IncidenceDailyRS2014: Incidence estimator using rs2014 method implemented using...

In cturbelin/ifnBase: InfluenzaNet Data Analysis Base

Incidence estimator using rs2014 method implemented using daily agregatation

Description

Incidence estimator using rs2014 method implemented using daily agregatation

Incidence estimator using rs2014 method implemented using daily agregatation

Details

Input: Input data are expected to have some columns & some fixes. They are loaded and prepared using load_results_for_incidence

Parameters:

ignore.first.delay

Number of days form his first survey befotre to include a participant (not compatible with ignore.first)

ignore.first.only.new

Ignore first rule only for new participant (uses intake$first.season column

exclude.same

should exclude syndrom if same episode is on (partcipant still active)

exclude.same.delay

max delay to exclude syndrom if same (not excluded if over this delay)

active.max.freq

max delay between 2 surveys (in weeks)

active.day.before

Number of week before each computed week to count active participants

active.day.after

Number of week after each computed week to count active participants

active.min.surveys

min number of surveys for each participant (not active if less)

active.use.mean

Use mean number of active participant over the windows [active.day.before, active.day.after]

Public fields

weekly

weekly data (loaded using load_results_for_incidence)

intake

intake data (loaded using load_results_for_incidence)

participant

data.frame() with all available participants and commputed criterias used during computation

params

parameters for computation

syndromes

character vector of column names containing syndromes classification for each weekly

profiler

profiler

verbose

logical show verbose message

design

design stratification from design_incidence

output

vector of character, see IncidenceRS2014

Methods

Public methods

• IncidenceDailyRS2014$new()

• IncidenceDailyRS2014$prepare()

• IncidenceDailyRS2014$compute_date()

• IncidenceDailyRS2014$compute()

• IncidenceDailyRS2014$clone()

---

Method new()

instanciate object

Usage

IncidenceDailyRS2014$new(
  weekly,
  intake,
  syndromes,
  params,
  design,
  output = c("inc")
)

Arguments

weekly

data

intake

intake data

syndromes

syndromes column names in weekly

params

list of parameters for computing

design

design_incidence

output

list of output types to compute

syndroms

compatibility

---

Method prepare()

Prepare data before to compute Prepare participants data to be able to apply selection rules

Usage

IncidenceDailyRS2014$prepare()

---

Method compute_date()

Internal function Estimate incidence with rs2014 method for a given date

Usage

IncidenceDailyRS2014$compute_date(date)

Arguments

date

date to compute

---

Method compute()

Compute weekly incidence for all requested weeks Apply the full algorithm for rs2014 incidence computation prepare data and then compute for each week by calling estimate_incidence_rs2014_week

Usage

IncidenceDailyRS2014$compute(dates = NULL, verbose = T, progress = T)

Arguments

dates

dates to compute, if NULL will compute on all dates available in weekly data

verbose

show verbose messages if TRUE

progress

show progress

---

Method clone()

The objects of this class are cloneable with this method.

Usage

IncidenceDailyRS2014$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

cturbelin/ifnBase documentation built on Aug. 26, 2024, 12:54 p.m.