Output Files

Documented in upgrade_plt_xml

#' Upgrading _plt.xml file(s) to a newer version
#'
#' @param file Path of an plant (*_plt.xml) file or a vector of
#' @param out_dir Output directory path of the generated files
#' @param param_newform_file Path of the param_newform.xml file corresponding
#' to the file version
#' @param param_gen_file Path of the param_gen.xml file corresponding
#' to the file version
#' @param stics_version Name of the STICS version (VX.Y format)
#' @param target_version Name of the STICS version to upgrade files to
#' (VX.Y format)
#' @param check_version Perform version consistency between `stics_version`
#' and the file version, for finally checking if an upgrade is possible
#' allowed to the target_version. If TRUE, param_gen_file is mandatory.
#' @param overwrite logical (optional),
#' TRUE for overwriting file if it exists, FALSE otherwise
#' @param ... Additional input arguments
#'
#' @return None
#'
#' @export
#'
#' @details See get_stics_versions_compat() for listing versions
#'
#' @examples
#'
#' dir_path <- get_examples_path(file_type = "xml", stics_version = "V9.2")
#'
#' upgrade_plt_xml(
#'   file = file.path(dir_path,"file_plt.xml"),
#'   out_dir = tempdir(),
#'   param_newform_file = file.path(dir_path, "param_newform.xml"),
#'   param_gen_file = file.path(dir_path, "param_gen.xml")
#' )
#'
upgrade_plt_xml <- function(file,
                            out_dir,
                            param_newform_file,
                            param_gen_file,
                            stics_version = "V9.2",
                            target_version = "V10.0",
                            check_version = TRUE,
                            overwrite = FALSE,
                            ...) {



  # For verifying output dir existence
  check_dir <- TRUE
  args_list <- list(...)
  if ("check_dir" %in% names(args_list)) check_dir <- args_list$check_dir
  if (check_dir) {
    if (!dir.exists(out_dir)) dir.create(out_dir)
    # for checking only once when multiple files are treated !
    check_dir <- FALSE
  }

  # checking version
  if (check_version) {
    min_version <- get_version_num("V9.1")

    # extracting or detecting the STICS version corresponding to the xml file
    # based on param_gen.xml file content
    file_version <- check_xml_file_version(file[1],
                                           stics_version,
                                           param_gen_file = param_gen_file
    )


    if (!file_version && is.null(param_gen_file)) {
      stop("param_gen_file must be provided! ")
    }

    if (!file_version) {
      stop(
        "The input version ", stics_version,
        " does not match file version ",
        attr(file_version, "version"), " \n", file[1]
      )
    }

    # Compatibility checks between version and update to target_version
    ver_num <- get_version_num(stics_version)
    if (ver_num < min_version) {
      stop(
        "Files from the version ", stics_version,
        " cannot be converted to the version ", target_version
      )
    }


    # for checking only once when multiple files are treated !
    check_version <- FALSE
  }


  # Treating a files list
  if (length(file) > 1) {
    lapply(file, function(x) {
      upgrade_plt_xml(
        file = x,
        out_dir = out_dir,
        param_newform_file = param_newform_file,
        param_gen_file = param_gen_file,
        stics_version = stics_version,
        target_version = target_version,
        check_version = check_version,
        overwrite = overwrite,
        check_dir = check_dir
      )
    })
    return(invisible())
  }

  # local initialization, before loadinf RData
  jvc_data <- NULL

  # Loading the old xml file
  old_doc <- xmldocument(file = file)


  # Setting file STICS version
  set_xml_file_version(old_doc, new_version = target_version,
                       overwrite = overwrite)


  # Parameters to move to varietal parameters ----------------------------------
  #
  # Coming from other formalisms than varietal ones
  # Storing parameters values to set them to varietal ones
  param_names_to_varietal <- c(
    "phobase", "phosat", "stdordebour", "bdens", "hautbase", "hautmax",
    "dlaimax", "dlaimaxbrut", "innsen", "rapsenturg", "extin", "ktrou", "temin",
    "teopt", "slamax", "tigefeuil", "nbjgrain", "nbgrmin", "vitircarb",
    "vitircarbT", "stdrpnou", "nbinflo", "inflomax", "pentinflores",
    "vitpropsucre", "vitprophuile", "vitirazo",
    "tgellev10", "tgeljuv10", "tgelveg10",
    "psisto", "psiturg",
    "deshydbase"
  )
  param_values_to_varietal <- get_param_value(old_doc, param_names_to_varietal)

