river-data-core 0.2.2

Common types & traits for the in the river-data platform
Documentation 
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# Source: cnet-data-portal (MIT, mclement18)
# File: app/utils/calculation_functions.R
# Lines: 469-511
#
# Verbatim copy — do not modify. See generate_fixtures.R for the
# standalone version used to produce golden test values.

calcBenthicAFDM <- function(df, ...) {
  # Check for the presence of the correct columns
  allColumns <- sum(
    grepl(
      paste(
        c('lab_chla_sizeA_rep',
          'lab_chla_sizeB_rep',
          'lab_chla_sizeC_rep',
          'lab_chla_tot_vol_rep',
          'lab_chla_vol_filtrated_rep',
          'afdm_g_filter_rep'),
        collapse = '|'
      ),
      colnames(df)
    )
  ) == 6
  
  if (nrow(df) == 1 & allColumns) {
    # Get values
    lab_chla_sizeA_rep <- df %>% select(starts_with('lab_chla_sizeA_rep')) %>% pull()
    lab_chla_sizeB_rep <- df %>% select(starts_with('lab_chla_sizeB_rep')) %>% pull()
    lab_chla_sizeC_rep <- df %>% select(starts_with('lab_chla_sizeC_rep')) %>% pull()
    lab_chla_tot_vol_rep <- df %>% select(starts_with('lab_chla_tot_vol_rep')) %>% pull()
    lab_chla_vol_filtrated_rep <- df %>% select(starts_with('lab_chla_vol_filtrated_rep')) %>% pull()
    afdm_g_filter_rep <- df %>% select(starts_with('afdm_g_filter_rep')) %>% pull()
    
    # If no NAs, calculate AFDM per m2
    if (!any(is.na(c(lab_chla_sizeA_rep, lab_chla_sizeB_rep, lab_chla_sizeC_rep, lab_chla_tot_vol_rep, lab_chla_vol_filtrated_rep, afdm_g_filter_rep)))) {
      return(
        convertToUnitPerM2(
          afdm_g_filter_rep,
          c(lab_chla_sizeA_rep, lab_chla_sizeB_rep, lab_chla_sizeC_rep),
          lab_chla_vol_filtrated_rep,
          lab_chla_tot_vol_rep
        )
      )
    }
  }
  
  
  # If nothing is returned, return 'KEEP OLD'
  'KEEP OLD'
}