コード例 #1
0
ファイル: fit_pyddm.py プロジェクト: LNDG/zurich_data
    def setup_model(self):
        """
        Function to setup model. 
        """
        class DriftCoherence(ddm.models.Drift):
            name = "Drift depends linearly on coherence"
            # Parameter that should be included in the ddm
            required_parameters = ["driftcoherence"]
            # Task Parameter, i.e. coherence
            required_conditions = ["coherence"]

            # Define the get_drift function
            def get_drift(self, conditions, **kwargs):
                return self.driftcoherence * conditions['coherence']

        # Set up Model with Drift depending on Coherence
        model = Model(
            name='Noise Model - Drift varies with coherence',
            drift=DriftCoherence(driftcoherence=Fittable(minval=0, maxval=20)),
            noise=NoiseConstant(noise=1),
            bound=BoundConstant(B=Fittable(minval=.1, maxval=1.5)),
            overlay=OverlayChain(overlays=[
                OverlayNonDecision(nondectime=Fittable(minval=0, maxval=.4)),
                OverlayPoissonMixture(pmixturecoef=.02, rate=1)
            ]),
            dx=.01,
            dt=.01,
            T_dur=2)
        return model
コード例 #2
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ファイル: degee2020.py プロジェクト: ntardiff/PyDDM
def make_model(sample, model_settings):
    
    # model components:
    z = make_z(sample=sample, 
                z_depends_on=model_settings['depends_on']['z'])
    drift = make_drift(sample=sample, 
                        drift_bias=model_settings['drift_bias'], 
                        v_depends_on=model_settings['depends_on']['v'], 
                        b_depends_on=model_settings['depends_on']['b'])
    a = make_a(sample=sample, 
                urgency=model_settings['urgency'], 
                a_depends_on=model_settings['depends_on']['a'], 
                u_depends_on=model_settings['depends_on']['u'])
    t = make_t(sample=sample, 
                t_depends_on=model_settings['depends_on']['t'])
    T_dur = model_settings['T_dur']

    # limits:
    ranges = {
            'z':(0.05,0.95),               # starting point
            'v':(0,5),                     # drift rate
            'b':(-5,5),                    # drift bias
            'a':(0.1,5),                   # bound
            # 'u':(-T_dur*10,T_dur*10),    # hyperbolic collapse
            'u':(0.01,T_dur*10),           # hyperbolic collapse
            't':(0,2),                     # non-decision time
            }

    # put together:
    if model_settings['start_bias']:
        initial_condition = z(**{param:Fittable(minval=ranges[param[0]][0], maxval=ranges[param[0]][1]) for param in z.required_parameters})
    else:
        initial_condition = z(**{'z':0.5})
    model = Model(name='stimulus coding model / collapsing bound',
                IC=initial_condition,
                drift=drift(**{param:Fittable(minval=ranges[param[0]][0], maxval=ranges[param[0]][1]) for param in drift.required_parameters}),
                bound=a(**{param:Fittable(minval=ranges[param[0]][0], maxval=ranges[param[0]][1]) for param in a.required_parameters}),
                overlay=OverlayChain(overlays=[t(**{param:Fittable(minval=ranges[param[0]][0], maxval=ranges[param[0]][1]) for param in t.required_parameters}),
                                                OverlayUniformMixture(umixturecoef=0)]),
                                                # OverlayPoissonMixture(pmixturecoef=.01, rate=1)]),
                noise=NoiseConstant(noise=1),
                dx=.005, dt=.01, T_dur=T_dur)
    return model
def DDM_FIT(RT, ANSWER):
    df = []

    # RT is scalles to seconds, the function takes seconds
    df = pd.DataFrame({'RT': RT / 1000, 'correct': ANSWER})
    df.head()
    sample = Sample.from_pandas_dataframe(df,
                                          rt_column_name="RT",
                                          correct_column_name="correct")
    model = Model(
        name='Model',
        drift=DriftConstant(drift=Fittable(minval=6, maxval=25)),
        noise=NoiseConstant(
            noise=1.5),  #(noise=Fittable(minval=0.5, maxval=2.5)),
        bound=BoundConstant(B=2.5),
        overlay=OverlayChain(overlays=[
            OverlayNonDecision(nondectime=Fittable(minval=0, maxval=.8)),
            OverlayPoissonMixture(pmixturecoef=.02, rate=1)
        ]),
        dx=.001,
        dt=.01,
        T_dur=2)