  # nodes existing outside of 'cultivar parameters' formalism
  nodes_to_rm <- lapply(param_names_to_varietal, function(x) {
    get_nodes(
      old_doc,
      path = paste0("//formalisme[@nom!='cultivar parameters']//param[@nom='",
                    x, "']")
    )
  })

  # Checking nodes : all must be not NULL
  nodes_null <- unlist(lapply(nodes_to_rm, is.null))
  if (any(nodes_null)) stop("missing nodes, not a v9.1 or 9.2 _plt.xml file")

  # Removing nodes
  lapply(nodes_to_rm, function(x) XML::removeNodes(x))


  # Already exist in varietal parameters
  # Storing parameters values before applying new varietal parameters structure
  param_names_keep <- c(
    "stlevamf", "stamflax", "stlevdrp", "stflodrp", "stdrpdes", "pgrainmaxi",
    "adens", "croirac", "durvieF", "jvc", "sensiphot", "stlaxsen", "stsenlan",
    "nbgrmax", "stdrpmat", "afruitpot", "dureefruit"
  )

  param_values_keep <- get_param_value(old_doc, param_names_keep)

  # Checking values: list names ==  param_names_keep
  if (!all(param_names_keep %in% names(param_values_keep))) {
    stop("Missing values, , not a v9.1 or 9.2 _plt.xml file")
  }


  # General plant parameters ---------------------------------------------------
  #
  # adding codephot_part
  new_node <- XML::xmlParseString(
    '<option choix="2" nom="effect of decreasing photoperiod on
    biomass allocation" nomParam="codephot_part">
    <choix code="1" nom="yes"/>
    <choix code="2" nom="no"/>
    </option>',
    addFinalizer = TRUE
  )

  # test if the node exists
  node_exists <- !is.null(get_nodes(old_doc,
                                    '//option[@nomParam="codephot_part"]'))

  if (node_exists) stop(
    "codephot_part already exists, not a v9.1 or 9.2 _plt.xml file")

  parent_node <- get_nodes(
    old_doc,
    '//option[@nomParam="codephot"]/choix[@code="1"]')[[1]]

  XML::addChildren(parent_node, XML::xmlClone(new_node))


  # moving nbfeuilplant
  node_to_move <- get_nodes(old_doc, path = "//param[@nom='nbfeuilplant']")[[1]]
  prev_sibling <- get_nodes(old_doc, path = "//param[@nom='laiplantule']")[[1]]

  XML::addSibling(prev_sibling, node_to_move)



  # Recalculating irazomax
  irazomax_calc <- calc_irazomax(
    get_param_value(old_doc, "irmax")$irmax,
    param_values_to_varietal$vitircarb,
    param_values_to_varietal$vitirazo)

  new_node <- XML::xmlParseString(
    paste0('<param format="real" max="1.0" min="0.01" nom="irazomax">',
           irazomax_calc,
           "</param>"),
    addFinalizer = TRUE
  )

  # adding irazomax node
  parent_node <- get_nodes(old_doc,
                           path = "//formalisme[@nom='yield formation']")[[1]]
  XML::addChildren(parent_node, new_node, at = 0)


  message(old_doc@name,
          ": be aware that irazomax is a new parameter and its value (",
          irazomax_calc,
          ")\nis estimated using some other parameters values.\n",
          paste0("But this value needs to be ajusted according to ",
                 "species and varieties "), "\n")


  # moving irmax
  node_to_move <- get_nodes(old_doc, path = "//param[@nom='irmax']")[[1]]
  parent_node <- get_nodes(
    old_doc,
    path = "//option[@nomParam='codeir']/choix[@code='1']")[[1]]

  XML::addChildren(parent_node, node_to_move)



  # add codedisrac option node
  new_node <- XML::xmlParseString(
    '<option choix="2" nom="Standard root distribution" nomParam="codedisrac">
    <choix code="1" nom="yes">
    <param format="real" max="0.01" min="0.00001" nom="kdisrac">0.00158</param>
    <param format="real" max="1.0" min="0.0" nom="alloperirac">0.23</param>
    </choix>
    <choix code="2" nom="no"/>
    </option>',
    addFinalizer = TRUE
  )
  # before sibling
  # <option choix="2" nom="N effect on root distribution" nomParam="codazorac">
  prev_sibling <- get_nodes(old_doc, '//option[@nomParam="codazorac"]')[[1]]
  XML::addSibling(prev_sibling, new_node, after = FALSE)


