UME 1.6.1b

Archiving in Zenodo (CITATION.cff fixed)

UME 1.6.1a

Archiving in Zenodo

UME 1.6.1

Submitted to CRAN.

New features

• calc_isotope_pattern() returns exact mass, nominal mass, probability,
  relative abundance, molecular formula (mf), and isotope-specific molecular
  formula (mf_iso) for each isotope peak.
• inchi_to_mf(): Extracts molecular formula string from an InChI code.
• check_neutral_mf(): Is a given string for a neutral molecular formula correct?
  • Added optional pre-validation of molecular formulas via check_neutral_mf() in convert_molecular_formula_to_data_table().
    Invalid, charged, or non-formula inputs now produce informative error messages.
  • Introduced robust parsing of molecular formulas based on masses,
    supporting a wide range of elements and isotope labels without hard-coded symbol lists.
• calc_nm() and related workflows now correctly preserve input order and
  duplicate formulas when character vectors are supplied.

Stability and bug fixes

• convert_molecular_formula_to_data_table()
  • Added new argument isotope_default. Unspecific element notation such as Mo can now be resolved either to the
    most abundant isotope ("most_abundant", default) or to the lightest isotope ("lightest").
  • Fixed parsing errors for formulas containing multi-letter element symbols (such as `Mg) that were previously misinterpreted.
  • Fixed incorrect splitting of multi-letter element symbols without counts (e.g. "Mo" was parsed as "M" + "o")
  • Resolved internal inconsistencies related to isotope handling and duplicate detection.
  • Fixed inconsistency where masses were calculated using the correct isotope but column names still reflected the lightest isotope
  • Original input order and duplicate molecular formulas are now preserved.
  • Improved handling of repeated element or isotope tokens such as C2H5OH or Cl3[37Cl2][37Cl4].
• create_isotope_expanded_table() now also accepts character vectors of
  molecular formulas as input.
• convert_data_table_to_molecular_formulas() was rewritten to preserve
  original row order and duplicate entries using internal row identifiers.
• check_neutral_mf()
  • Fixed length mismatch in data.table assignment when handling non-empty entries
  • Improved robustness for inputs containing NA values

Improvements

• uplot_ms()
  • Replaced .SD[order()]-based data reduction with a faster data.table::frank()-based ranking approach
  • Significantly improved performance for large peak lists (10⁵–10⁶+ peaks), especially when using data_reduction < 1
  • Reduced memory overhead by avoiding repeated sorting and subsetting operations