

Current state of operations

Chantel, Ian, and Melissa Monk use markdown. Kelli and Aaron (for hake) use LaTex. There is no single template, but rather one-off constructions of the same thing.

Concerns

  • The code will be too complicated
  • ADA compliance
  • People might be afraid to move to LaTex

Tasks

  • Chantel will update the executive summary code to create csv files for each table using r4ss
  • Kelli will create some wrapper code to generate an executive summary
  • Kelli asked Kristin Marshall to document what she does and doesn't like about the assessment documents she has to read for the SSC to get ideas about what the template should and should not have

Timeline

Meet again after CAPAM in New Zealand.

2019-10-24

Attendees - Kelli Johnson &

Interactive stock assessment documents

DFO is starting to produce interactive stock assessment documents using Shiny to create an app. A web search led to me finding other groups that summarize their data using Shiny as well, e.g., NWFSC Economics Program, IPHC, AKFIN.

Goal

Produce a stock assessment document using LaTex that populates an interactive document available via html and a pdf that is a static, but complete, document similar to what reviewers and managers are used to reading.

2020-06-22

Attendees - Kelli Johnson & Chantel Wetzel

Topic - Create user friendly assessment template with automated table/figure functionality

  • Discussed the end goal of having both html and pdf documents for users to access. The pdf is of highest priority right now because pdf documents are mandatory for archiving and necessary for people to review the document in a printed version. We can add functionality along the way that provides html output, but this should not be our main focus. Thus, rmd files should be able to provide what we need at the moment and it will allow more people to feel comfortable with the process.
  • What items (e.g., diagnostics) is every assessment required to have? How can we automate this? Discussed creating a package with wrapper function to run all standard model diagnostic runs, create tables and figures for the document (profiles, jitter, retrospectives). This will allow for a standardize output product which can be incorporated easily in the assessment documentation product. A potential name of this package would be m4ss and it could be stored in the r4ss community.
  • In that same vain, create standardized paragraphs for items that are included across assessments (e.g., basic survey description) and standardized figure captions.

Goal: Create sa4ss package for writing assessments and creating standardized input/output which will reduce user work load or recreating the same items across assessments.

To-Do

  • Find example documents/interfaces that can be used as a model for our document
  • Create list of items to include: standardized paragraphs, package for standardized model diagnostics/tasks, package for document creation.
  • bib files
    • Create and push draft bib file that contains all previous assessments
    • Create and push draft bib file of relevant peer reviewed journal articles
    • Create a template entry in each bib file to structure all entries
  • Create flow chart of how items will interlink across the project.

2020-08-11

Attendees - Kelli Johnson, Chantel Wetzel

Goal: Touch base regarding sa4ss and nwfscDiag

To-Do

  • Run sa4ss and nwfscDiag on a model other than simple (KFJ)
  • fix parameter names and bounds of profile in profiling function
  • found that knitr::combine_words() produces an oxford comma list.
Clone this wiki locally