R/mean.adjust.R

In covid19-dashboard-us/STEM: Spatio-Temporal Epidemic Model

mean.adjust <- function(mfit, new.data = list(), index, 
  b1.type = "cons", adj.type = "infec"){
  mpred.terms <- predict(mfit, new.data, type = "terms", se.fit = FALSE)
  W = log(as.matrix(new.data$I) + 1)
  mpred.terms[index$index.1, 1] = index$thrd1
  mpred.terms[index$index.2, 1] = index$thrd2
  if(b1.type == "vary"){
    mpred.terms[index$index.3, 2] = 0
    mpred.terms[index$index.4, 2] = W[index$index.4]
  }
  
  mpred.gsvcm = rowSums(mpred.terms) 
  if(adj.type == "infec"){
    mpred.gsvcm = mpred.gsvcm + log(new.data$S.ratio)
  }
  theta <- mfit$family$getTheta()
  p.gsvcm <- 1 - exp(-exp(theta[1] + exp(theta[2]) * mpred.gsvcm))    
  pred = p.gsvcm * exp(mpred.gsvcm)
  return(pred)
}