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remeta.model.ReMeta

ReMeta

Usage 
rem = remeta.ReMeta()

for a default model, or otherwise:

cfg = remeta.Configuration()
cfg.<some_setting> = <some_value>
rem = remeta.ReMeta(cfg)

Parameters:

Name Type Description Default
cfg Configuration

Configuration object. If None is passed, the default configuration (but see kwargs).

 None
**kwargs

kwargs entries are passed to the Configuration

 {}
Source code in remeta/model.py 
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def __init__(
    self,
    cfg: Configuration = None,
    **kwargs
):
    """

    Usage:
        ```
        rem = remeta.ReMeta()
        ```

        for a default model, or otherwise:

        ```
        cfg = remeta.Configuration()
        cfg.<some_setting> = <some_value>
        rem = remeta.ReMeta(cfg)
        ```

    Args:
        cfg: Configuration object. If None is passed, the default configuration (but see kwargs).
        **kwargs: kwargs entries are passed to the Configuration

    """

    if cfg is None:
        # Set configuration attributes that match keyword arguments
        cfg_kwargs = {k: v for k, v in kwargs.items() if k in Configuration.__dict__}
        self.cfg = Configuration(**cfg_kwargs)
    else:
        self.cfg = cfg
        for k, v in kwargs.items():
            if k in Configuration.__dict__:
                setattr(self.cfg, k, v)
    self.cfg.setup()

    self.modeldata = ModelData(cfg=self.cfg)
    self.data = None
    self.result = None

    self.type1_is_fitted = False
    self.type2_is_fitted = False

.fit()

Usage 
rem = ReMeta()
rem.fit(stimuli, choices, confidence)

Parameters:

Name Type Description Default
stimuli list[float] | list[list[float]] | NDArray[float]

1d or 2d array or list of signed stimulus intensities

 required
choices list[float] | list[list[float]] | NDArray[float]

1d or 2d array or list of choices (coded as -1/1 or 0/1)

 required
confidence list[float] | list[list[float]] | NDArray[float]

1d or 2d array or list of confidence ratings (normalized to the range 0-1)

 None
verbosity int

verbosity level (possible values: 0, 1, 2)

 1
silence_warnings bool

if True, warnings during model fitting are supressed.

 False
Source code in remeta/model.py 
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def fit(
    self,
    stimuli: list[float] | list[list[float]]  | np.typing.NDArray[float],
    choices: list[float] | list[list[float]]  | np.typing.NDArray[float],
    confidence: list[float] | list[list[float]]  | np.typing.NDArray[float] = None,
    verbosity: int = 1,
    silence_warnings: bool = False
):
    """

    Usage:
        ```
        rem = ReMeta()
        rem.fit(stimuli, choices, confidence)
        ```

    Args:
        stimuli: 1d or 2d array or list of signed stimulus intensities
        choices: 1d or 2d array or list of choices (coded as -1/1 or 0/1)
        confidence: 1d or 2d array or list of confidence ratings (normalized to the range 0-1)
        verbosity: verbosity level (possible values: 0, 1, 2)
        silence_warnings: if `True`, warnings during model fitting are supressed.
    """

    self.data = Data(self.cfg, stimuli, choices, confidence)

    self.result = Summary(self.data, self.cfg)

    self.fit_type1(verbosity=verbosity, store_final_results=self.cfg.skip_type2, silence_warnings=silence_warnings)

    if not self.cfg.skip_type2:
        self.fit_type2(verbosity=verbosity, silence_warnings=silence_warnings)

.fit_type1()

Usage 
rem = ReMeta()
rem.fit_type1(stimuli, choices)

Parameters:

Name Type Description Default
stimuli None | list[float] | list[list[float]] | NDArray[float]

1d or 2d array or list of signed stimulus intensities

 None
choices None | list[float] | list[list[float]] | NDArray[float]

1d or 2d array or list of choices (coded as -1/1 or 0/1)

 None
confidence None | list[float] | list[list[float]] | NDArray[float]

1d or 2d array or list of confidence ratings (normalized to the range 0-1)

 None
store_final_results bool

if True, save final results. Mostly used internally - will be set to False, if followed by fit_type2.

 True
verbosity int

verbosity level (possible values: 0, 1, 2)

 1
silence_warnings bool

if True, warnings during model fitting are supressed.

 False
Source code in remeta/model.py 
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def fit_type1(
    self,
    stimuli: None | list[float] | list[list[float]]  | np.typing.NDArray[float] = None,
    choices: None | list[float] | list[list[float]]  | np.typing.NDArray[float] = None,
    confidence: None | list[float] | list[list[float]]  | np.typing.NDArray[float] = None,
    store_final_results: bool = True,
    verbosity: int = 1,
    silence_warnings: bool = False
):
    """

    Usage:
        ```
        rem = ReMeta()
        rem.fit_type1(stimuli, choices)
        ```

