R/calculate_knot_areas.R

In James-Thorson/FishStatsUtils: Utilities (shared code and data) for FishStats spatio-temporal modeling toolbox

#' Calculate areas and covariates for a given triangulated mesh
#'
#' \code{calculate_knot_areas} builds outputs for a given triangulated mesh used for approximating spatial variation
#'
#' @inheritParams make_mesh

#' @param Data_Extrap the output from e.g., \code{Extrapolation_List <- Prepare_WCGBTS_Extrapolation_Data_Fn()} using slot \code{Extrapolation_List$Data_Extrap}
#' @param Covariates character vector giving names of columns from Data_Extrap that should be used as covariates (default="none", which results in a design matrix with one columns of 1s)
#' @param a_el a matrix with \code{nrow(Data_Extrap)} rows and l columns, giving the area within the l-th stratum for the e-th row of Data_Extrap

#' @return Tagged list containing distance metrics
#' \describe{
#'   \item{a_xl}{A data frame with areas for each knot and each strattum}
#' }

#' @export
calculate_knot_areas <-
function( loc_x,
          Data_Extrap,
          Covariates = "none",
          a_el = NULL ){

  # Calculate a_el if missing
  if( is.null(a_el) ){
    a_el = rep(1,nrow(Data_Extrap))
  }

  # Nearest extrapolation grid for each knot
  if( all(c("E_km","N_km") %in% colnames(loc_x)) ) NN_Extrap = RANN::nn2( data=loc_x[,c('E_km','N_km')], query=Data_Extrap[,c('E_km','N_km')], k=1 )
  if( all(c("Lon","Lat") %in% colnames(loc_x)) ) NN_Extrap = RANN::nn2( data=loc_x[,c('Lon','Lat')], query=Data_Extrap[,c('Lon','Lat')], k=1 )

  # Calculate area for each knot
  a_xl = matrix(NA, ncol=ncol(a_el), nrow=nrow(loc_x), dimnames=list(NULL,colnames(a_el)))
  for(l in 1:ncol(a_xl)){
    a_xl[,l] = tapply(a_el[,l], INDEX=factor(NN_Extrap$nn.idx,levels=1:nrow(loc_x)), FUN=sum)
    a_xl[,l] = ifelse( is.na(a_xl[,l]), 0, a_xl[,l] )
  }

  # Calculate covariate for each knot
  # Covariate j at location x is the average value in the extrapolation_grid for all grid cells s that are nearest to location x
  if( length(Covariates)==1 && Covariates=="none" ){
    X_xj = cbind( "Dummy"=rep(0,nrow(loc_x)) )
  }else{
    X_xj = matrix(NA, ncol=length(Covariates), nrow=nrow(loc_x))
    for(j in 1:ncol(X_xj)){
      X_xj[,j] = tapply(Data_Extrap[,Covariates[j]], INDEX=factor(NN_Extrap$nn.idx,levels=1:nrow(loc_x)), FUN=mean, na.rm=TRUE)
    }
  }

  # Return stuff
  Return = list( "X_xj"=X_xj, "a_xl"=a_xl, "NN_Extrap"=NN_Extrap )
}