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

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, [n_ratings, ...])

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
linearize	bool	Perform stimulus linearization	False
n_ratings	int	Numer of discrete confidence ratings (only relevant if modeling of confidence criteria is enabled)	None
linearize_kwargs	dict	Keyword arguments for stimulus linearization	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

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,
    n_ratings : int = None,
    linearize: bool = False,
    linearize_kwargs: dict = None,
    verbosity: int = 1,
    silence_warnings: bool = False
):
    """

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

    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)
        linearize: Perform stimulus linearization
        n_ratings: Numer of discrete confidence ratings (only relevant if modeling of confidence criteria is enabled)
        linearize_kwargs: Keyword arguments for stimulus linearization
        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)

    if linearize or self.cfg.optim_type1_linearize:
        self._linearize_stimuli(linearize_kwargs=linearize_kwargs, verbosity=verbosity,
                                silence_warnings=silence_warnings)

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

    self.fit_type1(verbosity=verbosity, _store_final_results=self.cfg.skip_type2,
                   silence_warnings=silence_warnings,
                   _called_from_fit=True)

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

    return self

.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
linearize	bool	Perform stimulus linearization	False
linearize_kwargs	dict	Keyword arguments for stimulus linearization	None
verbosity	int	verbosity level (possible values: 0, 1, 2)	1
silence_warnings	bool	if True, warnings during model fitting are supressed.	False
_store_final_results	bool	if True, save final results. Internal parameter - will be set to False, if followed by fit_type2.	True
_called_from_fit	bool	internal variable passed by self.fit()	False

Source code in remeta/model.py

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,
    linearize: bool = False,
    linearize_kwargs: dict = None,
    verbosity: int = 1,
    silence_warnings: bool = False,
    _store_final_results: bool = True,
    _called_from_fit: 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)
        linearize: Perform stimulus linearization
        linearize_kwargs: Keyword arguments for stimulus linearization
        verbosity: verbosity level (possible values: 0, 1, 2)
        silence_warnings: if `True`, warnings during model fitting are supressed.
        _store_final_results: if `True`, save final results. Internal parameter - will be set to `False`,
            if followed by `fit_type2`.
        _called_from_fit: internal variable passed by self.fit()
    """

    if self.data is None or not _called_from_fit:
        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 linearize or self.cfg.optim_type1_linearize:
                self._linearize_stimuli(linearize_kwargs=linearize_kwargs, verbosity=verbosity,
                                        silence_warnings=silence_warnings)
    if verbosity >= 1:
        print(f'Dataset characteristics:')
        print(f'{TAB}No. subjects: {self.data.n_subjects}')
        print(f"{TAB}No. samples: {np.array2string(np.array(self.data.n_samples).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: {min(map(lambda x: np.min(x), self.data.c_conf)):.3f},"
                  f" max: {max(map(lambda x: np.max(x), self.data.c_conf)):.3f})")

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

    if verbosity:
        print('\n+++ Type 1 level +++')

    fits_type1_subject, fit_type1_group = None, None
    if self.cfg._paramset_type1.n_params > 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.n_subjects >= 8)
        def subject_loop(s):
            with warnings.catch_warnings():
                # warnings.filterwarnings('ignore', category=UserWarning, module=r'scipy\.optimize.*', message=r'delta_grad == 0\.0\.')
                warnings.filterwarnings('ignore', category=UserWarning, module=r'scipy\.optimize.*')
                if (verbosity > 0) and (self.data.n_subjects > 1):
                    print(f'{TAB} Subject {s + 1} / {self.data.n_subjects}')
                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,
                    force_hessian_uncertainty=self.cfg.optim_force_hessian_uncertainty,
                    verbosity=verbosity, silence_warnings=silence_warnings
                )
        if not use_multiproc_for_subject_loop or Parallel is None:
            if use_multiproc_for_subject_loop and not silence_warnings:
                warnings.warn('Multiprocessing is enabled, but joblib is not installed.')
            fits_type1_subject = [None for _ in range(self.data.n_subjects)]
            for s in range(self.data.n_subjects):
                fits_type1_subject[s] = subject_loop(s)
        else:
            fits_type1_subject = Parallel(n_jobs=self.cfg._optim_num_cores)(
                delayed(subject_loop)(s) for s in range(self.data.n_subjects)
            )

        # Store single-subject results
        params_subject = [fits_type1_subject[s].x for s in range(self.data.n_subjects)]
        params_hessian_subject = [fits_type1_subject[s].hessian for s in range(self.data.n_subjects)]
        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.n_subjects)]),
            silence_warnings=silence_warnings
        )

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

        if self.data.n_subjects > 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,
                    n_subjects=self.data.n_subjects,
                    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,
                    random_effect_method=self.cfg.optim_type1_random_effect_method,
                    include_posterior_variance=self.cfg.optim_type1_include_posterior_variance,
                    verbosity=verbosity
                )

                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.n_subjects)],
                    params_se=[fit_type1_group.x_se[s] for s in range(self.data.n_subjects)],
                    params_cov=[fit_type1_group.x_cov[s] for s in range(self.data.n_subjects)],
                    pop_mean_sd=fit_type1_group.x_re_pop_mean_sd,
                    execution_time=fit_type1_group.execution_time,
                    silence_warnings=silence_warnings
                )

        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')

    return self

.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

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

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

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
    )