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

NMRPipe simulation and processing

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