Package 'intervalcalc'

Fitting Data for Interval Calculation

Description

This function takes data from the prep_interval_data function and fits it to a series of speficied distributions

Usage

fit_interval_data(
  interval_data,
  distribution = c("gamma", "gamma-trunc"),
  stan_opts = list(),
  return_raw = FALSE
)

Arguments

interval_data	a named list containing the interval data
distribution	a string vector indicating the distributions with which to fit the data
stan_opts	a named list with additional options passed to CmdStanR
return_raw	a logical, should the samples be returned

---

Serial Interval Data from Nishiura et al

Description

Serial Interval Data from Nishiura et al

Usage

nishiura

Format

a data.frame with 28 rows and 10 columns

V1

Row number

SIClassification

Certainty of the Classification

DiagnosisCounty

County of Diagnosis

InfectorOnset

Onset for index case

InfecteeOnset

Onset for infected individual

ER

Symptom interval for infector

EL

Symptom interval for infector

SL

Symptom interval for infectee

SR

Symptom interval for infectee

Source

Source for the data

Source

Supporting materials for Nishiura H, Linton NM, Akhmetzhanov AR 2020 "Serial interval of novel coronavirus (COVID-19) infections" International journal of infectious diseases 93: 284–6 (doi:10.1016/j.ijid.2020.02.060)

---

Prepare Interval Data

Description

This function can be used to prepare data for fitting

Usage

prep_interval_data(dat)

Arguments

dat	a data.frame with columes named er, el sl,sr

Value

a named list for use with fit_interval_data

---