Function reference • fitnmr

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

Reference

Package overview

Spectrum reading, plotting, and analysis

Low-level fitting and plotting

Modifying parameter lists for fits

High-level fitting and plotting

High-level fitting using resonances, nuclei, and couplings tables

NMRPipe simulation and processing

Postprocessing and assignment

Deprecated

Internal