R/merge_covariates.R

In wpgp/popRF: Random Forest-Informed Population Disaggregation

#' Merging covariates.
#'
#' @param input.countries list countries 
#' @param covariates.var.names list of covariates names 
#' @param covariates details of the covariates
#' @param rfg.countries.tag tag for the project
#' @param rfg.countries.merged directory to save merged rasters
#' @param verbose is logical. TRUE or FALSE: flag indicating whether to print 
#'        intermediate output from the function on the console, which might be 
#'        helpful for model debugging. Default is \code{verbose} = TRUE.
#' @param log is logical. TRUE or FALSE: flag indicating whether to print 
#'        intermediate output from the function on the log.txt file. 
#'        Default is \code{log} = FALSE.
#' @importFrom terra sprc
#' @importFrom terra rast
#' @importFrom terra merge
#' @noRd 
#' @rdname merge_covariates
#' @return A data.frame merged covariates
#' @examples
#' \dontrun{
#' merge_covariates( covariates.var.names, 
#'                  covariates, 
#'                  rfg.countries.tag, 
#'                  rfg.countries.merged)
#' }
merge_covariates <- function(input.countries,
                             covariates.var.names, 
                             covariates, 
                             rfg.countries.tag, 
                             rfg.countries.merged, 
                             verbose = FALSE,
                             log = FALSE){
  
  
  rfg.input.countries <- input.countries
  
  log_info("MSG",
           paste0("Start merging covariates"),
           verbose=verbose,
           log=log) 
  
  covariates_merged <- list()
  
  
  for ( i in 1:length(covariates.var.names) ) {  
    
    cname <- covariates.var.names[[i]]
    
    list_of_tiffs <- c()
    for ( ic in 1:length(rfg.input.countries) ) {
      
      country <- rfg.input.countries[[ic]]
      rst <- paste0(covariates[[country]][[cname]][["dataset_path"]])
      list_of_tiffs <- append(list_of_tiffs, rst, 1)
      rtype <- covariates[[country]][[cname]][["dataset_summary"]]
      
    }
    
    dstfile <- file.path(rfg.countries.merged,
                         paste0(rfg.countries.tag,
                                "_",
                                cname,
                                ".tif"))
    
    if (!file.exists(dstfile)){
      
      
      # gdalwarp(srcfile=list_of_tiffs,
      #          of = "GTiff",
      #          dstfile=dstfile,
      #          co=c("COMPRESS=LZW", "BLOCKXSIZE=512",
      #           "BLOCKYSIZE=512", "TILED=YES", "BIGTIFF=YES"),
      #          s_srs=crs(raster(rst)),
      #          output_Raster=TRUE,
      #          overwrite=TRUE,
      #          verbose=FALSE) 
      
      terra::merge(x = terra::sprc(list_of_tiffs),
                   first = TRUE,
                   na.rm = TRUE,
                   filename = dstfile,
                   overwrite = TRUE,
                   wopt = list(filetype = "GTiff", 
                               gdal = c("COMPRESS=LZW",
                                        "BLOCKXSIZE=512",
                                        "BLOCKYSIZE=512",
                                        "TILED=YES",
                                        "BIGTIFF=YES")))
      
      
      
    }
    
    #covariates_merged[[rfg.countries.tag]][[cname]][["path"]] <- dstfile
    covariates_merged[[rfg.countries.tag]][[cname]] <- list(dataset_folder = dirname(dstfile), 
                                                            dataset_filename = basename(dstfile),
                                                            dataset_description = cname,
                                                            dataset_summary = rtype,
                                                            dataset_country = cname,
                                                            dataset_class = cname,
                                                            dataset_path  = dstfile 
    )
    
    
    if (verbose){
      if ( i != length(covariates.var.names)){
        
        progress_message(x=i, 
                         max=length(covariates.var.names), 
                         label=paste0("Merging ", cname))  
        
      }else{
        
        progress_message(x=i, 
                         max=length(covariates.var.names), 
                         label=paste0("Merging complete                     " ))
        
      }
    }      
    
    
    
  } 
  
  #log_info("MSG", paste0("Completed merging covariates"),
  # verbose=verbose, log=log) 
  return(covariates_merged)
  
}