  # Changing varietal section structure ----------------------------------------
  #
  # Remove nodes from old doc for varietal content (under variete nodes)
  nodes_to_rm <- get_nodes(old_doc, path = "//variete/*")
  lapply(nodes_to_rm, function(x) XML::removeNodes(x))

  # Add under each variete node new nodes
  var_nodes <- XML::xmlParseString(
    '<formalismev nom="phenological stages">
			<param format="real" max="6000.0" min="0.0" nom="stlevamf">275</param>
			<param format="real" max="6000.0" min="0.0" nom="stamflax">375</param>
			<param format="real" max="6000.0" min="0.0" nom="stlevdrp">837</param>
			<param format="real" max="500.0" min="0.0" nom="stflodrp">0</param>
			<param format="real" max="900.0" min="0.0" nom="stdrpdes">700</param>
			<param format="integer" max="70" min="0" nom="jvc">55</param>
			<optionv nom="codebfroid">
				<param code="3" format="real" max="20000.0" min="0.0"
				nom="stdordebour">0</param>
			</optionv>
			<optionv nom="codephot">
				<param code="1" format="real" max="1.0" min="0.0"
				nom="sensiphot">0</param>
				<param code="1" format="real" max="24.0" min="0.0"
				nom="phobase">6.3</param>
				<param code="1" format="real" max="24.0" min="0.0"
				nom="phosat">20</param>
			</optionv>
</formalismev>
<formalismev nom="leaves">
			<param format="real" max="0.0" min="-2.0" nom="adens">-0.6</param>
			<param format="real" max="200.0" min="1.0" nom="bdens">7.00000</param>
			<param format="real" max="2.0" min="0.0" nom="hautbase">0.00000</param>
			<param format="real" max="5.0" min="0.1" nom="hautmax">1.2</param>
			<param format="real" max="2.0" min="0.2" nom="khaut">0.70</param>
			<param format="real" max="500.0" min="10.0" nom="durvieF">200</param>
			<optionv nom="codlainet">
				<param code="1" format="real" max="6000.0" min="0.0"
				nom="stlaxsen">675.</param>
				<param code="1" format="real" max="6000.0" min="0.0"
				nom="stsenlan">110.</param>
				<param code="1" format="real" max="0.5" min="5.0E-6"
				nom="dlaimax">0.00047</param>
				<param code="2" format="real" max="0.5" min="5.0E-6"
				nom="dlaimaxbrut">0.00047</param>
				<param code="2" format="real" max="1.0" min="-2.0"
				nom="innsen">0.17</param>
				<param code="2" format="real" max="1.5" min="0.5"
				nom="rapsenturg">0.50</param>
			</optionv>
</formalismev>
<formalismev nom="radiation interception">
			<optionv nom="codetransrad">
				<param code="1" format="real" max="1.5" min="0.1"
				nom="extin">0.50</param>
				<param code="2" format="real" max="2.0" min="0.1"
				nom="ktrou">1.00</param>
			</optionv>
</formalismev>
<formalismev nom="shoot biomass growth">
			<param format="real" max="15.0" min="-10.0" nom="temin">0.0</param>
			<param format="real" max="30.0" min="10.0" nom="teopt">12.0</param>
</formalismev>
<formalismev nom="biomass partitioning">
			<param format="real" max="500.0" min="50.0" nom="slamax">350</param>
			<param format="real" max="3.0" min="0.0" nom="tigefeuil">0.50</param>
</formalismev>
<formalismev nom="yield formation">
			<param format="real" max="5.0" min="0.0"
			nom="pgrainmaxi">0.03970</param>
			<param format="real" max="0.01" min="0.0010"
			nom="vitpropsucre">0.00000</param>
			<param format="real" max="0.01" min="0.0010"
			nom="vitprophuile">0.00000</param>
			<param format="real" max="0.04" min="0.0010"
			nom="vitirazo">0.01450</param>
		    <param format="real" max="0.02" min="-0.02"
		    nom="deshydbase">0.008000</param>
			<optionv nom="codeindetermin">
				<param code="1" format="integer" max="40" min="5"
				nom="nbjgrain">30</param>
				<param code="1" format="real" max="10000.0" min="0.0"
				nom="nbgrmin">6000</param>
				<param code="1" format="real" max="1000000.0" min="0.0"
				nom="nbgrmax">30000</param>
				<param code="1" format="real" max="2000.0" min="0.0"
				nom="stdrpmat">700</param>
				<optionv code="1" nom="codeir">
					<param code="1" format="real" max="0.02" min="0.001"
					nom="vitircarb">0.0107</param>
					<param code="2" format="real" max="0.002" min="5.0E-5"
					nom="vitircarbT">0</param>
				</optionv>
				<param code="2" format="real" max="20.0" min="0.5"
				nom="afruitpot">.00000</param>
				<param code="2" format="real" max="2000.0" min="10.0"
				nom="dureefruit">.00000</param>
				<param code="2" format="real" max="6000.0" min="0.0"
				nom="stdrpnou">-999</param>
				<optionv code="2" nom="codcalinflo">
					<param code="1" format="real" max="100.0" min="0.0"
					nom="nbinflo">-999</param>
				    <param code="2" format="real" max="100.0" min="0.0"
				    nom="inflomax">-999</param>
					<param code="2" format="real" max="10.0" min="0.0"
					nom="pentinflores">-999</param>
				</optionv>
			</optionv>
</formalismev>
<formalismev nom="roots">
			<param format="real" max="0.5" min="0.0" nom="croirac">0.12</param>
</formalismev>
<formalismev nom="frost">
			<optionv nom="codgellev">
				<param code="2" format="real" max="0.0" min="-25.0"
				nom="tgellev10">-4.0</param>
			</optionv>
			<optionv nom="codgeljuv">
				<param code="2" format="real" max="0.0" min="-25.0"
				nom="tgeljuv10">-10.0</param>
			</optionv>
			<optionv nom="codgelveg">
				<param code="2" format="real" max="0.0" min="-25.0"
				nom="tgelveg10">-4.5</param>
			</optionv>
</formalismev>
<formalismev nom="water stress">
			<param format="real" max="25.0" min="1.0" nom="psisto">15</param>
			<param format="real" max="15.0" min="1.0" nom="psiturg">4</param>
			<param format="real" max="0.3" min="0.05" nom="swfacmin">0.1</param>
</formalismev>',
    addFinalizer = TRUE
  )


