Typhoid vignette

[kristinawlai]

I finished the typhoid vignette withe the simulated data and moved the references.bib to the vignettes folder. However, Kristen recommended using the South Sudan data for this vignette so it's real data. The simulated data doesn't have age groups, so it's just overall incidence. I can make those updates, but wanted to get this version pushed out first to have something. Would it be useful to have an overall vignette and an age-specific vignette? Or perhaps include both in the same vignette?

[kristinawlai]

@d-morrison Uh oh checks are failing now. Did I use an older version before your fixes?

[d-morrison]

@d-morrison Uh oh checks are failing now. Did I use an older version before your fixes?

@kristinawlai:

The relevant error is:

could not find function "load_all"

The load_all function is only for in-development code. The finalized vignettes should use library(serocalculator) instead. Try making that change; to test on your local computer, first run the install() command in the Console, then replace load_all() with library(serocalculator), then run the test() command in the Console. If the output of test() is all tests passed, then the tests on github should also pass.

[d-morrison]

(see my reply re: check errors)

[kristinawlai]

@d-morrison I removed load_all() and devtools() from typhoid-seroincidence.rmd and tutorial.rmd, but there are still errors. When I use test() in my console there are no errors either, but it has been running so quickly that I don't trust it. Any tips?

[d-morrison]

@d-morrison I removed load_all() and devtools() from typhoid-seroincidence.rmd and tutorial.rmd, but there are still errors. When I use test() in my console there are no errors either, but it has been running so quickly that I don't trust it. Any tips?

@kristinawlai Looks like there is a reference to the "seroincidence" package somewhere: in the checks, there is a message:

Error: Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
4 nodes produced errors; first error: there is no package called ‘seroincidence’
```

[kristinawlai]

@d-morrison the checks pass now! This is the only warning I saw when checking on my desktop and I'm not quite sure what to do with it. Maybe just a function name issue?

W checking for code/documentation mismatches (1.8s)
Functions or methods with usage in documentation object 'incidence.age' but not in code:
'incidence.age'

[kristinawlai]

Closing this since all updates were moved to the typhoid_vignette_hack branch