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Detect bare molecular formulas

Source: R/cleaning_pipeline.R
detect_bare_formulas.Rd

Uses an element-token regex to identify bare molecular formulas (H2O, NaCl, CuSO4). Bare formulas are blocked because they lack chemical context needed for curation. Detected formulas are moved to formula_blocked_{col} columns and name set to NA.

Usage

detect_bare_formulas(df, name_cols, isotope_lookup = NULL)

Arguments

df

Dataframe with name columns

name_cols

Character vector of Name-tagged column names

isotope_lookup

Optional isotope lookup from load_isotope_lookup(). Known isotope shortcodes are not blocked as bare formulas.

Value

List with cleaned_data and audit_trail

Examples

df <- tibble::tibble(chemical_name = c("H2O", "acetone", "NaCl"))
detect_bare_formulas(df, c("chemical_name"))
#> $cleaned_data
#> # A tibble: 3 × 3
#>   chemical_name cleaning_flag       formula_blocked_chemical_name
#>   <chr>         <chr>               <chr>                        
#> 1 NA            BLOCK: bare formula H2O                          
#> 2 acetone       NA                  NA                           
#> 3 NA            BLOCK: bare formula NaCl                         
#> 
#> $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 detect_bare_formula H2O            [NA]      Bare molecu…
#> 2      3 chemical_name detect_bare_formula NaCl           [NA]      Bare molecu…
#>