estimate.R: Estimate reproduction number (R0 or Rt) for one incidence...

In R0: Estimation of R0 and Real-Time Reproduction Number from Epidemics

Estimate reproduction number (R0 or Rt) for one incidence dataset using available methods

Description

Estimate R_{0} or R(t) for an incidence dataset using the methods implemented in the R0 package.

Usage

estimate.R(
  epid = NULL,
  GT = NULL,
  t = NULL,
  begin = NULL,
  end = NULL,
  date.first.obs = NULL,
  time.step = 1,
  AR = NULL,
  pop.size = NULL,
  S0 = 1,
  methods = NULL,
  checked = TRUE,
  ...
)

Arguments

epid	Object containing epidemic curve data.
GT	Generation time distribution from generation.time().
t	Vector of dates at which incidence was observed.
begin	Begin date for estimation. Can be an integer or a date (YYYY-mm-dd or YYYY/mm/dd).
end	End date for estimation. Can be an integer or a date (YYYY-mm-dd or YYYY/mm/dd).
date.first.obs	Optional date of first observation, if t not specified.
time.step	Optional. If date of first observation is specified, number of day between each incidence observation.
AR	Attack rate as a percentage from total population.
pop.size	Population size in which the incident cases were observed. See more details in est.R0.AR() documentation.
S0	Initial proportion of the population considered susceptible.
methods	Vector of methods to be used for R/R0/Rt estimation. Must be provided as c("method 1", "method 2", ...).
checked	Internal flag used to check whether integrity checks were ran or not.
...	Parameters passed to inner functions.

Details

Currently, supported methods are Exponential Growth (EG), Maximum Likelihood (ML), Attack Rate (AR), Time-Dependant (TD), and Sequential Bayesian (SB). The corresponding references from the literature are available below.

This function acts as a front-end and will prepare relevant inputs to pass them to internal estimation routines. In particular, all inputs will undergo validation through integrity.checks() and the checked flag (defaulting as TRUE here) will be passed to internal estimation routines. Any warning raised by integrity.checks() should warrant careful thinking and investigation.

Value

A list with components:

estimates	List containing all results from called methods.
epid	Epidemic curve.
GT	Generation Time distribution function.
t	Date vector.
begin	Begin date for estimation.
end	End date for estimation.

Author(s)

Pierre-Yves Boelle, Thomas Obadia

References

est.R0.AR() : Dietz, K. "The Estimation of the Basic Reproduction Number for Infectious Diseases." Statistical Methods in Medical Research 2, no. 1 (March 1, 1993): 23-41.
est.R0.EG() : Wallinga, J., and M. Lipsitch. "How Generation Intervals Shape the Relationship Between Growth Rates and Reproductive Numbers." Proceedings of the Royal Society B: Biological Sciences 274, no. 1609 (2007): 599.
est.R0.ML() : White, L.F., J. Wallinga, L. Finelli, C. Reed, S. Riley, M. Lipsitch, and M. Pagano. "Estimation of the Reproductive Number and the Serial Interval in Early Phase of the 2009 Influenza A/H1N1 Pandemic in the USA." Influenza and Other Respiratory Viruses 3, no. 6 (2009): 267-276.
est.R0.SB() : Bettencourt, L.M.A., and R.M. Ribeiro. "Real Time Bayesian Estimation of the Epidemic Potential of Emerging Infectious Diseases." PLoS One 3, no. 5 (2008): e2185.
est.R0.TD() : Wallinga, J., and P. Teunis. "Different Epidemic Curves for Severe Acute Respiratory Syndrome Reveal Similar Impacts of Control Measures." American Journal of Epidemiology 160, no. 6 (2004): 509; Cauchemez S., and Valleron AJ. "Estimating in Real Time the Efficacy of Measures to Control Emerging Communicable Diseases" American Journal of Epidemiology 164, no. 6 (2006): 591.

Examples

#Loading package
library(R0)

## Outbreak during 1918 influenza pandemic in Germany)
data(Germany.1918)
mGT <- generation.time("gamma", c(3, 1.5))
estR0 <- estimate.R(Germany.1918, mGT, begin=1, end=27, methods=c("EG", "ML", "TD", "AR", "SB"), 
                  pop.size=100000, nsim=100)

attributes(estR0)
## $names
## [1] "epid"      "GT"        "begin"     "end"       "estimates"
## 
## $class
## [1] "R0.sR"

## Estimates results are stored in the $estimates object
estR0
## Reproduction number estimate using  Exponential Growth  method.
## R :  1.525895[ 1.494984 , 1.557779 ]
## 
## Reproduction number estimate using  Maximum Likelihood  method.
## R :  1.383996[ 1.309545 , 1.461203 ]
## 
## Reproduction number estimate using  Attack Rate  method.
## R :  1.047392[ 1.046394 , 1.048393 ]
## 
## Reproduction number estimate using  Time-Dependent  method.
## 2.322239 2.272013 1.998474 1.843703 2.019297 1.867488 1.644993 1.553265 1.553317 1.601317 ...
## 
## Reproduction number estimate using  Sequential Bayesian  method.
## 0 0 2.22 0.66 1.2 1.84 1.43 1.63 1.34 1.52 ...


## If no date vector nor date of first observation are provided, results are the same
## except time values in $t are replaced by index

R0 documentation built on Sept. 26, 2023, 5:10 p.m.