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TAF Rules and Recommendations

As a general framework, TAF allows a wide variety of analyses to run on the TAF server. At the same time, some level of uniformity is useful. A few rules and recommendations have been developed for TAF, to establish a workflow that allows anyone to run and review (read and understand) the analysis.

Breaking a rule results in an error. The TAF server will not run the analysis until such an issue is improved.

Not following a recommendation can either result in a warning or a note. A warning is an issue that should be relatively straightforward for the user to improve. A note, on the other hand, is a flag that may be related to an intentional feature in an unusal TAF analysis.

There are three points in time when TAF rules and recommendations are checked: the first scan (before anything is run), the middle scan (after the boot procedure), and final scan (after R scripts have run).

1. First scan

Examines files before anything is run

1.1 Rules

1.1.1 Files

(a) R scripts use the uppercase .R file extension:

  • *.R

(b) The metadata files DATA.bib and SOFTWARE.bib can only exist in these file locations:

  • boot/DATA.bib
  • boot/SOFTWARE.bib

1.1.2 Content

(a) These functions cannot appear in TAF scripts, except in a custom boot script:

  • .libPaths
  • download
  • download.file
  • install_github
  • install.packages
  • process.bib
  • taf.boot

(b) All text files that have non-ASCII characters must be encoded as UTF-8:

  • enc.latin1

(c) Each TAF script should only write to its corresponding directory:

  • data.R writes to data
  • model.R writes to model
  • output.R writes to output
  • report.R writes to report

1.2 Recommendations (warn)

1.3 Recommendations (note)

(a) This string should not appear in TAF scripts, except in a custom boot script:

  • http (except stockassessment.org?)

(b) Rounding functions should not be used in data.R, model.R, or output.R:

  • icesRound(
  • round(
  • rnd(

1.3.1 Files

(a) The following files are expected to exist:

  • data.R
  • model.R
  • output.R
  • boot/DATA.bib

(b) Authors in SOFTWARE.bib are spelled out as {First M Last and First M Last and First M Last}, so the author field has no commas:

  • ,

2. Middle scan

Examines files that were created during the boot procedure

3. Final scan

Examines files that were created by the R scripts

https://www.ietf.org/rfc/rfc2119.txt