R: Multidimensional Nuclear Magnetic Resonance Peak Fitting and Analysis

# Multidimensional Nuclear Magnetic Resonance Peak Fitting and Analysis

## Documentation for package ‘fitnmr’ version 1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Code demos. Use demo() to run them.

## Help Pages

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