Include examples in functions

[andybeet]

I have been adding examples to all of the functions i am reviewing so a user knows how to use the function. As a new user to Rpath i am finding this exercise very helpful in understanding how the package/functions works

For example, one of the functions i was reviewing (extract.node) can only be used if 3 other Rpath functions have been run prior. Having an example showing this, is valuable (in my opinion), for future users.

For those unfamiliar with Rpackage development you can add examples using code like below:

#' @examples
#' # Read in Rpath parameter file and balance model
#' Rpath <- rpath(Ecosense.EBS)
#' # Create a 50 yr Rpath scenario
#' Rsim.scenario <- rsim.scenario(Rpath, Ecosense.EBS, years = 1:50)
#' # Run a scenario
#' Rsim.output <- rsim.run(Rsim.scenario, method = "RK4", years = 1:50)
#' # Extracts group (node) specific data from the simulation run
#' group <- extract.node(Rsim.output,Rpath$Group['Squids'])

This code will be executed in the help documentation

Is this something we want to make as a standard?

[SarahJWeisberg]

I think so...my only thought is maybe we want to use the Anchovy Bay model (AB) as our example, as this is a relatively simple model commonly used for teaching EwE -- and it might be easier for a new user to follow along with a simple parameter set.

The downside is we might not have ready examples for some of the more complex functionality.

@kaydin What do you think?

[kaydin]

"Smallest" is good and Anchovy Bay is a good default, but as found in the extract.node conversation we might need to check on features that are illustrated (e.g. multiple detritus groups, stanzas).

[sgaichas]

I was planning to add examples for the ecosim.R functions and am happy to use any standard format the group agrees on

[SarahJWeisberg]

I was planning to add examples for the ecosim.R functions and am happy to use any standard format the group agrees on

Do you have thoughts on which example model might be best to point to?

[sgaichas]

ideally I think it would be the smallest one we could use to test all the features currently in the package; I'm not sure which one that is