Nb outbreak walk

[nsbatra]

Revised R4Epis website walk-through to align with current code in skeleton.Rmd.

Also made a few minor changes to the outbreak templates, aligning some code with piping, e.g.

linelist_cleaned$sex <- fct_explicit_na(linelist_cleaned$sex, "M", "F")

change to:

linelist_cleaned <- linelist_cleaned %>% mutate(sex = fct_explicit_na(sex)

[nsbatra]

This is super weird. I don't remember changing this at all in the Rmd!!

On Mon, Aug 29, 2022 at 9:40 AM Alex Spina @.***> wrote:

@.**** commented on this pull request.

In inst/rmarkdown/templates/cholera_outbreak/skeleton/skeleton.Rmd https://github.com/R4EPI/sitrep/pull/305#discussion_r956991373:

@@ -739,11 +743,12 @@ linelist_cleaned$age_group <- age_categories(linelist_cleaned$age_years,

to combine different age categories use the following function

this prioritises the smaller unit, i.e. if given months and years, will return months first

-## generally, these delineations are NOT used for cholera

+## generally, these delineations are NOT used for measles.

here too ...

— Reply to this email directly, view it on GitHub https://github.com/R4EPI/sitrep/pull/305#pullrequestreview-1088202623, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMN4O7Z7UTOMSA27LHFUAODV3RSP3ANCNFSM573WZJ2A . You are receiving this because you authored the thread.Message ID: @.***>

[nsbatra]

@aspina7 I know you want to try to wrap this up this weekend, so I've pushed my progress on the walkthroughs, including the new data copying functions.

In brief each of the datasets is accessible internally via the data/ folder, and externally via the extdata/ folder. The R functions allpw easy "download" of the external versions of the datasets (explained in the walkthrough), while the internal versions of the datasets are used to actually render the walkthroughs.

The walkthroughs themselves are still being finished, but nothing else remaining to be written should impact the structure of the package.

[aspina7]

also pls remove spaces is vignette names according to zhian https://github.com/R4EPI/sitrep/pull/304#issuecomment-1231868161

[aspina7]

@nsbatra - fixed download function for shapefiles and reduced code duplication by moving to an internal generic function, also moved all to one script so easier for oversight

[aspina7]

merging for now as per https://github.com/R4EPI/sitrep/pull/305#issuecomment-1236044241