  # adding var nodes under each "variete" node
  var_parent_nodes <- get_nodes(old_doc, path = "//variete")
  lapply(var_parent_nodes,
         function(x) {
           XML::addChildren(x,
                            kids = XML::xmlChildren(XML::xmlClone(var_nodes)))
         }
  )

  #
  # Set values of all kept parameter values (removed nodes or moved)
  # to new nodes
  # param_values_to_varietal
  set_param_value(old_doc, param_names_to_varietal, param_values_to_varietal)
  set_param_value(old_doc, param_names_keep, param_values_keep)


  # Special case: jvc not any more under an option choice
  # Checking values for jvc, if == -999, and replacing with
  # a value set in new files provided with JavaSTICS
  # Values stores in a jvc.RData in the package.
  #
  #
  # If the file name is the same as a provided plt file.
  # Get values
  # - get variete from current file
  # - intersect names with those in loaded RData file
  # - set values for parameters == -999 for common varieties
  # to those loaded

  load(
    file.path(
      get_examples_path(file_type = "xml_param",
                        stics_version = target_version
      ),
      "jvc_data.RData")
  )

  # get varieties
  current_var <- get_param_value(old_doc, "variete")

  if (basename(file) %in% names(jvc_data)) {

    common_var <-
      jvc_data[[basename(file)]][["variete"]] %in% current_var$variete

    if (any(common_var)) {
      values <- get_param_value(old_doc, param_name = "jvc",
                                parent_name = "variete",
                                parent_sel_attr = current_var[common_var])$jvc

      values_999_ids <- which(values == -999)
      if (length(values_999_ids) > 0) {
        jvc_values <- jvc_data[[basename(file)]]$jvc[common_var][values_999_ids]
        set_param_value(old_doc,
                        param_name = "jvc",
                        param_value = jvc_values,
                        ids = values_999_ids)
      }
    }
  }

  # In case of the file name not found in the list for the V10 version
  # Check if still any -999 values
  values <- get_param_value(old_doc, "jvc")$jvc
  values_999_ids <- which(values == -999)
  if (length(values_999_ids) > 0)
    message(old_doc@name,
            paste0(": be aware that jvc is from now a mandatory parameter",
                   "and its value must be fixed !\n"),
            "for all varieties: \n", current_var[values_999_ids], "\n")



