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ModelFitter Parameters

Parameters of ModelFitter:

NameTypeDefaultRestrictionsDescription
fit_algorithmstringsimplesimple, simplest, waveletFitting algorithm type (internal parameter).
max_iterationint500min: 1Maximum number of iterations for fitting with Levenberg-Marquardt algorithm.
deltaAbsErrorfloat0.0001min: 0Absolute error used by the Levenberg-Marquardt algorithm.
deltaRelErrorfloat0.0001min: 0Relative error used by the Levenberg-Marquardt algorithm.
tolerance_stdev_bounding_boxfloat3min: 0Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data
intensity_cutoff_factorfloat0.05min: 0 max: 1Cutoff peaks with a predicted intensity below intensity_cutoff_factor times the maximal intensity of the model
feature_intensity_sumint1min: 0 max: 1Determines what is reported as feature intensity.
1: the sum of peak intensities;
0: the maximum intensity of all peaks
min_num_peaks:finalint5min: 1Minimum number of peaks left after cutoff. If smaller, feature will be discarded.
min_num_peaks:extendedint10min: 1Minimum number of peaks after extension. If smaller, feature will be discarded.
rt:interpolation_stepfloat0.2min: 0Step size in seconds used to interpolate model for RT.
mz:interpolation_stepfloat0.03min: 0.001Interpolation step size for m/z.
mz:model_type:firstint0min: 0Numeric id of first m/z model fitted (usually indicating the charge state), 0 = no isotope pattern (fit a single gaussian).
mz:model_type:lastint4min: 0Numeric id of last m/z model fitted (usually indicating the charge state), 0 = no isotope pattern (fit a single gaussian).
quality:typestringCorrelationCorrelationType of the quality measure used to assess the fit of model vs data.
quality:minimumfloat0.65min: 0 max: 1Minimum quality of fit, features below this threshold are discarded.
isotope_model:stdev:firstfloat0.04min: 0First standard deviation to be considered for isotope model.
isotope_model:stdev:lastfloat0.12min: 0Last standard deviation to be considered for isotope model.
isotope_model:stdev:stepfloat0.04min: 0Step size for standard deviations considered for isotope model.
isotope_model:averagines:Cfloat0.0443min: 0Number of C atoms per Dalton of the mass.
isotope_model:averagines:Hfloat0.007min: 0Number of H atoms per Dalton of the mass.
isotope_model:averagines:Nfloat0.0012min: 0Number of N atoms per Dalton of the mass.
isotope_model:averagines:Ofloat0.013min: 0Number of O atoms per Dalton of the mass.
isotope_model:averagines:Sfloat0.00037min: 0Number of S atoms per Dalton of the mass.
isotope_model:isotope:trim_right_cutofffloat0.001min: 0Cutoff for averagine distribution, trailing isotopes below this relative intensity are not considered.
isotope_model:isotope:maximumint100min: 1Maximum number of isotopes being used for the IsotopeModel.
isotope_model:isotope:distancefloat1.000495min: 0Distance between consecutive isotopic peaks.

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