CovidTimeseriesProvider: General covid processing

In terminological/uk-covid-datatools: Functions for sourcing, cleaning and calculating Rt for uk covid timeseries data

Description

General covid processing

General covid processing

Super classes

ukcovidtools::PassthroughFilesystemCache -> ukcovidtools::DataProvider -> CovidTimeseriesProvider

Methods

Public methods

• CovidTimeseriesProvider$new()

• CovidTimeseriesProvider$setTruncation()

• CovidTimeseriesProvider$trimNAs()

• CovidTimeseriesProvider$complete()

• CovidTimeseriesProvider$completeAllRegions()

• CovidTimeseriesProvider$fillAbsent()

• CovidTimeseriesProvider$fillAbsentAllRegions()

• CovidTimeseriesProvider$fillAbsentByRegion()

• CovidTimeseriesProvider$fixDatesAndNames()

• CovidTimeseriesProvider$timeseriesQA()

• CovidTimeseriesProvider$describeErrors()

• CovidTimeseriesProvider$describe()

• CovidTimeseriesProvider$clone()

Inherited methods

• ukcovidtools::PassthroughFilesystemCache$getDaily()

• ukcovidtools::PassthroughFilesystemCache$getHashCached()

• ukcovidtools::PassthroughFilesystemCache$getSaved()

• ukcovidtools::PassthroughFilesystemCache$unloadCache()

• ukcovidtools::DataProvider$ageCatToFactor()

• ukcovidtools::DataProvider$ageToAgeCat()

• ukcovidtools::DataProvider$breakFromCats()

• ukcovidtools::DataProvider$cutByAge()

• ukcovidtools::DataProvider$download()

• ukcovidtools::DataProvider$downloadAndUntar()

• ukcovidtools::DataProvider$downloadAndUnzip()

• ukcovidtools::DataProvider$downloadDaily()

• ukcovidtools::DataProvider$labelsFromBreaks()

• ukcovidtools::DataProvider$normaliseAgeCat()

• ukcovidtools::DataProvider$normaliseGender()

---

Method new()

New timeseries provider pipeline

Usage

CovidTimeseriesProvider$new(providerController, ...)

Arguments

providerController

the provider controller

...

for compatibility

Returns

the provider

---

Method setTruncation()

Usage

CovidTimeseriesProvider$setTruncation(listDays)

---

Method trimNAs()

Usage

CovidTimeseriesProvider$trimNAs(r0Timeseries)

---

Method complete()

Take a set of timeseries and add in missing dates as NAs. Preserves source, type, statistic differences in timeseries length. intially Fills all regions to be the same length but with trim trailing NAs

Usage

CovidTimeseriesProvider$complete(covidTimeseries)

Returns

a covidTimeseriesFormat dataframe

---

Method completeAllRegions()

Take a set of timeseries and add in missing dates as NAs. Preserves source, type, statistic differences in timeseries length. intially Fills all regions to be the same length but with trim trailing NAs

Usage

CovidTimeseriesProvider$completeAllRegions(covidTimeseries)

Returns

a covidTimeseriesFormat dataframe

---

Method fillAbsent()

Usage

CovidTimeseriesProvider$fillAbsent(covidTimeseries, completeDates = FALSE)

---

Method fillAbsentAllRegions()

Take a set of regional timeseries, finds the full list of regions and the whole timeseries and fills any missing values with zero (if incidence) or the previous value (if cumulative) explicitly filling in missing values. This is suitable for use for a incidence derived from a line list where some dates and regions will not be observed

Usage

CovidTimeseriesProvider$fillAbsentAllRegions(covidTimeseries)

Returns

a covidTimeseriesFormat dataframe

---

Method fillAbsentByRegion()

Take a set of timeseries and fills any missing values with zero (if incidence) or the previous value (if cumulative) explicitly filling in zeros for missing values. This is suitable for use for a incidence derived from a line list where some dates will not be observed. It does not enforce that something has been observed in all regions.

Usage

CovidTimeseriesProvider$fillAbsentByRegion(covidTimeseries)

Returns

a covidTimeseriesFormat dataframe

---

Method fixDatesAndNames()

Take a set of timeseries and fixes any non standard names, truncates time series by truncate days. intially Fills all regions to be the same length but with trim trailing NAs

Usage

CovidTimeseriesProvider$fixDatesAndNames(covidTimeseries, truncate = NULL)

Returns

a covidTimeseriesFormat dataframe

---

Method timeseriesQA()

Check timeseries conforms

Usage

CovidTimeseriesProvider$timeseriesQA(covidTimeseries)

---

Method describeErrors()

Usage

CovidTimeseriesProvider$describeErrors(covidTimeseries, valueVar = "value")

---

Method describe()

Usage

CovidTimeseriesProvider$describe(covidTimeseries, ...)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

CovidTimeseriesProvider$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

terminological/uk-covid-datatools documentation built on June 24, 2021, 8:16 p.m.