  # Adding new nodes
  #
  # codemortalracine
  # after <option choix="1" nom="driving temperature" nomParam="codetemprac">
  new_node <- XML::xmlParseString(
    '<option choix="2" nom="calculation of the root death at cutting date
    for grasslands" nomParam="codemortalracine">
	<choix code="1" nom="function of dry matter production between
	two successives cut">
		<param format="real" max="1.0" min="0.0" nom="coefracoupe">0.5</param>
	</choix>
    <choix code="2" nom="no specific root death at cutting"/>
</option>',
    addFinalizer = TRUE
  )

  prev_sibling <- get_nodes(old_doc, "//*[@nomParam='codetemprac']")[[1]]
  XML::addSibling(prev_sibling, XML::xmlClone(new_node))


  # code_WangEngel
  # in <choix code="1" nom="daily temperatures">
  new_node <- XML::xmlParseString(
    '<option choix="2" nom=" Wang et Engel (1998)" nomParam="code_WangEngel">
	<choix code="1" nom="Wang et Engel">
		<param format="real" max="30" min="0" nom="tdoptdeb">11.7</param>
	</choix>
	<choix code="2" nom="no"/>
</option>',
    addFinalizer = TRUE
  )

  parent_node <- get_nodes(old_doc,
                           "//*[@nomParam='codegdhdeb']/choix[@code='1']")[[1]]
  XML::addChildren(parent_node, new_node)


  # Adding 2 option nodes
  # in <formalisme nom="partitioning of biomass in organs">
  #
  new_nodes <- XML::xmlParseString(
    '<option choix="2" nom="Simulation of Nitrogen and Carbon reserves"
    nomParam="code_acti_reserve">
      <choix code="1" nom="yes">
      <param format="real" max="1.0" min="0.0" nom="propresP">0.47</param>
      <param format="real" max="1.0" min="0.0" nom="PropresPN">0.6</param>
      <param format="real" max="1.0" min="0.0" nom="Efremobil">0.05</param>
      <param format="real" max="1.0" min="0.0" nom="Propres">0.10</param>
      <param format="real" max="1.0" min="0.0" nom="tauxmortresP">0.0025</param>
      <param format="real" max="50.0" min="0.0" nom="Parazoper">25</param>
      <param format="real" max="100.0" min="0.0" nom="ParazoTmorte">30</param>
      <param format="real" max="0.1" min="0" nom="inilai">0.001</param>
      </choix>
      <choix code="2" nom="no">
      <param format="real" max="100.0" min="0.0" nom="resplmax">0.66</param>
      </choix>
      </option>
    <option choix="2" nom="Calculation of the stem elongation stage for
    perenial grasslands" nomParam="codemontaison">
		<choix code="1" nom="yes"/>
		<choix code="2" nom="no"/>
</option>
<option choix="2" nom="Simulation of tiller dynamics for grasslands"
nomParam="codedyntalle">
	<choix code="1" nom="yes">
		<option choix="1" nom="Choice of the ratio used to calculate
		tiller mortality" nomParam="codetranspitalle">
			<choix code="1" nom="et/etm"/>
			<choix code="2" nom="ep/eop"/>
		</option>
			<param format="real" max="0.00001" min="0.0000025"
			nom="SurfApex">0.000005</param>
			<param format="real" max="0.04" min="0.01"
			nom="SeuilMorTalle">0.02</param>
			<param format="real" max="0.2" min="0.1"
			nom="SigmaDisTalle">0.1</param>
			<param format="real" max="0.01" min="0.00001"
			nom="VitReconsPeupl">0.001</param>
			<param format="real" max="1200" min="400"
			nom="SeuilReconsPeupl">800</param>
			<param format="real" max="5000" min="3000"
			nom="MaxTalle">4000.0</param>
			<param format="real" max="2.0" min="0.5"
			nom="SeuilLAIapex">1.0</param>
			<param format="real" max="10.0" min="1.0"
			nom="tigefeuilcoupe">5.0</param>
	</choix>
	<choix code="2" nom="no"/>
</option>',
    addFinalizer = TRUE
  )

  parent_node <- get_nodes(
    old_doc,
    "//formalisme[@nom='partitioning of biomass in organs']"
  )[[1]]
  XML::addChildren(parent_node, kids = unlist(XML::xmlChildren(new_nodes)))


