Update {epiparameter} usage

[CarmenTamayo]

Changes in epiparameter usage to update template contents to the latest version of the package:

• Changed pathogen to disease on in the params section (both label and description) of the .Rmd to avoid confusion, since epidist uses diseases rather than pathogens
• Changed epidist() to epidist_db() to extract from database (lines 380-385)
• Changed epidist$params to as.list(get_parameters(si_epiparameter)) (line 387)<- as.list so it can be used with function on line 406
• Changed to family(epidist) to extract distribution name (line 388)
• Changed lines 389 and 390 to extract mean and sd from summary statistics
• Changed {epiparameter} version on renv
• Changed {epitrix} to {epiparameter} when converting summary statistics to distribution parameters
• Changed {distcrete} to {epiparameter} when discretising distribution
• Removed {epitrix} and {distcrete} as they've now been replaced by {epiparameter} functions
• Changed param from "use_epiparameter" to "use_epiparameter_database" now that {epiparameter} is used also when this param = FALSE
• Updated epiparameter usage in code chunks to estimate Rt (EpiNow2, R0)

[Bisaloo]

Please also update the epiparameter version number for renv:

episoap/inst/rmarkdown/templates/transmissibility/skeleton/skeleton.Rmd

Line 79 in 724ce0d

"epiverse-trace/epiparameter@fd250ce", # nolint

You can find the value to use by running sessioninfo::package_info("epiparameter"), which will tell you which version is installed on your local computer.

[Bisaloo]

Could you also update epiparameter usage in the EpiNow2 child document?

[CarmenTamayo]

Could you also update epiparameter usage in the EpiNow2 child document?
yes, that's on my to-do list, to update the usage also on the rmd chunks

[Bisaloo]

Suggested change

	si <- epiparameter::discretise(si_epiparameter)
	si_x <- seq(1L, to = si$prob_dist$qf(0.999), by = 1L)
	si <- as.function(si_epiparameter)
	si_x <- seq(1L, to = quantile(si_epiparameter, 0.999), by = 1L)

Note however that in the case use_epiparameter_database = FALSE, the object si_epiparameter does not exist.

[CarmenTamayo]

@joshwlambert @Bisaloo hi both, do you think we could merge this PR? the only issue I've not been able to resolve is issue #127 , where I'm unsure how {epiparameter} could be used to update what's now being done by epitrix/distcrete
Other than that, this could be merged after being reviewed

[joshwlambert]

@CarmenTamayo I will review this afternoon and get back to you by EOD.

[joshwlambert]

Thanks for making these updates @CarmenTamayo! Mostly looks really good. I've left a few comments throughout the changes with some comments and questions.

[joshwlambert]

Given the number of commits to number of files changed I think this PR would be a good candidate for a squash merge.

[Bisaloo]

Please also add yourself as a package author (role = "aut") in the DESCRIPTION before we merge this @CarmenTamayo 🙏

episoap/DESCRIPTION

Lines 4 to 9 in 0b7406f

	Authors@R: c(
	person("Hugo", "Gruson", , "hugo.gruson+R@normalesup.org", role = c("aut", "cre", "cph"),
	comment = c(ORCID = "0000-0002-4094-1476")),
	person("Thibaut", "Jombart", role = "aut"),
	person("data.org", role = "fnd")
	)

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 73.07%. Comparing base (e21a7c8) to head (f5dd10b).

❗ Current head f5dd10b differs from pull request most recent head 916e8e3. Consider uploading reports for the commit 916e8e3 to get more accurate results

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #100   +/-   ##
=======================================
  Coverage   73.07%   73.07%           
=======================================
  Files           4        4           
  Lines          26       26           
=======================================
  Hits           19       19           
  Misses          7        7           

☔ View full report in Codecov by Sentry.
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[CarmenTamayo]

Please also add yourself as a package author (role = "aut") in the DESCRIPTION before we merge this @CarmenTamayo 🙏

episoap/DESCRIPTION

Lines 4 to 9 in 0b7406f

	Authors@R: c(
	person("Hugo", "Gruson", , "hugo.gruson+R@normalesup.org", role = c("aut", "cre", "cph"),
	comment = c(ORCID = "0000-0002-4094-1476")),
	person("Thibaut", "Jombart", role = "aut"),
	person("data.org", role = "fnd")
	)

Done here 013a44d

[joshwlambert]

Not sure why the test-reports workflow is failing, looking at the setup-r-dependencies@v2 output from sessionInfo() neither {episoap} or it's dependencies for the templates are being installed, even though they were on previous actions runs when the workflow passed. Could use the setup-renv@2 workflow (https://github.com/r-lib/actions/tree/v2-branch/setup-renv) to ensure the packages required to build the reports are installed with their correct versions. @Bisaloo & @chartgerink let me know if you think this is a suitable fix?

[chartgerink]

@joshwlambert - are we confident that's the underlying problem, really? If the workflow worked before and has not changed, it feels like something else must be causing this. I just re-ran the workflow and it seems like there is a different problem that requires some debugging to make the action

Quitting from lines 215-230 [unnamed-chunk-2] (skeleton.Rmd)
Error in `value[[3L]]()`:
! Package 'ggplot2' version 3.5.0 cannot be unloaded:
 Error in unloadNamespace(package) : namespace 'ggplot2' is imported by 'episoap' so cannot be unloaded
Backtrace:

To fix the workflow, I would see what changed since the last time the workflow succeeded and find the root cause.

[joshwlambert]

@chartgerink I think the misunderstanding is because I was looking at the first test report workflow to fail. It seems the error in recent workflow failures is different.

The packages being installed by setup-r-dependencies are the most recent versions, or at least newer than specified in the skeleton.Rmd lock file. The error seems to be that the action cannot unload the newer version. This would presumably be resolved by just installing the versions specified in the lock file in the first place, but I'm unsure how to do this without pulling the lock file into a renv.lock file and using the setup-renv workflow mentioned above.

What's the best approach?