SyndromeProviderCovid: Syndrome Provider with COVID-19 like definitions

In cturbelin/ifnBase: InfluenzaNet Data Analysis Base

Syndrome Provider with COVID-19 like definitions

Description

Syndrome Provider with COVID-19 like definitions

Syndrome Provider with COVID-19 like definitions

Details

To run need weekly with get_columns_for_incidence() column list

Super class

ifnBase::SyndromeProvider -> SyndromeProviderCovid

Public fields

pain.age.limit

age under which pain & headache will exluded from defintion

use.sudden

logical, use sudden feature to build the syndrome

definitions

character vector of definitions to output

Methods

Public methods

• SyndromeProviderCovid$new()

• SyndromeProviderCovid$syndromes()

• SyndromeProviderCovid$check_definitions()

• SyndromeProviderCovid$compute()

• SyndromeProviderCovid$clone()

Inherited methods

• ifnBase::SyndromeProvider$compute_age()
• ifnBase::SyndromeProvider$is_sudden()

---

Method new()

instanciate object

Usage

SyndromeProviderCovid$new(pain.age.limit = 5, use.sudden = TRUE)

Arguments

pain.age.limit

age to take into account of subjectives symptoms

use.sudden

use sudden appearance of symptoms in the definitions, if FALSE will be considered as always sudden

---

Method syndromes()

Get available syndromes names

Usage

SyndromeProviderCovid$syndromes()

Returns

character()

---

Method check_definitions()

Update definitions list to compute

Usage

SyndromeProviderCovid$check_definitions(definitions)

Arguments

definitions

character vector of definition name to compute

---

Method compute()

Compute definitions for all syndromes

Usage

SyndromeProviderCovid$compute(weekly, intake, definitions = NULL)

Arguments

weekly

weekly data

intake

intake data with at least 'person_id', 'age' column

definitions

character vector of definition to use

use.sudden

logical if TRUE use is_sudden, otherwise consider it's always TRUE

Returns

data.frame with each computed syndrome in column, and "id" column from weekly

---

Method clone()

The objects of this class are cloneable with this method.

Usage

SyndromeProviderCovid$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

## Not run: 
 season = 2017
 weekly = survey_load_results("weekly", get_columns_for_incidence(), season=season)
 intake = survey_load_results("weekly", c('timestamp','date.birth'))
 weekly = recode_weekly(weekly)
 intake = recode_intake(intake)
 provider = SyndromeProviderCovid$new()
 r = provider$compute(weekly, intake)

## End(Not run)

cturbelin/ifnBase documentation built on Nov. 5, 2023, 12:54 p.m.