R/get_ncmean.R

In momentuHMM: Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models

get_ncmean <- function(distnames,fullDM,circularAngleMean,nbStates){
  nc <- meanind <- vector('list',length(distnames))
  names(nc) <- names(meanind) <- distnames
  for(i in distnames){
    nc[[i]] <- apply(fullDM[[i]],1:2,function(x) !all(unlist(x)==0))
    if(!isFALSE(circularAngleMean[[i]])) {
      meanind[[i]] <- which((apply(fullDM[[i]][1:nbStates,,drop=FALSE],1,function(x) !all(unlist(x)==0))))
      # deal with angular covariates that are exactly zero
      if(length(meanind[[i]])){
        angInd <- which(is.na(match(gsub("cos","",gsub("sin","",colnames(nc[[i]]))),colnames(nc[[i]]),nomatch=NA)))
        sinInd <- colnames(nc[[i]])[which(grepl("sin",colnames(nc[[i]])[angInd]))]
        nc[[i]][meanind[[i]],sinInd]<-ifelse(nc[[i]][meanind[[i]],sinInd],nc[[i]][meanind[[i]],sinInd],nc[[i]][meanind[[i]],gsub("sin","cos",sinInd)])
        nc[[i]][meanind[[i]],gsub("sin","cos",sinInd)]<-ifelse(nc[[i]][meanind[[i]],gsub("sin","cos",sinInd)],nc[[i]][meanind[[i]],gsub("sin","cos",sinInd)],nc[[i]][meanind[[i]],sinInd])
      }
    }
  }
  list(nc=nc,meanind=meanind)
}