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Expand isotope shortcodes to canonical Name-Mass format (vectorized)

Source: R/cleaning_pipeline.R
expand_isotope_shortcodes.Rd

Two-pass approach applied column-at-a-time:

  1. Naked shortcode expansion: u234 -> Uranium-234 (using cached isotope lookup)

  2. Spelled-out normalization: radium 226 -> Radium-226 Plus special case: unat -> WARNING flag (unresolvable natural uranium mixture)

Usage

expand_isotope_shortcodes(df, name_cols, isotope_lookup = NULL)

Arguments

df

Dataframe with name columns

name_cols

Character vector of Name-tagged column names

isotope_lookup

Optional pre-built lookup from load_isotope_lookup(). If NULL, falls back to building from ComptoxR::pt$isotope directly.

Value

List with cleaned_data (tibble) and audit_trail (tibble)

Details

Exclusions per ISOT-03:

  • Carbon backbone patterns (C12H22O11) - NOT expanded

  • Deuterium d-prefix patterns (d-glucose) - NOT expanded

  • Isotope prefixes in compound names (14C-glucose) - NOT expanded

Examples

df <- tibble::tibble(chemical_name = c("u234", "radium 226", "C12H22O11"))
expand_isotope_shortcodes(df, c("chemical_name"))
#> $cleaned_data
#> # A tibble: 3 × 3
#>   chemical_name cleaning_flag isotope_dtxsid
#>   <chr>         <chr>         <chr>         
#> 1 Uranium-234   isotope_match DTXSID40891752
#> 2 Radium-226    isotope_match DTXSID3051202 
#> 3 C12H22O11     NA            NA            
#> 
#> $audit_trail
#> # A tibble: 2 × 6
#>   row_id field         step                      original_value new_value reason
#>    <int> <chr>         <chr>                     <chr>          <chr>     <chr> 
#> 1      1 chemical_name expand_isotope_shortcodes u234           Uranium-… Isoto…
#> 2      2 chemical_name expand_isotope_shortcodes radium 226     Radium-2… Isoto…
#>