    # Fitting this will also be fast because PyDDM can automatically
    # determine that DriftCoherence will allow an analytical solution.
    fit_model = fit_adjust_model(sample=sample,
                                 model=model,
                                 fitting_method="differential_evolution",
                                 lossfunction=LossRobustBIC,
                                 verbose=False)

    param = fit_model.get_model_parameters()

    Drift = np.asarray(param[0])
    Delay = np.asarray(param[1])

    return Drift, Delay
コード例 #4
0
ファイル: roitman_shadlen.py プロジェクト: ntardiff/PyDDM

# Define a model which uses our new DriftCoherence defined above.
from ddm import Model, Fittable
from ddm.functions import fit_adjust_model, display_model
from ddm.models import NoiseConstant, BoundConstant, OverlayChain, OverlayNonDecision, OverlayPoissonMixture

model_rs = Model(
    name='Roitman data, drift varies with coherence',
    drift=DriftCoherence(driftcoh=Fittable(minval=0, maxval=20)),
    noise=NoiseConstant(noise=1),
    bound=BoundConstant(B=Fittable(minval=.1, maxval=1.5)),
    # Since we can only have one overlay, we use
    # OverlayChain to string together multiple overlays.
    # They are applied sequentially in order.  OverlayNonDecision
    # implements a non-decision time by shifting the
    # resulting distribution of response times by
    # `nondectime` seconds.
    overlay=OverlayChain(overlays=[
        OverlayNonDecision(nondectime=Fittable(minval=0, maxval=.4)),
        OverlayPoissonMixture(pmixturecoef=.02, rate=1)
    ]),
    dx=.001,
    dt=.01,
    T_dur=2)

# Fitting this will also be fast because PyDDM can automatically
# determine that DriftCoherence will allow an analytical solution.
fit_model_rs = fit_adjust_model(sample=roitman_sample,
                                model=model_rs,
                                verbose=False)
display_model(fit_model_rs)
コード例 #5
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ファイル: simple.py プロジェクト: ntardiff/PyDDM
# Simple demonstration of PyDDM.

# Create a simple model with constant drift, noise, and bounds.
from ddm import Model
from ddm.models import DriftConstant, NoiseConstant, BoundConstant, OverlayNonDecision, ICPointSourceCenter
from ddm.functions import fit_adjust_model, display_model

model = Model(name='Simple model',
              drift=DriftConstant(drift=2.2),
              noise=NoiseConstant(noise=1.5),
              bound=BoundConstant(B=1.1),
              overlay=OverlayNonDecision(nondectime=.1),
              dx=.001, dt=.01, T_dur=2)

# Solve the model, i.e. simulate the differential equations to
# generate a probability distribution solution.
display_model(model)
sol = model.solve()

# Now, sample from the model solution to create a new generated
# sample.
samp = sol.resample(1000)

# Fit a model identical to the one described above on the newly
# generated data so show that parameters can be recovered.
from ddm import Fittable, Fitted
from ddm.models import LossRobustBIC
from ddm.functions import fit_adjust_model
model_fit = Model(name='Simple model (fitted)',
                  drift=DriftConstant(drift=Fittable(minval=0, maxval=4)),
                  noise=NoiseConstant(noise=Fittable(minval=.5, maxval=4)),
コード例 #6
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ファイル: ddmdiagram.py プロジェクト: mwshinn/CanD
# End canvas initialization

##### DDM SCHEMATIC #####

# Begin default unit
c.add_unit("absolute2", Vector(1, 1, "absolute"), Point(0, 1, "absolute"))
c.set_default_unit("absolute2")
# End default unit

# Begin other axes
c.add_axis("ddm", Point(0.3, 6.5), Point(3.7, 7.6))
c.add_axis("evidence", Point(0.3, 6.2), Point(3.7, 6.4))
# End other axes

# Begin model simulation
model = Model(drift=DriftConstant(drift=0.8), dt=0.01, dx=0.01)
sim_trial = model.simulate_trial(seed=8)
sim_trial[20:] = -sim_trial[20:] * 1.6
sim_trial = sim_trial[0:38]
# End model simulation

