Chain size data for pneumonic plague

Nishiura et al. (2012) report 19 outbreaks with more than one case of pneumonic plague since 1900. Given the collection process, analysis must condition on seeing chains of size >= 2. Further, the chain of size 5009 should either be treated as censored (at size 5009) or re-coded to Inf.

data(pneumonic_plague)

Format

Vector of all chain sizes.

Source

https://doi.org/10.1016/j.jtbi.2011.10.039

References

Nishiura H, Yan P, Sleeman CK, Mode CJ (2012). "Estimating the transmission potential of super-critical processes based on the final size distribution of minor outbreaks." Journal of Theoretical Biology 294: 48–55.

Examples

if (FALSE) { # \dontrun{
data(pneumonic_plague)

# Fit with censoring
model <- compile_nbbp_homogenous()
fit_nbbp_homogenous_bayes(
  pneumonic_plague,
  model,
  condition_geq = rep(2, 19),
  censor_geq = c(rep(NA, 3), 5009, rep(NA, 15))
)

# Fit with re-coding
pneumonic_plague[pneumonic_plague == 5009] <- Inf
fit_nbbp_homogenous_bayes(
  pneumonic_plague,
  model,
  condition_geq = rep(2, 19)
)
} # }