est.R0.SB | R Documentation |
Estimate R by a sequential Bayesian method, using known data up to a point in time as a Bayesian prior for the next iteration (see details).
est.R0.SB(
epid,
GT,
t = NULL,
begin = NULL,
end = NULL,
date.first.obs = NULL,
time.step = 1,
force.prior = FALSE,
checked = FALSE,
...
)
epid |
Object containing epidemic curve data. |
GT |
Generation time distribution from |
t |
Vector of dates at which incidence was observed. |
begin |
At what time estimation begins (unused by this method, just there for plotting purposes). |
end |
At what time estimation ends (unused by this method, just there for plotting purposes). |
date.first.obs |
Optional date of first observation, if |
time.step |
Optional. If date of first observation is specified, number of day between each incidence observation. |
force.prior |
Set to any custom value to force the initial prior as a uniform distribution on [0 ; value]. |
checked |
Internal flag used to check whether integrity checks were ran or not. |
... |
Parameters passed to inner functions. |
For internal use. Called by estimate.R()
.
Initial prior is an unbiased uniform distribution for R, between 0 and the maximum of incid(t+1) - incid(t). For each subsequent iteration, a new distribution is computed for R, using the previous output as new prior.
The 95% confidence intervan is achieved by a cumulative sum of the posterior distirbution of R and corresponds to the 2.5-th and 97.5-th percentiles.
A list with components:
R |
vector of R values. |
conf.int |
95% confidence interval for estimates. |
proba.Rt |
A list with successive distribution for R throughout the outbreak. |
GT |
Generation time distribution used in the computation. |
epid |
Original epidemic data. |
begin |
Begin date for the fit. |
begin.nb |
Index of begin date for the fit. |
end |
End date for the fit. |
end.nb |
Index of end date for the fit. |
pred |
Predictive curve based on most-likely R value. |
data.name |
Name of the data used in the fit. |
call |
Complete call used to generate results. |
method |
Method for estimation. |
method.code |
Internal code used to designate method. |
This is the implementation of the method provided by Bettencourt & Ribeiro (2008).
Pierre-Yves Boelle, Thomas Obadia
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.
#Loading package
library(R0)
## Data is taken from the paper by Nishiura for key transmission parameters of an institutional
## outbreak during 1918 influenza pandemic in Germany)
data(Germany.1918)
mGT <- generation.time("gamma", c(3,1.5))
SB <- est.R0.SB(Germany.1918, mGT)
## Results will include "most likely R(t)" (ie. the R(t) value for which the computed probability
## is the highest), along with 95% CI, in a data.frame object
SB
# Reproduction number estimate using Real Time Bayesian method.
# 0 0 2.02 0.71 1.17 1.7 1.36 1.53 1.28 1.43 ...
SB$Rt.quant
# Date R.t. CI.lower. CI.upper.
# 1 1918-09-29 0.00 0.01 1.44
# 2 1918-09-30 0.00 0.01 1.42
# 3 1918-10-01 2.02 0.97 2.88
# 4 1918-10-02 0.71 0.07 1.51
# 5 1918-10-03 1.17 0.40 1.84
# 6 1918-10-04 1.70 1.09 2.24
# 7 1918-10-05 1.36 0.84 1.83
# 8 1918-10-06 1.53 1.08 1.94
# 9 1918-10-07 1.28 0.88 1.66
# 10 1918-10-08 1.43 1.08 1.77
# ...
## "Plot" will provide the most-likely R value at each time unit, along with 95CI
plot(SB)
## "Plotfit" will show the complete distribution of R for 9 time unit throughout the outbreak
plotfit(SB)
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