MetawardProcessingPipeline: Process metawards output

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

Description

Process metawards output

Process metawards output

Super classes

ukcovidtools::PassthroughFilesystemCache -> ukcovidtools::DataProvider -> MetawardProcessingPipeline

Methods

Public methods

• MetawardProcessingPipeline$new()

• MetawardProcessingPipeline$readSpatialFile()

• MetawardProcessingPipeline$loadAgeTimeMatrix()

• MetawardProcessingPipeline$applyAgeTimeMatrix()

• MetawardProcessingPipeline$loadDefaultAgeTimeMatrices()

• MetawardProcessingPipeline$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()

Usage

MetawardProcessingPipeline$new(providerController, ...)

---

Method readSpatialFile()

loads a spatial model file

Usage

MetawardProcessingPipeline$readSpatialFile(fname, ignoreErrors = FALSE)

Arguments

fname

- a filename containing a ward based metaward model .dat file

Returns

a data frame containing the simulation results

---

Method loadAgeTimeMatrix()

loads an age time matrix from a csv

Usage

MetawardProcessingPipeline$loadAgeTimeMatrix(url)

Arguments

url

- a url or filename for a csv file

Returns

a data frame containing the filter

---

Method applyAgeTimeMatrix()

applies a age time matrix to a dataframe containing an incidence, an age category column, and a date column

Usage

MetawardProcessingPipeline$applyAgeTimeMatrix(
  inputDf,
  matrixDf,
  oldIncidenceVar = "incidence",
  newIncidenceVar = "incidence",
  oldDateVar = "date",
  newDateVar = "date",
  ageCatVar = "ageGroup"
)

Arguments

inputDf

- an input df containing an incidence col, a date col and a ageCategory col this must be grouped

matrixDf

- a dataframe containing a sparse matrix of probabilities where age is labelled

oldIncidenceVar

- the name of the input incidence col

newIncidenceVar

- the name of the output incidence col

oldDateVar

- the name of the input date column

newDateVar

- the name of the output date column

ageCatVar

- the age category variable

Details

Make sure your age categories are the saem as the matrix you are applying The age time matrix can implement a delay, aggregate over time and or filter by age

Returns

a data frame containing the simulation results

---

Method loadDefaultAgeTimeMatrices()

loads a ventilator demand matrices

Usage

MetawardProcessingPipeline$loadDefaultAgeTimeMatrices()

Returns

a list of matrices

---

Method clone()

The objects of this class are cloneable with this method.

Usage

MetawardProcessingPipeline$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.