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rmeanmedianconfidence-intervalellipsis

How to get values inside (...) and take mean?

I am using package R0. I am trying to replicate the example provided in CRAN pdf but not getting exactly same result as provided in pdf.

code:

library(R0)
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
# ...

I have three queries.

  1. The last command SB$Rt.quant shows NULL in output. How can I get exactly the same result as in the example?

  2. How can I get values hidden in (...) for both command: SB and SB$Rt.quant?

  3. How can I take mean and median of SB and get confidence interval of related mean and median of SB?

Solution

  • The arguments have been changed now. You have to use SB$conf.int to get the confidence interval like

    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)
SB
SB$conf.int

    Then you can use write.csv(SB$conf.int) to print all the values. If you want to have both R and confidence interval as like the example in the R0 pdf document you can use the following code

    cbind(Rt=SB$R, SB$conf.int)

    Reading 3rd question, I think you can get the mean by using SB$R and the median function is not available in the package. The confidence interval is already available through SB$conf.int.