emei: Spatiotemporal models of variability

stmv_timeseries_smooth = function(p, dat, sloc=sloc, distance=distance, datvarsout=c("id", p$stmv_variables$TIME, p$stmv_variables$LOCS, p$stmv_variables$Y)) {

  # static vars .. don't need to look up
    datgridded = dat # only the static parts .. time has to be a uniform grid so reconstruct below

    p_coord_names = p$stmv_variables$LOCS[1:2]

    ids = array_map( "xy->1", datgridded[, p_coord_names], gridparams=p$gridparams ) # 100X faster than paste / merge
    todrop = which(duplicated( ids) )
    if (length(todrop>0)) datgridded = datgridded[-todrop,]
    ids=todrop=NULL

    tokeep = c(p$stmv_variables$LOCS )
    if (exists("weights", dat) ) tokeep = c(tokeep, "weights")

    if (p$nloccov > 0) {
      for (ci in 1:p$nloccov) {
        vn = p$stmv_variables$local_cov[ci]
        pu = stmv_attach( p$storage_backend, p$ptr$Pcov[[vn]] )
        nts = ncol(pu)
        if ( nts==1 ) tokeep = c(tokeep, vn )
      }
    }

    datgridded = datgridded[ , tokeep ]
    datgridded_n = nrow(datgridded)
    nts = vn = NULL

    # add temporal grid
    if ( exists("TIME", p$stmv_variables) ) {
      datgridded = cbind( datgridded[ rep.int(1:datgridded_n, p$nt), ],
                      rep.int(p$prediction_ts, rep(datgridded_n, p$nt )) )
      names(datgridded)[ ncol(datgridded) ] = p$stmv_variables$TIME
      datgridded = cbind( datgridded, stmv_timecovars ( vars=p$stmv_variables$local_all, ti=datgridded[,p$stmv_variables$TIME]  ) )
    }

    if (p$nloccov > 0) {
      # add time-varying covars .. not necessary except when covars are modelled locally
      for (ci in 1:p$nloccov) {
        vn = p$stmv_variables$local_cov[ci]
        pu = stmv_attach( p$storage_backend, p$ptr$Pcov[[vn]] )
        nts = ncol(pu)
        if ( nts== 1) {
          # static vars are retained in the previous step
        } else if ( nts == p$ny )  {
          datgridded$iy = datgridded$yr - p$yrs[1] + 1 #yr index
          datgridded[,vn] = pu[ cbind(datgridded$i, datgridded$iy) ]
         } else if ( nts == p$nt) {
          datgridded$it = p$nw*(datgridded$tiyr - p$yrs[1] - p$tres/2) + 1 #ts index
          datgridded[,vn] = pu[ cbind(datgridded$i, datgridded$it) ]
        }
      } # end for loop
      nts = vn = NULL
    } # end if

    rownames(datgridded) = NULL

    ts_gam = stmv__gam( p, dat, datgridded ) # currently only a GAM is enabled for the TS component

    if (is.null( ts_gam)) return(NULL)
    if (ts_gam$stmv_stats$rsquared < p$stmv_rsquared_threshold ) return(NULL)

    # range checks
    rY = range( dat[,p$stmv_variables$Y], na.rm=TRUE)
    toosmall = which( ts_gam$predictions$mean < rY[1] )
    toolarge = which( ts_gam$predictions$mean > rY[2] )
    if (length(toosmall) > 0) ts_gam$predictions$mean[toosmall] =  NA
    if (length(toolarge) > 0) ts_gam$predictions$mean[toolarge] =  NA

    # overwrite dat with interpolated predictions
    datgridded = ts_gam$predictions
    rownames(datgridded) = NULL
    ts_gam = NULL

    names(datgridded)[which(names(datgridded)=="mean")] = p$stmv_variables$Y
    names(datgridded)[which(names(datgridded)=="sd")] = paste(p$stmv_variables$Y, "sd", sep=".")

    windowsize.half = trunc(distance/p$pres) + 1L
    pa_w = -windowsize.half : windowsize.half # default window size
    # pa_w = pa_w[ -length(pa_w)] # must be even
    pa_w_n = length(pa_w)
    adims = c(p$nt, pa_w_n, pa_w_n )
    datgridded$id = array_map( "3->1",
      coords = trunc( cbind(
        ( (datgridded[,p$stmv_variables$TIME ] - p$prediction_ts[1] ) / p$tres) + 1L ,
        ( windowsize.half + (datgridded[,p$stmv_variables$LOCS[1]] - sloc[1]) / p$pres) + 1L,
        ( windowsize.half + (datgridded[,p$stmv_variables$LOCS[2]] - sloc[2]) / p$pres) + 1L)),
      dims=adims )
    o = which( datgridded$id > prod(adims)  | datgridded$id <= 0 ) # remove the area outside the aoi
    if (length(o) > 0 ) datgridded = datgridded[-o,]

    ddup = which(duplicated(datgridded$id))

    if ( length( ddup) > 0 ) {
      dups = unique(datgridded$id[ddup])
      for ( i in dups ) {
        j = which( datgridded$id== i)
        meanvalue = mean( datgridded[j, p$stmv_variables$Y], na.rm=TRUE)
        datgridded[j, p$stmv_variables$Y] = NA
        datgridded[j[1], p$stmv_variables$Y] = meanvalue
      }
      datgridded = datgridded[ which(is.finite(datgridded[, p$stmv_variables$Y]) ) , ]
    }

    out = list()
    out$pa_w_n = pa_w_n
    out$windowsize.half = windowsize.half
    out$adims = adims
    out$xM = array( NA, dim=adims )
    out$xM[datgridded$id] = datgridded[,p$stmv_variables$Y]

    if(0){
    # ignore this for now .. as it is unlikely to be used ..
    # prediction covariates i.e., independent variables/ covariates
      pvars = c("plon", "plat", "id")
      if (p$nloccov > 0) {
        # .. not necessary except when covars are modelled locally
        for (ci in 1:p$nloccov) {
          vn = p$stmv_variables$local_cov[ci]
          pu = NULL
          pu = stmv_attach( p$storage_backend, p$ptr$Pcov[[vn]] )
          nts = ncol(pu)
          if ( nts== 1 ) {
            pvars = c( pvars, vn )
            datgridded[,vn] = pu[datgridded$i]  # ie. a static variable
          }
        }
      }
      datgridded = datgridded[, pvars]
      datgridded = cbind( datgridded, stmv_timecovars ( vars=p$stmv_variables$local_all, ti=datgridded[,p$stmv_variables$TIME]  ) )

      if (p$nloccov > 0) {
        # add time-varying covars .. not necessary except when covars are modelled locally
        for (ci in 1:p$nloccov) {
          vn = p$stmv_variables$local_cov[ci]
          pu = NULL
          pu = stmv_attach( p$storage_backend, p$ptr$Pcov[[vn]] )
          nts = ncol(pu)
          if ( nts == p$ny )  {
            datgridded$iy = datgridded$yr - p$yrs[1] + 1 #yr index
            datgridded[,vn] = pu[ cbind(datgridded$i, datgridded$iy) ]
            message("Need to check that datgriddeda order is correct")
          } else if ( nts == p$nt ) {
            datgridded$it = p$nw*(datgridded$tiyr - p$yrs[1] - p$tres/2) + 1 #ts index
            datgridded[,vn] = pu[ cbind(datgridded$i, datgridded$it) ]
            message("Need to check that data order is correct")
          } else if (nts==1) { } #nothing to do .. already processed above }
        }
      }

    }

      out$datgridded= datgridded[, datvarsout ]

    return(out)

}