jidea-110 New time series

[EmmaLRussell]

This branch adds time series for new (daily) values for infections, hospitalisations, deaths and vaccinations, using daedalus's get_incidence and get_new_vaccinations methods.

It also adds metadata for the new time series, and for groupings of time series. This might overkill, but I wanted the API to provide as much information as possible so that the front end could be as generic as possible - but also has the option to pick and choose which metadata it wants to use. The idea here is that related time_series are grouped together into time_series_groups, and each time series in a group takes a particular "role" ie total or daily. The role the time series takes in a group is its key in time_series_groups.times_series, and the top level time_series_roles provides metadata for the roles (currently just label but could add description too). Could also add descriptions for the time series groups, just let me know.

[david-mears-2]

Is there no way to specify that this object's keys must be 'time_series_role's? If not, what good does it do to define the time_series_roles array?

[EmmaLRussell]

I don't think so, in the schema. The reason for putting in the time_series_roles array was to include metadata, which the front end might choose to use i.e. label.

[pratikunterwegs]

Thanks @EmmaLRussell - just a couple of comments from me, but otherwise feel free to merge this once David okays it.

[pratikunterwegs]

The code here definitely works, but here's a suggestion to cut down calls to get_incidence():

model_results = daedalus("GBR", "sars_cov_1")

# already has all three time series in long format
incidences = get_incidence(output)

# pivot to wide format
incidences_wide = tidyr::pivot_wider(
  incidences, id_cols = "time", names_from = "measure"
)

# get timeseries, e.g.
time_series$new_infections = incidences_wider$daily_infections

[pratikunterwegs]

Could "New deaths" and "New vaccinations" be capitalised to follow the previous few labels? Only an issue if these are going to be displayed in the front end, otherwise don't bother!

[david-mears-2]

The house style I'm going for is actually to only capitalize once per title: so it's New Infections and New Hospitalisations that need to change.

[david-mears-2]

Suggested change

	{ "id": "new_infections", "label": "New Infections", "description": "Number of new infections per day" },
	{ "id": "new_hospitalisations", "label": "New Hospitalisations", "description": "Number of patients who are hospitalised per day" },
	{ "id": "new_deaths", "label": "New deaths", "description": "Number of deaths per day" },
	{ "id": "new_vaccinations", "label": "New vaccinations", "description": "Number of vaccinations per day" }
	{ "id": "new_infected", "label": "New infections", "description": "Number of new infections per day" },
	{ "id": "new_hospitalised", "label": "New hospitalisations", "description": "Number of patients who are hospitalised per day" },
	{ "id": "new_dead", "label": "New deaths", "description": "Number of deaths per day" },
	{ "id": "new_vaccinated", "label": "New vaccinations", "description": "Number of vaccinations per day" }

It's neat how the t_s_groups have nouns as their ids while time_series themselves have adjectives as ids -- helps us avoid the ids colliding. So let's regularise on that and have all the time_series adjectives where possible.

[david-mears-2]

A suggestion of an edited description to align with the description of the corresponding total (and to be more accurate):

Suggested change

	{ "id": "new_infections", "label": "New Infections", "description": "Number of new infections per day" },
	{ "id": "new_hospitalisations", "label": "New Hospitalisations", "description": "Number of patients who are hospitalised per day" },
	{ "id": "new_deaths", "label": "New deaths", "description": "Number of deaths per day" },
	{ "id": "new_vaccinations", "label": "New vaccinations", "description": "Number of vaccinations per day" }
	{ "id": "new_infections", "label": "New Infections", "description": "Number of new infections per day" },
	{ "id": "new_hospitalisations", "label": "New Hospitalisations", "description": "Number of new patients in need of hospitalisation per day" },
	{ "id": "new_deaths", "label": "New deaths", "description": "Number of deaths per day" },
	{ "id": "new_vaccinations", "label": "New vaccinations", "description": "Number of vaccinations per day" }

[david-mears-2]

Thanks for getting this out of the door so quickly. See comments.