# Begin ddm plot
ax = c.ax("ddm")
ax.plot(model.t_domain()[0:len(sim_trial)], sim_trial, c="k")
ax.axhline(1, c=color_bound, clip_on=False)
ax.axhline(-1, c=color_bound, clip_on=False)
ax.set_ylabel("Decision variable")
set_up_plot(ax)
# End ddm plot

# Begin ddm annotate
コード例 #7
0
ファイル: pyddm_tools.py プロジェクト: jwdegee/accumodels
def make_model_one_accumulator(sample, model_settings):

    # # components:
    # z = make_z_one_accumulator(sample=sample,
    #             a_depends_on=model_settings['depends_on']['a'])
    # drift = make_drift_one_accumulator(sample=sample,
    #                 drift_bias=model_settings['drift_bias'],
    #                 leak=model_settings['leak'],
    #                 v_depends_on=model_settings['depends_on']['v'],
    #                 b_depends_on=model_settings['depends_on']['b'],
    #                 k_depends_on=model_settings['depends_on']['k'],
    #                 a_depends_on=model_settings['depends_on']['v'],)
    # bound = BoundConstant
    # t = NonDecisionTime
    # n = NoisePulse(noise=1)

    # # limits:
    # ranges = {

    #         # 'v':(0.99,1.01),               # drift rate
    #         # 'b':(-0.21,-0.19),             # drift bias
    #         # 'k':(2.39,2.41),               # leak
    #         # 'z':(0.75,0.999),              # starting point --> translates into bound heigth 0-5
    #         'v':(0,5),                     # drift rate
    #         'b':(-5,5),                    # drift bias
    #         'k':(0,5),                     # leak
    #         'a':(0.1,5),                   # bound
    #         't':(0,.1),                    # non-decision time
    #         }

    # # initialize params:
    # a_params = {param:Fittable(minval=ranges[param[0]][0], maxval=ranges[param[0]][1]) for param in z.required_parameters}
    # drift_params = {param:Fittable(minval=ranges[param[0]][0], maxval=ranges[param[0]][1]) for param in drift.required_parameters if not 'a' in param}
    # drift_params = {**drift_params, **a_params}

    # # put together:
    # model = Model(name='one accumulator model',
    #             IC=z(**a_params),
    #             drift=drift(**drift_params),
    #             bound=bound(B=10),
    #             overlay=OverlayChain(overlays=[t(**{param:Fittable(minval=ranges[param[0]][0], maxval=ranges[param[0]][1]) for param in t.required_parameters}),
    #                                             # OverlayUniformMixture(umixturecoef=0)
    #                                             # OverlayUniformMixture(umixturecoef=0.01)
    #                                             OverlayPoissonMixture(pmixturecoef=.02, rate=1)
    #                                             ]),
    #             noise=n,
    #             dx=.01, dt=.01, T_dur=T_dur)

    # parameters:
    ranges = {
        # 'v':(0.99,1.01),               # drift rate
        # 'b':(-0.21,-0.19),             # drift bias
        # 'k':(2.39,2.41),               # leak
        # 'z':(0.75,0.999),              # starting point --> translates into bound heigth 0-5
        'v': (0, 25),  # drift rate
        'b': (-5, 5),  # drift bias
        'k': (0, 5),  # leak
        'a': (0.1, 5),  # bound
        't': (0, .1),  # non-decision time
        'lapse': (0.001, 0.999),  # lapse rate
        'mixture': (0.001, 0.999),  # mixture rate
    }

    a0_value = Fittable(minval=ranges['a'][0],
                        maxval=ranges['a'][1],
                        default=1)
    a1_value = Fittable(minval=ranges['a'][0],
                        maxval=ranges['a'][1],
                        default=1)
    v0_value = Fittable(minval=ranges['v'][0],
                        maxval=ranges['v'][1],
                        default=1)
    v1_value = Fittable(minval=ranges['v'][0],
                        maxval=ranges['v'][1],
                        default=1)