    Args:
        stimuli: 1d or 2d array or list of signed stimulus intensities
        choices: 1d or 2d array or list of choices (coded as -1/1 or 0/1)
        confidence: 1d or 2d array or list of confidence ratings (normalized to the range 0-1)
        store_final_results: if `True`, save final results. Mostly used internally - will be set to `False`,
            if followed by `fit_type2`.
        verbosity: verbosity level (possible values: 0, 1, 2)
        silence_warnings: if `True`, warnings during model fitting are supressed.
    """

    if self.data is None:
        if stimuli is None or choices is None:
            raise ValueError('If the data attribute of the ReMeta instance is None, at least stimuli '
                             'and choices have to be passed to fits_type1_subject()')
        else:
            self.data = Data(self.cfg, stimuli, choices, confidence)

    if verbosity >= 1:
        print(f'Dataset characteristics:')
        print(f'{TAB}No. subjects: {self.data.nsubjects}')
        print(f"{TAB}No. samples: {np.array2string(np.array(self.data.nsamples).squeeze(), separator=', ', threshold=3)}")
        print(f'{TAB}Accuracy: {100*self.data.stats.accuracy:.1f}% correct')
        print(f"{TAB}d': {self.data.stats.dprime:.3f}")
        print(f"{TAB}Choice bias: {100*self.data.stats.choice_bias:.1f}%")
        if not self.cfg.skip_type2 and not store_final_results:
            print(f"{TAB}Mean confidence: {self.data.stats.mean_confidence:.3f} "
                  f"(min: {np.min(self.data.c_conf):.3f}, max: {np.max(self.data.c_conf):.3f})")

    self.result = Summary(self.data, self.cfg)

    if verbosity:
        print('\n+++ Type 1 level +++')
    with warnings.catch_warnings():
        warnings.filterwarnings('ignore', category=UserWarning, module='scipy.optimize',
                                message='delta_grad == 0.0. Check if the approximated function is linear. If the '
                                        'function is linear better results can be obtained by defining the Hessian '
                                        'as zero instead of using quasi-Newton approximations.')

        fits_type1_subject, fit_type1_group = None, None
        if self.cfg._paramset_type1.nparams > 0:

            if verbosity:
                print(f'{SP2}Subject-level estimation (MLE)')
                tind = timeit.default_timer()

            # Single-subject fits via MLE
            use_multiproc_for_subject_loop = (self.cfg._optim_num_cores >= 8) and (self.data.nsubjects >= 8)
            def subject_loop(s):
                return subject_estimation(
                    self.compute_type1_negll, self.cfg._paramset_type1, args=[s],
                    gridsearch=self.cfg.optim_type1_gridsearch,
                    scipy_solvers=self.cfg.optim_type1_scipy_solvers,
                    num_cores=1 if use_multiproc_for_subject_loop else self.cfg._optim_num_cores,
                    minimize_along_grid=self.cfg.optim_type1_minimize_along_grid,
                    global_minimization=self.cfg.optim_type1_global_minimization,
                    # fine_gridsearch=self.cfg.optim_type1_fine_gridsearch,
                    verbosity=verbosity
                )
            if use_multiproc_for_subject_loop:
                with DillPool(self.cfg._optim_num_cores) as pool:
                    fits_type1_subject = pool.map(subject_loop, range(self.data.nsubjects))
            else:
                fits_type1_subject = [None for _ in range(self.data.nsubjects)]
                for s in range(self.data.nsubjects):
                    if (verbosity > 0) and (self.data.nsubjects > 1):
                        print(f'{TAB} Subject {s + 1} / {self.data.nsubjects}')
                    fits_type1_subject[s] = subject_loop(s)
            # Store single-subject results
            params_subject = [fits_type1_subject[s].x for s in range(self.data.nsubjects)]
            params_hessian_subject = [fits_type1_subject[s].hessian for s in range(self.data.nsubjects)]
            self.result.type1.subject.store(
                'type1', self.cfg, self.data, self.compute_type1_negll, params_subject,
                hessian=params_hessian_subject, fit=fits_type1_subject,
                execution_time=np.sum([fits_type1_subject[s].execution_time for s in range(self.data.nsubjects)])
            )

            if verbosity:
                print(f'{TAB}.. finished ({timeit.default_timer() - tind:.1f} secs).')

            if self.data.nsubjects > 1:
                idx_fe = np.array([i for i, p in enumerate(self.cfg._paramset_type1.parameters_flat.values()) if p.group == 'fixed'])
                idx_re = np.array([i for i, p in enumerate(self.cfg._paramset_type1.parameters_flat.values()) if p.group == 'random'])
                if (len(idx_fe) > 0) or (len(idx_re) > 0):

                    fit_type1_group = group_estimation(
                        fun=self.compute_type1_negll,
                        nsubjects=self.data.nsubjects,
                        params_init=params_subject,
                        bounds=self.cfg._paramset_type1.bounds,
                        idx_fe=idx_fe,
                        idx_re=idx_re,
                        num_cores=self.cfg._optim_num_cores,
                        max_iter=30, sigma_floor=1e-3,
                        verbosity=verbosity,
                        # tau=0.05
                    )

