Return a list of options for an ABfit analysis.
abfit_opts(
init_damping = 5,
maxiters = 1024,
max_shift_pre = 0.078,
max_shift_fine = NULL,
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 = FALSE,
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 = NULL,
max_basis_damping_broad = NULL,
ahat_calc_method = "lh_pnnls",
prefit_phase_search = TRUE,
freq_reg = NULL,
freq_reg_naa = NULL,
lb_reg = NULL,
asym_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,
lb_init_approx_fit = FALSE,
zf_offset = NULL
)initial value of the Gaussian global damping parameter (Hz). Very poorly shimmed or high field data may benefit from a larger value.
The maximum number of iterations to run for the detailed fit.
The maximum allowable global shift to be applied in the approximate (pre-fit) phases of analysis (ppm).
The maximum allowable global shift to be applied in the detailed fit phase of analysis (ppm).
maximum permitted value of the global damping parameter (Hz).
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.
manually set the the baseline smoothness parameter.
downfield frequency limit for the fitting range (ppm).
upfield frequency limit for the fitting range (ppm).
zero pad the data to twice the original length before fitting.
manually set the the baseline smoothness parameter (ED per ppm).
automatically determine the level of baseline smoothness.
spline basis density (signals per ppm).
adjust the spline basis density in the detailed fit phase, based on the required level of smoothness, to reduce computation time.
add the fitted spline functions to the fit result.
maximum allowable value of the asymmetry parameter.
maximum allowable frequency shift for individual basis signals (ppm).
maximum allowable Lorentzian damping factor for individual basis signals (Hz).
maximum iterations for the coarse (pre-)fit.
optimisation method for the coarse (pre-)fit.
minimum value for the candidate baseline flexibility analyses (ED per ppm).
minimum value for the candidate baseline flexibility analyses (ED per ppm).
number of candidate baseline analyses to perform.
level of baseline flexibility to use in the coarse fitting stage of the algorithm (ED per ppm).
remove broad signals in the coarse fitting stage of the algorithm.
perform a pre-alignment step before coarse fitting.
maximum allowable shift in the pre-alignment step (ppm).
a vector of prominent spectral frequencies used in the pre-alignment step (ppm).
spectral region to estimate the noise level (ppm).
method to determine the optimal smoothness.
modification factor for the AIC calculation. Larger values result in less flexible baselines.
use a analytical approximation to the jacobian in the detailed fitting stage.
downfield frequency limit for the fitting range in the coarse fitting stage of the algorithm (ppm).
upfield frequency limit for the fitting range in the coarse fitting stage of the algorithm (ppm).
apply and optimise a frequency dependant phase term.
initial value for the frequency dependant phase term (ms).
maximum allowable change from the initial frequency dependant phase term (ms).
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.
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.
method to calculate the metabolite amplitudes. May be one of: "lh_pnnls" or "ls".
perform a 1D search for the optimal phase in the prefit stage of the algorithm.
frequency shift parameter.
frequency shift parameter for NAA and NAAG.
individual line broadening parameter.
lineshape asymmetry parameter.
include more fitting parameters in the fit table, e.g. individual shift and damping factors for each basis set element.
include raw fitting parameters in the fit table. For advanced diagnostic use only.
input raw fitting parameters. For advanced diagnostic use only.
optimize the global line-broadening term only.
limits for the line-breading term as a percentage of the starting value when optim_lw_only is TRUE.
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.
apply lb_init to the basis during the approximate iterative fit.
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.
full list of options.
opts <- abfit_opts(ppm_left = 4.2, noise_region = c(-1, -3))