Package index • metabodecon

Deconvolution

Functions to deconvolute a spectrum into its individual peaks.

read_spectrum(): Read one or more spectra from Disk

read_spectra(): Read one or more spectra from Disk

plot_spectrum() experimental: Plot Spectrum

plot_spectra(): Plot Spectra

draw_spectrum(): Draw Spectrum

deconvolute() generate_lorentz_curves() generate_lorentz_curves_sim(): Deconvolute one or more NMR spectra

Alignment

Functions to align multiple spectra.

align(): Align Spectra

combine_peaks(): Combine Peaks

dohCluster(): Cluster Based Peak Alignment

gen_feat_mat(): Generate Feature Matrix.

get_ppm_range(): Get PPM Range covered by Spectra

speaq_align(): Align Signals using 'speaq'

Datasets

Functions to download and/or find example datasets.

datadir(): Return path to metabodecon's data directory

datadir_persistent(): Persistent Data Directory

datadir_temp(): Temporary Data Directory

download_example_datasets(): Download metabodecon Example Datasets

metabodecon_file(): Return Path to File or Directory in metabodecon Package

sim: The Sim Dataset

sap: The SAP Dataset

tmpdir(): Temporary Session Directory

Utility

Utility functions, e.g. for converting between units or for calculating y values for a given lorentz curve.

as_spectrum() as_ispec() as_idecon() as_decon0() as_decon1() as_decon2() as_spectra() as_ispecs() as_idecons() as_decons0() as_decons1() as_decons2(): Convert to a Metabodecon Class

is_spectrum() is_ispec() is_idecon() is_decon0() is_decon1() is_decon2() is_align() is_spectra() is_ispecs() is_idecons() is_decons0() is_decons1() is_decons2() is_aligns(): Is an Object from a Metabodecon Class?

print(<spectrum>) print(<ispec>) print(<idecon>) print(<decon1>) print(<decon2>) print(<align>) print(<spectra>) print(<ispecs>) print(<idecons>) print(<decons1>) print(<decons2>) print(<aligns>): S3 Methods for Printing Metabodecon Objects

convert_pos() convert_width(): Convert from unit A to unit B

evalwith(): Evaluate an expression with predefined global state

make_spectrum(): Create a Spectrum Object

metabodecon_classes: Metabodecon Classes

simulate_spectrum() experimental: Simulate a 1D NMR Spectrum

transp(): Make transparent

tree(): Print the Structure of a Directory Tree

width(): Calculate the Width of a Numeric Vector

Deprecated

Deprecated functions. These functions should no longer be used. They will be retained for a short period of time to give users time to migrate to their replacement function, but will be removed in future releases of the package.

get_data_dir() deprecated: Retrieve directory path of an example dataset

MetaboDecon1D() deprecated: Deconvolute 1D NMR spectrum

calculate_lorentz_curves(): Calculate lorentz curves for each analyzed spectrum

plot_lorentz_curves_save_as_png() deprecated: Plot lorentz curves for variable range

plot_spectrum_superposition_save_as_png() deprecated: Plot spectrum approx for variable range

plot_triplets() deprecated: Plot peak triplets for variable range