Missing info in EpiNow2 chunk

[CarmenTamayo]

@Bisaloo there's a Rmd code chunk that just says "missing for now" in the EpiNow2 section of the template, should this be removed? the code above it does generate the plot with regional estimates so I'm not sure whether this was a typo or if there's actually some information that needs to be added

episoap/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiNow2.Rmd

Line 109 in 2b56ffb

# Missing for now

[Bisaloo]

The idea was to add a boxplot/mustache plot, such as the same one we are provided in the chunk with the same name in the EpiEstim child document:

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

Lines 148 to 165 in a44eda5

	```{r rt-plot-estimates-group}
	# Plot of latest estimates
	res_epiestim_group %>%
	filter(end == max(end)) %>%
	ggplot(aes(y = .data[[group_var]]), fill = custom_grey) +
	geom_point(aes(x = median), color = dark_green) +
	geom_errorbar(aes(xmin = lower, xmax = upper), color = dark_green) +
	geom_vline(xintercept = 1, color = dark_pink) +
	labs(
	title = "Latest estimates of Rt",
	subtitle = sprintf(
	"As of %s",
	format(max(get_dates(dat_i_day)), "%d %B %Y")
	),
	y = "",
	x = "Instantaneous Reproduction Number (Rt)"
	)
	```

The overall concept was to have a perfect match (or as good as possible) match across the different package options.

[CarmenTamayo]

So should I add this as well? Or was there a blocker for this at the time that I should be aware of?
Also, I'm not able to knit the template with EpiNow2 because of a lock file error, but at least on the Rmd I see that the chunk starts with an "Explanation" section that appears to be empty- what did you envision to include here? an overview of the package and how it's used to estimate transmissibility? should I add it too?

episoap/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiNow2.Rmd

Line 11 in a44eda5

### Explanations

[Bisaloo]

So should I add this as well? Or was there a blocker for this at the time that I should be aware of?

As far as I remember, it was mostly a lack of time to do it at the time. It would be great if you can add it.

chunk starts with an "Explanation" section that appears to be empty- what did you envision to include here?

It was added to match perfectly what is present in the i2extras child document. I'm no longer sure what the best solution is here. Maybe this section should be removed from all child documents, including i2extras, in line with what we discussed in #120.

[CarmenTamayo]

This has been addressed in #144 by adding a corresponding section of explanations for the other Rmd chunks (EpiNow2, EpiEstim, R0)