updated priors vignette so that it works, exported required functions

[dlebauer]

Updated the prior vignette so that it can compile. This required exporting a few functions from the PEcAn.priors function. Or perhaps these were incorrectly identified as S3 methods.

Motivation and Context

To get the vignette working again.

Review Time Estimate

• Immediately
• Within one week
• When possible

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• My change requires a change to the documentation.
• I have updated the CHANGELOG.md.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.

[infotroph]

@dlebauer Overall this looks great. Thanks for getting it working again!

To get Travis tests passing, I think it should suffice to add MASS to the Imports section of the DESCRIPTION file. (Note that the check failure is only detecting the undeclared import, not running the vignette code -- making Travis actually build vignettes is a separate issue discussed in #2437).

Once tests pass, I'm happy to merge this, but a longer-term consideration that can wait for a different PR: This vignette uses a lot of external packages that aren't currently listed as dependencies for the Priors package -- I see at least dplyr, DEoptim, fitdistrplus, rjags, rriskDistributions. These need to be declared as package dependencies, so we should (1) consider whether they add enough to the vignette to be worth the installation footprint or whether we can show usage effectively without them, then (2) remove any we can live without and (3) declare the rest in Suggests.

[dlebauer]

No idea! I think I just used devtools::document()

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_______________________ *David LeBauer* Director of Data Sciences Arizona Experiment Station THE UNIVERSITY OF ARIZONA Bioscience Research Labs, 207 1230 N Cherry Ave | Tucson, AZ 85721 Office: 520-621-4381 dlebauer@email.arizona.edu orcid <https://orcid.org/0000-0001-7228-053X> | twitter <https://twitter.com/dlebauer> | github <https://github.com/dlebauer> | linkedin <https://www.linkedin.com/in/dlebauer/>

[infotroph]

my version of Roxygen wants to re-add these S3 method declarations. How did you persuade it to treat these as regular functions?

No idea! I think I just used devtools::document()

@dlebauer Huh, weird. Well, I'd say fix the missing MASS declaration and see if the build passes -- if it does, the problem was on my end. If it complains about files changing during the build, then we'll need to revisit this

[infotroph]

@dlebauer Can you estimate when you'll have time to finish this? I'd like to use the priors package as a test case for #2437, but it'd be preferable to have this merged first to avoid conflict / take advantage of your work

[dlebauer]

@infotroph I've added MASS to imports

regarding the dependencies ... I think fitdistrplus, rjags, and rriskDistributions are critical to the vignette - since the vignette shows how to use these packages to come up with priors. DEoptim could possibly be replaced with optim and dplyr could certainly be replaced. But then this brings up the question of whether it is worthwhile to refactor code just to reduce dependencies (especially in vignettes, or in the case of dplyr, where the package is installed elsewhere in the PEcAn build).

[dlebauer]

Thanks for your help @infotroph! Finally can merge!