  # <formalisme nom="roots">
  # rayon
  #
  new_node <- XML::xmlParseString(
    '<param format="real" max="0.07" min="0.005" nom="rayon">0.02</param>'
  )
  prev_sibling <- get_nodes(old_doc, "//*[@nom='contrdamax']")[[1]]
  XML::addSibling(prev_sibling, new_node)

  # adding 2 option nodes
  new_nodes <- XML::xmlParseString(
    '<option choix="2" nom="Preferential allocation of biomass to roots
    in case of water or N stress" nomParam="code_stress_root">
    <choix code="1" nom="yes"/>
    <choix code="2" nom="no"/>
    </option>
    <option choix="2" nom="rootdeposition activation"
    nomParam="code_rootdeposition">
    <choix code="1" nom="yes">
    <param format="real" max="60.0" min="10.0" nom="parazorac">-999</param>
    <option choix="2" nom="simulation of 2 roots classes"
    nomParam="code_diff_root">
    <choix code="1" nom="yes">
    <param format="real" max="4.0" min="0.0" nom="lvmax">-999</param>
    <param format="real" max="10.0" min="1.0" nom="rapdia">-999</param>
    <param format="real" max="0.80" min="0.05" nom="RTD">-999</param>
    <param format="real" max="1.0" min="0.0" nom="propracfmax">-999</param>
    </choix>
    <choix code="2" nom="no"/>
    </option>
    </choix>
    <choix code="2" nom="no"/>
    </option>',
    addFinalizer = TRUE
  )

  parent_node <- get_nodes(old_doc, "//choix[@nom='true density']")[[1]]

  XML::addChildren(parent_node, kids = unlist(XML::xmlChildren(new_nodes)))


  # -----------------------------------------------------------
  # Update param values
  #
  # from param_gen.xml
  # khaut, rayon
  param_gen_values <- get_param_xml(
    file = param_gen_file,
    param = c("rayon", "khaut")
  )[[1]]
  set_param_value(old_doc,
                  param_name = c("rayon", "khaut"),
                  param_value = param_gen_values)


  # from param_newform.xml
  # coefracoupe(1), coefracoupe(2) -> coefracoupe
  param_newform_values <- get_param_xml(
    file = param_newform_file,
    param = c("coefracoupe(1)", "coefracoupe(2)")
  )[[1]]

  if (length(unique(unlist(param_newform_values))) > 1)
    stop(
      "Multiple values of coefracoupe in param_gen.xml file")

  set_param_value(old_doc, param_name = "coefracoupe",
                  param_value = param_newform_values[[1]])


  # Updating other values than nodes values (i.e. nodes attributes values)
  #
  # Changing param min / max wrong attributes values
  # hautbase => 0.1
  # <param format="real" max="2.0" min="0.0" nom="hautbase">0</param>
  nodes_to_change <- get_nodes(old_doc, path = "//param[@nom='hautbase']")
  if (!is.null(nodes_to_change)) {
    set_attrs_values(old_doc, path = "//param[@nom='hautbase']",
                     attr_name = "min", values_list = "0.1")
  }
  #
  # Changing options' "choix",  "nom" attribute values
  #
  # oui to yes, non to no
  nodes_to_change <- get_nodes(old_doc, path = "//choix[@nom='oui']")
  if (!is.null(nodes_to_change)) {
    set_attrs_values(old_doc, path = "//choix[@nom='oui']", attr_name = "nom",
                     values_list = "yes")
  }
  nodes_to_change <- get_nodes(old_doc, path = "//choix[@nom='non']")
  if (!is.null(nodes_to_change)) {
    set_attrs_values(old_doc, path = "//choix[@nom='non']", attr_name = "nom",
                     values_list = "no")
  }




  # Writing to file _plt.xml
  out_plt <- file.path(out_dir, basename(file))
  write_xml_file(old_doc, out_plt, overwrite)



  XML::free(old_doc@content)
  invisible(gc(verbose = FALSE))
}




calc_irazomax <- function(irmax, vitircarb, vitirazo) {

  irazomax <- (irmax / vitircarb) * vitirazo

  irazomax <- pmin(1., irazomax)

  if (is.nan(irazomax) || irazomax > 1) irazomax <- 1

  return(round(irazomax, digits = 3))
}