                    self.result.type1.init_group()
                    self.result.type1.group.store(
                        'type1', self.cfg, self.data, self.compute_type1_negll,
                        params=[fit_type1_group.x[s] for s in range(self.data.nsubjects)],
                        params_se=[fit_type1_group.x_se[s] for s in range(self.data.nsubjects)],
                        params_cov=[fit_type1_group.x_cov[s] for s in range(self.data.nsubjects)],
                        pop_mean_sd=fit_type1_group.x_re_pop_mean_sd,
                        execution_time=fit_type1_group.execution_time
                    )

        self.result.type1.store(cfg=self.cfg, data=self.data, fun=self.compute_type1_negll)
        if verbosity:
            self.result.type1.report_fit(self.cfg)
        self.type1_is_fitted = True

    if store_final_results:
        self.result.store(store_type1_only=True)

    if verbosity:
        print('Type 1 level finished')

.plot_psychometric()

Invoke remeta.plotting.plot_psychomtric on the ReMeta instance.

Usage 
rem = ReMeta()
rem.fit(stimuli, choices, confidence)
rem.plot_psychometric()

Parameters:

Name Type Description Default
sub_ind int

subject index (only applicable if group data were fitted)

 0
model_prediction bool

if True, plot model predictions

 True
**kwargs

Pass parameters to remeta.plotting.plot_psychomtric

 {}
Source code in remeta/model.py 
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def plot_psychometric(
    self,
    sub_ind: int = 0,
    model_prediction: bool = True,
    **kwargs
):
    """
    Invoke `remeta.plotting.plot_psychomtric` on the `ReMeta` instance.

    Usage:
        ```
        rem = ReMeta()
        rem.fit(stimuli, choices, confidence)
        rem.plot_psychometric()
        ```

    Args:
        sub_ind: subject index (only applicable if group data were fitted)
        model_prediction: if `True`, plot model predictions
        **kwargs: Pass parameters to `remeta.plotting.plot_psychomtric`
    """

    # self._check_fit()
    plot_psychometric(
        self.data.x_stim[sub_ind], self.data.d_dec[sub_ind],
        params=self.result.params[sub_ind] if model_prediction else None,
        cfg=self.cfg, **kwargs
    )

.plot_stimulus_versus_confidence()

Invoke remeta.plotting.plot_stimulus_versus_confidence on the ReMeta instance.

Usage 
rem = ReMeta()
rem.fit(stimuli, choices, confidence)
rem.plot_stimulus_versus_confidence()

Parameters:

Name Type Description Default
sub_ind int

subject index (only applicable if group data were fitted)

 0
model_prediction bool

if True, plot model predictions

 True
**kwargs

Pass parameters to remeta.plotting.plot_stimulus_versus_confidence

 {}
Source code in remeta/model.py 
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def plot_stimulus_versus_confidence(
    self,
    sub_ind: int = 0,
    model_prediction: bool = True,
    **kwargs
):
    """
    Invoke `remeta.plotting.plot_stimulus_versus_confidence` on the `ReMeta` instance.

    Usage:
        ```
        rem = ReMeta()
        rem.fit(stimuli, choices, confidence)
        rem.plot_stimulus_versus_confidence()
        ```

    Args:
        sub_ind: subject index (only applicable if group data were fitted)
        model_prediction: if `True`, plot model predictions
        **kwargs: Pass parameters to `remeta.plotting.plot_stimulus_versus_confidence`
    """
    # self._check_fit()
    plot_stimulus_versus_confidence(
        self.data.x_stim[sub_ind], self.data.c_conf[sub_ind],self.data.d_dec[sub_ind],
        params=self.result.params[sub_ind] if model_prediction else None,
        model_prediction=model_prediction,
        cfg=self.cfg, **kwargs
    )

.plot_confidence_histogram()

Invoke remeta.plotting.plot_confidence_histogram on the ReMeta instance.

Usage 
rem = ReMeta()
rem.fit(stimuli, choices, confidence)
rem.plot_confidence_histogram()

Parameters:

Name Type Description Default
sub_ind int

subject index (only applicable if group data were fitted)

 0
model_prediction bool

if True, plot model predictions

 True
**kwargs

Pass parameters to remeta.plotting.plot_confidence_histogram

 {}
Source code in remeta/model.py 
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def plot_confidence_histogram(
    self,
    sub_ind: int = 0,
    model_prediction: bool = True,
    **kwargs
):
    """
    Invoke `remeta.plotting.plot_confidence_histogram` on the `ReMeta` instance.

    Usage:
        ```
        rem = ReMeta()
        rem.fit(stimuli, choices, confidence)
        rem.plot_confidence_histogram()
        ```

    Args:
        sub_ind: subject index (only applicable if group data were fitted)
        model_prediction: if `True`, plot model predictions
        **kwargs: Pass parameters to `remeta.plotting.plot_confidence_histogram`
    """
    # self._check_fit()
    plot_confidence_histogram(
        self.data.c_conf[sub_ind], self.data.x_stim[sub_ind], self.data.d_dec[sub_ind],
        params=self.result.params[sub_ind] if model_prediction else None,
        cfg=self.cfg, **kwargs
    )