R/build_CIs_regrxn_pois_comm.R

In brouwern/DRmencia: Data and code to replicate analyses for Latta, Brouwer, et al. 2018. PeerJ.

## Build prediction interval for regression data
### Poisson model (has "i" for overdisp)
### community data
buidCIs_regrxn_pois_comm <- function(mod, mod.type = "poisson"){
  #new data
  if(mod.type == "poisson"){
    newdat <- expand.grid(
      i = mod@frame$i[1]
      ,site = unique(mod@frame$site)[1]
      ,year = unique(mod@frame$year)[1]
      ,site.age.cent = unique(mod@frame$site.age.cent)
    )

  }

   if(mod.type != "poisson"){
    newdat <- expand.grid(
      #i = mod@frame$i[1]
      site = unique(mod@frame$site)[1]
      ,year = unique(mod@frame$year)[1]
      ,site.age.cent = unique(mod@frame$site.age.cent)
    )

  }

  #predict output
  out <- merTools::predictInterval(mod,
                                   newdata =   newdat,
                                   which = "fixed",
                                   level = 0.95,
                                   #n.sims = 10,
                                   stat = "median",
                                   include.resid.var = FALSE)
  #combine
  out <- cbind(newdat,out)

  return(out)
}