Package index • fitnmr

Package overview

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

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

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 of 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

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_sparse_2d(): Plot spectrum from 2D 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 map

height_assign(): Calculate mapping from assigned peak list onto an unknown peak list
read_nmrdraw_peak_tab(): Read an NMRDraw formatted peak table

extract_params(): Extract parameters from fit object for use with make_fit_input
get_spec_peak_int(): Get spectra for individual peaks

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
collapse_na_array(): Collapse blocks of NAs in an array with numeric dimension names