abfit_opts {spant}

Return a list of options for an ABfit analysis.

Description

Return a list of options for an ABfit analysis.

Usage

abfit_opts(
  init_damping = 5,
  maxiters = 1024,
  max_shift = 0.078,
  max_damping = 15,
  max_phase = 360,
  lambda = NULL,
  ppm_left = 4,
  ppm_right = 0.2,
  zp = TRUE,
  bl_ed_pppm = 2,
  auto_bl_flex = TRUE,
  bl_comps_pppm = 15,
  export_sp_fit = FALSE,
  max_asym = 0.25,
  max_basis_shift = 0.0078,
  max_basis_damping = 2,
  maxiters_pre = 1000,
  algo_pre = "NLOPT_LN_NELDERMEAD",
  min_bl_ed_pppm = NULL,
  max_bl_ed_pppm = 7,
  auto_bl_flex_n = 20,
  pre_fit_bl_ed_pppm = 1,
  remove_lip_mm_prefit = FALSE,
  pre_align = TRUE,
  max_pre_align_shift = 0.1,
  pre_align_ref_freqs = c(2.01, 3.03, 3.22),
  noise_region = c(-0.5, -2.5),
  optimal_smooth_criterion = "maic",
  aic_smoothing_factor = 5,
  anal_jac = TRUE,
  pre_fit_ppm_left = 4,
  pre_fit_ppm_right = 1.8,
  phi1_optim = FALSE,
  phi1_init = 0,
  max_dphi1 = 0.2,
  max_basis_shift_broad = 0.0078,
  max_basis_damping_broad = 2,
  ahat_calc_method = "lh_pnnls",
  prefit_phase_search = TRUE,
  freq_reg = NULL,
  lb_reg = NULL,
  output_all_paras = FALSE,
  output_all_paras_raw = FALSE,
  input_paras_raw = NULL,
  optim_lw_only = FALSE,
  optim_lw_only_limit = 20,
  lb_init = 0.001,
  zf_offset = NULL
)

Arguments

init_damping

initial value of the Gaussian global damping parameter (Hz). Very poorly shimmed or high field data may benefit from a larger value.

maxiters

The maximum number of iterations to run for the detailed fit.

max_shift

The maximum allowable shift to be applied in the optimisation phase of fitting (ppm).

max_damping

maximum permitted value of the global damping parameter (Hz).

max_phase

the maximum absolute permitted value of the global zero-order phase term (degrees). Note, the prefit_phase_search option is not constrained by this term.

lambda

manually set the the baseline smoothness parameter.

ppm_left

downfield frequency limit for the fitting range (ppm).

ppm_right

upfield frequency limit for the fitting range (ppm).

zp

zero pad the data to twice the original length before fitting.

bl_ed_pppm

manually set the the baseline smoothness parameter (ED per ppm).

auto_bl_flex

automatically determine the level of baseline smoothness.

bl_comps_pppm

spline basis density (signals per ppm).

export_sp_fit

add the fitted spline functions to the fit result.

max_asym

maximum allowable value of the asymmetry parameter.

max_basis_shift

maximum allowable frequency shift for individual basis signals (ppm).

max_basis_damping

maximum allowable Lorentzian damping factor for individual basis signals (Hz).

maxiters_pre

maximum iterations for the coarse (pre-)fit.

algo_pre

optimisation method for the coarse (pre-)fit.

min_bl_ed_pppm

minimum value for the candidate baseline flexibility analyses (ED per ppm).

max_bl_ed_pppm

minimum value for the candidate baseline flexibility analyses (ED per ppm).

auto_bl_flex_n

number of candidate baseline analyses to perform.

pre_fit_bl_ed_pppm

level of baseline flexibility to use in the coarse fitting stage of the algorithm (ED per ppm).

remove_lip_mm_prefit

remove broad signals in the coarse fitting stage of the algorithm.

pre_align

perform a pre-alignment step before coarse fitting.

max_pre_align_shift

maximum allowable shift in the pre-alignment step (ppm).

pre_align_ref_freqs

a vector of prominent spectral frequencies used in the pre-alignment step (ppm).

noise_region

spectral region to estimate the noise level (ppm).

optimal_smooth_criterion

method to determine the optimal smoothness.

aic_smoothing_factor

modification factor for the AIC calculation.

anal_jac

use a analytical approximation to the jacobian in the detailed fitting stage.

pre_fit_ppm_left

downfield frequency limit for the fitting range in the coarse fitting stage of the algorithm (ppm).

pre_fit_ppm_right

upfield frequency limit for the fitting range in the coarse fitting stage of the algorithm (ppm).

phi1_optim

apply and optimise a frequency dependant phase term.

phi1_init

initial value for the frequency dependant phase term (ms).

max_dphi1

maximum allowable change from the initial frequency dependant phase term (ms).

max_basis_shift_broad

maximum allowable shift for broad signals in the basis (ppm). Determined based on their name beginning with Lip or MM.

max_basis_damping_broad

maximum allowable Lorentzian damping for broad signals in the basis (Hz). Determined based on their name beginning with Lip or MM.

ahat_calc_method

method to calculate the metabolite amplitudes. May be one of: "lh_pnnls" or "ls".

prefit_phase_search

perform a 1D search for the optimal phase in the prefit stage of the algorithm.

freq_reg

frequency shift parameter.

lb_reg

individual line broadening parameter.

output_all_paras

include more fitting parameters in the fit table, e.g. individual shift and damping factors for each basis set element.

output_all_paras_raw

include raw fitting parameters in the fit table. For advanced diagnostic use only.

input_paras_raw

input raw fitting parameters. For advanced diagnostic use only.

optim_lw_only

optimize the global line-broadening term only.

optim_lw_only_limit

limits for the line-breading term as a percentage of the starting value when optim_lw_only is TRUE.

lb_init

initial Lorentzian line broadening value for the individual basis signals. Setting to 0 will clash with the minimum allowable value (eg hard constraint) during the detailed fit.

zf_offset

offset in number of data points from the end of the FID to zero-fill. Default is NULL and will automatically set this to 50 points when the FID distortion flag is set for the mrs_data.

Value

full list of options.

Examples

opts <- abfit_opts(ppm_left = 4.2, noise_region = c(-1, -3))