Multidimensional Nuclear Magnetic Resonance Peak Fitting and Analysis

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Documentation for package ‘fitnmr’ version 1.0

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fitnmr-package fitnmr Package Overview
abind_list Combine multi-dimensional arrays with lists
collapse_na Collapse strings of repeated NAs in a vector with numeric names
collapse_na_array Collapse blocks of NAs in an array with numeric dimension names
comb_vec_to_param_array Determine array of destination parameters from a source vector
contour_pipe Plot Spectra Contours
coupling_param_idx Get a list of logical arrays indicating which parameters correspond to scalar couplings
extract_params Extract parameters from fit object for use with make_fit_input
fitnmr fitnmr Package Overview
fit_footprint Determine the region of a spectrum containing the majority of the fit peaks
fit_peaks Fit peaks from a table of chemical shifts
fit_peak_cluster Fit a cluster of nearby peaks starting from a seed table of chemical shifts
fit_peak_iter Iterative Peak Fitting
get_spec_int Get arrays of spectral intensities for input, starting parameters, and fit peaks
get_spec_peak_int Get spectra for individual peaks
height_assign Calculate mapping from assigned peak list onto an unknown peak list
infer_acquisition_time Infer acquisition time for each dimension
infer_aliasing Infer which dimension was directly acquired
infer_direct Infer which dimension was directly acquired
infer_sweep_width Infer original sweep width for each dimension
limit_omega0_by_r2 Add upper/lower limits based on the r2 value
make_coupling_mat Make a multiplet matrix with weights and scalar coupling coefficients
make_fit_input Prepare input data structure for peak fitting
make_map Create a sparse axis map
make_param_list Make a parameter list for a set of spectra and chemical shifts
nmrpipe_ft Fourier transform a 1D FID
nmrpipe_fti Inverse Fourier transform a 1D spectrum
nmrpipe_ps Inverse Fourier transform a 1D spectrum
nmrpipe_sp Apply sine-based window function to a 1D FID
nmrpipe_zf Apply zero filling to a 1D FID
nmr_pipe Process an FID with NMRPipe
noise_estimate Estimate Noise
omega0_comb_source_idx Get the first index in the omega0 array corresponding to each TRUE value in omega0_idx
omega0_param_idx Get a list of logical arrays indicating which parameters correspond to peak positions
param_array_to_comb_vec Determine vector of source parameters from destination array via least squares
param_list_to_arg_list Convert a list of parameters for use with make_fit_input
param_list_to_peak_df Convert Fit to Data Frame
param_list_to_tables Convert a parameter list into a set of tables with resonance/nuclei/couplings
param_values Get/set a subset of fitting parameters specified by a list of logical vectors
param_values<- Get/set a subset of fitting parameters specified by a list of logical vectors
peak_bind Combine parameter lists referring to different peaks
peak_df_to_fit_input Convert a peak data frame to fit input
peak_df_to_param_list Convert a peak data frame to a parameter list
perform_fit Perform a fit with an input data structure
plot_fit_1d Plot a one dimensional peak fit
plot_fit_2d Plot a two dimensional peak fit
plot_peak_df Plot Peaks from a Peak Table
plot_resonances_1d Plot resonances from 1D fit
plot_resonances_2d Plot resonances from 2D fit
plot_resonances_3d Plot resonances from 3D fit
plot_sparse_1d Plot spectrum from 1D fit
plot_sparse_2d Plot spectrum from 2D fit
ppm_to_pts Convert PPM values to points
read_nmrdraw_peak_tab Read an NMRDraw formatted peak table
read_nmrpipe Read NMRPipe spectrum
resonance_to_param_list Convert data frame of resonances into a parameter list
sim_time_nd Simulate an FID using the NMRPipe SimTimeND function
spec_bind Combine parameter lists referring to different spectra
spec_overlap_mat Determine a matrix of fractional peak overlap
split_coupling_names Split string of scalar coupling names
tables_to_param_list Convert tables with resonance/nuclei/couplings to a parameter list
update_fit_bounds Update bounds on fitting parameters
whz_to_pts Convert widths in Hz into points
write_nmrdraw_peak_tab Write an NMRDraw formatted peak table