R/get_cosoilmoist_from_SDA.R

In soilDB: Soil Database Interface

#' @export
#' @rdname fetchSDA
#' @param impute replace missing (i.e. `NULL`) values with `"Not_Populated"` for categorical data, or the "RV" for numeric data or `201` cm if the "RV" is also`NULL` (default: `TRUE`)
get_cosoilmoist_from_SDA <- function(WHERE = NULL, duplicates = FALSE, impute = TRUE,
                                     stringsAsFactors = NULL
                                     ) {

  if (!missing(stringsAsFactors) && is.logical(stringsAsFactors)) {
    .Deprecated(msg = sprintf("stringsAsFactors argument is deprecated.\nSetting package option with `NASISDomainsAsFactor(%s)`", stringsAsFactors))
    NASISDomainsAsFactor(stringsAsFactors)
  }

  q.cosoilmoist <- paste("SELECT",
                         if (duplicates == FALSE) {
                           "DISTINCT"
                         } else {
                           "mu.mukey, c.cokey, "
                         },
                  "nationalmusym, muname, c.compname, c.comppct_r, drainagecl, month, flodfreqcl, 
                   pondfreqcl, soimoistdept_l, soimoistdept_r, soimoistdept_h, soimoistdepb_l, 
                   soimoistdepb_r, soimoistdepb_h, soimoiststat

  FROM legend l INNER JOIN
       mapunit mu ON mu.lkey = l.lkey INNER JOIN",
       if (duplicates == FALSE) {
          "(SELECT MIN(nationalmusym) nationalmusym2, MIN(mukey) AS mukey2
          FROM mapunit
          GROUP BY nationalmusym) AS mu2 ON mu2.nationalmusym2 = mu.nationalmusym INNER JOIN
          (SELECT compname, comppct_r, drainagecl, cokey, mukey AS mukey2 FROM component) AS c ON c.mukey2 = mu2.mukey2"
          } else {"(SELECT compname, comppct_r, drainagecl, cokey, mukey AS mukey2 FROM component) AS c ON c.mukey2 = mu.mukey"}
       , "LEFT OUTER JOIN
       comonth cm ON cm.cokey = c.cokey LEFT OUTER JOIN
       cosoilmoist csm ON csm.comonthkey = cm.comonthkey

  WHERE ", WHERE,

  "ORDER BY mu.muname, comppct_r DESC, compname DESC, month, soimoistdept_r ASC
  ;")

  # exec query
  d.cosoilmoist <- SDA_query(q.cosoilmoist)

  # set factor levels according to metadata domains
  d.cosoilmoist <- uncode(d.cosoilmoist)

  # prep dataset: rename columns, impute empty values, stringsAsFactors
  d.cosoilmoist <- .cosoilmoist_prep(d.cosoilmoist, impute = impute)

  # done
  return(d.cosoilmoist)
  }