Return a list of options for an ABfit analysis with regularision.

Usage

abfit_reg_opts(
  init_damping = 5,
  maxiters = 128,
  max_shift_pre = 0.078,
  max_shift_fine = 0.05,
  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,
  adaptive_bl_comps_pppm = TRUE,
  export_sp_fit = FALSE,
  max_asym = Inf,
  max_basis_shift = Inf,
  max_basis_damping = Inf,
  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 = NULL,
  max_basis_damping_broad = NULL,
  ahat_calc_method = "lh_pnnls",
  prefit_phase_search = TRUE,
  freq_reg = 0.004,
  freq_reg_naa = NULL,
  lb_reg = "lcm_compat",
  asym_reg = 0.1,
  output_all_paras = FALSE,
  output_all_paras_raw = FALSE,
  input_paras_raw = NULL,
  optim_lw_only = FALSE,
  optim_lw_only_limit = 20,
  lb_init = "lcm_compat",
  lb_init_approx_fit = FALSE,
  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_pre: The maximum allowable global shift to be applied in the approximate (pre-fit) phases of analysis (ppm).
max_shift_fine: The maximum allowable global shift to be applied in the detailed fit phase of analysis (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).
adaptive_bl_comps_pppm: adjust the spline basis density in the detailed fit phase, based on the required level of smoothness, to reduce computation time.
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. Larger values result in less flexible baselines.
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. The default value is set to max_basis_shift.
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. The default value is set to max_basis_damping.
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.
freq_reg_naa: frequency shift parameter for NAA and NAAG.
lb_reg: individual line broadening parameter.
asym_reg: lineshape asymmetry 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 (in Hz) for the individual basis signals. Setting to 0 will clash with the minimum allowable value (eg hard constraint) during the detailed fit.
lb_init_approx_fit: apply lb_init to the basis during the approximate iterative 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_reg_opts(ppm_left = 4.2, noise_region = c(-1, -3))