R/aer_in_geom_xml.R

In granar/granar: Generator of Root ANAtomy in R

#' @title Get the coordinate of the first cell center
#'
#'
#' @param sim The sim output list
#' @param path The geometry file for MECHA
#' @keywords root mecha
#' @export
#'

aer_in_geom_xml <- function(sim, path = "./MECHA/Projects/GRANAR/in/Maize_Geometry.xml"){

  require(xml2)
  if (is.null(path)) {
    warning("No path specified")
  }
  if(is.null(sim$id_aerenchyma)){
    warning("No aerenchyma id specified")
  }else{
    id_aerenchyma <- sim$id_aerenchyma
  }
  xml <- read_xml(path)

  aer <- xml_children(xml_find_all(xml, "//aerenchyma_range"))

  # newbee <- 'aerenchyma id="0"'
  if(length(sim$id_aerenchyma) == 0){
    message("no aerenchyma")
  }else{
    new_siblings <- paste0('aerenchyma id="',id_aerenchyma,'"')
    xml_add_sibling(aer, new_siblings)
  }

  xml_remove(aer[1])

  path <- paste0(c(unlist(stringr::str_split(path, ".xml"))[1]),"_aer.xml")

  write_xml(xml, path)
  return(TRUE)
}