add_known_mf            Add metainformation derived from ume::known_mf
add_missing_element_columns
                        Add Missing Isotope Columns to mfd
as_mfd                  Coerce input to UME molecular formula data
as_peaklist             Check format of peaklist
as_ume_matrix           Convert molecular formula data to a feature
                        matrix
assign_formulas         Molecular Formula Assignment
calc_data_summary       Create a Data Summary Table for Element Ratios
                        and Parameters
calc_dbe                Calculate Double Bond Equivalent (DBE)
calc_eval_params        Calculate UME Evaluation Parameters
calc_exact_mass         Calculate Exact Monoisotopic Mass of a Molecule
calc_ideg               Calculate Degradation Index (Ideg)
calc_isotope_pattern    Calculate Isotope Pattern
calc_iterr              Calculate terrestrial indeces Iterr and Iterr2
                        (after Medeiros et al. 2016)
calc_logratio           calc_logratio
calc_ma                 Calculate mass accuracy
calc_ma_abs             Calculate absolute mass accuracy range (ma)
calc_neutral_mass       Calculate neutral molecular mass
calc_nm                 Calculate Nominal Mass of a Molecule
calc_norm_int           Calculate Normalized Peak Intensities
calc_number_assignment
                        Calculate Number of Molecular Formula
                        Assignments per Peak
calc_pielou_evenness    Calculate Pielou's Evenness
calc_shannon_index      Calculate the Shannon Diversity Index
calc_simpson_index      Calculate the Simpson Diversity Index
calc_time_flattened_mfd
                        Create a time-flattened molecular formula data
                        table
check_neutral_mf        Check neutral molecular formulas
classify_files          Classify FTMS files into categories based on
                        filename patterns
color.palette           Create a Custom Interpolated Color Palette
convert_data_table_to_molecular_formulas
                        Convert Data Table with Element Counts to
                        Molecular Formulas
convert_molecular_formula_to_data_table
                        Convert Molecular Formulas to a Data Table of
                        Element Counts
create_isotope_expanded_table
                        Create an Expanded Table of Parent and Isotope
                        Daughter Formulas
create_ume_formula_library
                        Create a molecular formula library for UME
download_library        Download and Load a UME Formula Library
eval_isotopes           Evaluate isotope information
filter_int              Filter by (relative) peak magnitude
filter_mass_accuracy    Automated filter for mass accuracy
filter_mf_data          Filter molecular formula data by mass
                        spectrometric metadata
filter_multi_assignments
                        Filter multiple molecular formula assignments
                        by mass-error medians
get_isotope_info        Retrieve NIST element and isotope data
inchi_to_mf             Extract molecular formula from InChI string
is_ume_peaklist         Check whether an object is a UME peaklist
known_mf                Collection of known formulas, for which
                        additional information is available.
lib_demo                Demo formula library (200 - 300 Da, neutral
                        mass)
masses                  Masses: Elements and isotopes
mf_data_demo            mf_data_demo
order_columns           Order columns
peaklist_demo           Demo peak list
remove_blanks           Remove molecular formulas detected in blanks
remove_empty_columns    Remove empty columns
remove_id_columns       Remove columns that contain ID's
remove_unknown_columns
                        Remove columns that only have one specific
                        value
subset_known_mf         Subsetting known molecular formula categories
theme_uplots            theme_uplots
ume_assign_formulas     Complete formula assignment (wrapper function)
ume_filter_formulas     Complete Formula subsetting / filtering
                        (wrapper)
ume_name_dictionary     UME name dictionary
uplot_cluster           uplot_cluster
uplot_cvm               Carbon vs Mass (CvM) Diagram
uplot_dbe_minus_o_freq
                        Frequency Plot of DBE - O atoms
uplot_dbe_vs_c          Plot DBE vs Carbon Atoms
uplot_dbe_vs_ma         Plot DBE vs ppm with Option for Interactive
                        Plot
uplot_dbe_vs_o          Plot DBE vs Oxygen Atoms (cf. Herzsprung et al.
                        2014) with Option for Interactive Plot
uplot_freq              Frequency Plot of a Selected Variable
uplot_freq_ma           Histogram of Mass Accuracy
uplot_freq_vs_ppm       Mass Accuracy Frequency Histogram
uplot_hc_vs_m           H/C vs Molecular Mass Plot
uplot_heteroatoms       Heteroatom Combination vs Mass Accuracy
uplot_isotope_precision
                        Precision of Isotope Abundance
uplot_kmd               Kendrick Mass Defect (KMD) vs. Nominal Mass
                        Plot
uplot_lcms              Plot LC-MS Spectrum (or fallback MS if no RT
                        available)
uplot_ma_vs_mz          Plot Mass Accuracy vs m/z
uplot_ms                Plot Mass Spectrum
uplot_n_mf_per_sample   Number of Molecular Formulas per Sample Plot
uplot_pca               Plot PCA Results
uplot_ppm_avg           Plot Median of Mass Accuracy per Sample (ppm)
uplot_ratios            Molecular Formula Ratio Plot (Sample vs
                        Control)
uplot_reproducibility   Check Reproducibility of Sample Analyses
uplot_ri_vs_sample      Median Relative Intensity per Sample
uplot_vk                uplot_vk
ustats_outlier          Outlier detection using multiple statistical
                        tests
zero_filling            zero_filling
