R/warnparam.R

In frousseu/rNest: Estimating Nesting Chronology and Breeding Phenology in Birds

warnparam <-
function(x=x,param=nparam,prog=4,warn=warn){
                theosta<-c(nparam$cmax,nparam$laying*prog,nparam$incubation,nparam$rearing)
                sta<-names(x)
                laying<-length(which(sta=="laying"))
                incubation<-length(which(sta=="incubation"))
                rearing<-length(which(sta=="young"))
                obs<-c(prog,laying,incubation,rearing)
                if(warn$type=="percentage"){
                     varobs<-c(prog-theosta[1],(obs[-1]/theosta[-1])-1)
                }else{  #if warn$type=="days"
                     varobs<-c(prog-theosta[1],obs[-1]-theosta[-1])
                     }
                print(varobs)
                varobs<-c(ifelse(varobs[1]>0L,TRUE,FALSE),varobs[-1]>warn$over | varobs[-1]<(warn$under*(-1)))
                names(varobs)<-c("clutch","laying","incubation","young")
                return(list(warn=varobs,reject=any(varobs)))
                }