R/unknown_nbeggs.R

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

unknown_nbeggs <-
function(dat){
                  if(all(dat$eggs>=0 & dat$young>=0)){list(dat=dat,unknown=F)}
                  if(nrow(dat)==1 || all(dat$eggs%in%c(-1,0) & dat$young%in%c(-1,0))){
                       #dat[,c("eggs","young")]<-rep1(dat[,c("eggs","young")],dat$clutch[1])
                       return(list(dat=dat,unknown=T))
                       }
                  egg<-dat$eggs[dat$stage_code=="eggs"]
                  if(length(egg)==0 || all(egg>=0)){return(list(dat=dat,unknown=F))}
                  prog<-max(ifelse(dat$eggs==(-1),1,dat$eggs)+ifelse(dat$young==(-1),1,dat$young))
                  if(all(egg==(-1))){
                       #dat$eggs[dat$stage_code=="eggs"]<-prog
                       return(list(dat=dat,unknown=T))
                       }
                  
                  w<-which(dat$eggs>0 & dat$stage_code=="eggs")[1]
                  if(dat$eggs[w]==prog){return(list(dat=dat,unknown=T))}  #(2011/10/03 this unknown was changed to F because of nest 1040923)
                  if(dat$eggs[w]<prog){
                       ww<-match(-1,dat$eggs)
                       #if(ww<w){  #removed check bug test_20120301_122656
                       #     if((as.numeric(difftime(dat$date[w],dat$date[ww]))-1)>(dat$laying[1]*(dat$eggs[w]-1))){dat$eggs[ww]<-1}
                       #     }
                       dat<-dat[!(dat$eggs==(-1) & dat$stage_code=="eggs"),]
                       return(list(dat=dat[dat$eggs>=0,],unknown=F))  # anciennement un FALSE ici check bug test_20120301_130733 watch out, ici on ne conserve que les observations d'oeufs non négatives car ça fuck lorsqu'on a de l'incubation
                       #return(list(dat=dat,unknown=F))  # TEST on ne conserve que les observations d'oeufs non négatives car ça fuck lorsqu'on a de l'incubation
                       }
                  return(list(dat="negative numbers; not implemented yet",unknown=F))
                  }