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spant (version 1.1.0)

abfit_opts: 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 = 10,
  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 = 1,
  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 = 1,
  max_basis_damping_broad = 2
)

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 (Hz).

max_damping

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

max_phase

maximum permitted value of the global zero-order phase term (degrees).

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 (Hz).

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 (Hz). 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.

Value

full list of options.

Examples

Run this code
# NOT RUN {
opts <- abfit_opts(ppm_left = 4.2, noise_region = c(-1, -3))
# }

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