abfit_opts: Return a list of options for an ABfit analysis.
In neuroconductor-releases/spant: MR Spectroscopy Analysis Tools

Description Usage Arguments Value Examples

Return a list of options for an ABfit analysis.

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,
  ahat_calc_method = "lh_pnnls"
)

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