extract.node doc update

[andybeet]

Files updated

• Extract.r - this contains the extract.node() function

Details

• Updated the title and description
• Created autolinks to other functions mentioned in the documentation
• Expanded explanation of object output (how many variables in the list, their names, and definitions)
• Created an example of how you would use this function using one of the bundled rpath models

NOTE: The Discard item in the returned list has duplicate field names. (See discussion 103).

I created this PR for just the one function, as a test, to make sure i was doing what you were hoping i would. Please let me know if you are expecting anything else/different

[andybeet]

To test: switch to this branch, pull, build package, (depending on settings you may need to run devtools::document(), then run pkgdown::build_reference()).
Then navigate to the extract.node() documentation to view changes.

It should look something like this.

[andybeet]

I think the function extract_node is working as expected but the output from rsim.run may have an issue. See discussion

[SarahJWeisberg]

What does this comment mean?

[andybeet]

I have no idea

[SarahJWeisberg]

@kaydin Any ideas?

[kaydin]

This is a wholly Sean function and not one that's been part of my own practical workflow. It is out-of-date in at least one way: it doesn't include fishing from input forcing (ForcedF and ForcedCatch) which e.g. is how most of the catch in our current Bering/GOA models is input. Before detail bugfixes, might be worth an overall review of this function in terms of use (if anyone on team is using this in actual workflow, would love to know).

[andybeet]

ok, so maybe we merge this (since it is just documentation) and then create an issue to look into it further and fix any issues. Even though the group may not use extract.node, other R path users may use it. It has been in the package for a while

[andybeet]

i'll reach out @slucey and see if he has time to explain

[kaydin]

@andybeet agree we should not wholly delete it, just need to make sure it's reporting what it says (at most, deprecate with warning if need be).

[SarahJWeisberg]

ok, so maybe we merge this (since it is just documentation) and then create an issue to look into it further and fix any issues. Even though the group may not use extract.node, other R path users may use it. It has been in the package for a while

I like that idea! I have also never used this function before for what that's worth.