    if model_settings['drift_bias'] & (model_settings['depends_on']['b']
                                       == ['reward']):
        b0_value = Fittable(minval=ranges['b'][0],
                            maxval=ranges['b'][1],
                            default=0)
        b1_value = Fittable(minval=ranges['b'][0],
                            maxval=ranges['b'][1],
                            default=0)
    elif model_settings['drift_bias'] & (model_settings['depends_on']['b'] is
                                         None):
        b0_value = Fittable(minval=ranges['b'][0],
                            maxval=ranges['b'][1],
                            default=0)
        b1_value = b0_value
    else:
        b0_value = 0
        b1_value = 0

    if model_settings['leak'] & (model_settings['depends_on']['k']
                                 == ['reward']):
        k0_value = Fittable(minval=ranges['k'][0],
                            maxval=ranges['k'][1],
                            default=1)
        k1_value = Fittable(minval=ranges['k'][0],
                            maxval=ranges['k'][1],
                            default=1)
    elif model_settings['leak'] & (model_settings['depends_on']['k'] is None):
        k0_value = Fittable(minval=ranges['k'][0],
                            maxval=ranges['k'][1],
                            default=1)
        k1_value = k0_value
    else:
        k0_value = 0
        k1_value = 0

    if model_settings['lapse'] & (model_settings['depends_on']['lapse']
                                  == ['reward']):
        lapse0_value = Fittable(minval=ranges['lapse'][0],
                                maxval=ranges['lapse'][1],
                                default=0.1)
        lapse1_value = Fittable(minval=ranges['lapse'][0],
                                maxval=ranges['lapse'][1],
                                default=0.1)
    elif model_settings['lapse'] & (model_settings['depends_on']['lapse'] is
                                    None):
        lapse0_value = Fittable(minval=ranges['lapse'][0],
                                maxval=ranges['lapse'][1],
                                default=0.1)
        lapse1_value = lapse0_value
    else:
        lapse0_value = 0
        lapse1_value = 0

    if model_settings['mixture'] & (model_settings['depends_on']['mixture']
                                    == ['reward']):
        mixture0_value = Fittable(minval=ranges['mixture'][0],
                                  maxval=ranges['mixture'][1],
                                  default=0.1)
        mixture1_value = Fittable(minval=ranges['mixture'][0],
                                  maxval=ranges['mixture'][1],
                                  default=0.1)
    elif model_settings['mixture'] & (model_settings['depends_on']['mixture']
                                      is None):
        mixture0_value = Fittable(minval=ranges['mixture'][0],
                                  maxval=ranges['mixture'][1],
                                  default=0.1)
        mixture1_value = mixture0_value
    else:
        mixture0_value = 0
        mixture1_value = 0

    # components:
    starting_point_components = {'a0': a0_value, 'a1': a1_value}
    drift_components = {
        'v0': v0_value,
        'v1': v1_value,
        'k0': k0_value,
        'k1': k1_value,
        'b0': b0_value,
        'b1': b1_value,
        'a0': a0_value,
        'a1': a1_value,
    }
    mixture_components = {
        'mixture0': mixture0_value,
        'mixture1': mixture1_value
    }
    lapse_components = {'lapse0': lapse0_value, 'lapse1': lapse1_value}

    # build model:
    from ddm.models import DriftConstant, NoiseConstant, BoundConstant, OverlayChain, OverlayNonDecision, OverlayPoissonMixture, OverlayUniformMixture, InitialCondition, ICPoint, ICPointSourceCenter, LossBIC
    bound = BoundConstant
    a = StartingPoint_reward
    drift = DriftPulse_reward
    t = NonDecisionTime
    n = NoisePulse(noise=1)
    model = Model(
        name='one accumulator model',
        IC=a(**starting_point_components),
        drift=drift(**drift_components),
        bound=bound(B=10),
        overlay=OverlayChain(overlays=[
            t(t=0),
            # t(**{param:Fittable(minval=ranges[param[0]][0], maxval=ranges[param[0]][1]) for param in t.required_parameters}),
            OverlayExGaussMixture(**mixture_components),
            OverlayEvidenceLapse(**lapse_components),
        ]),
        noise=n,
        dx=model_settings['dx'],
        dt=model_settings['dt'],
        T_dur=model_settings['T_dur'])

    # # fit:
    # # model_fit = fit_adjust_model(sample=sample, model=model, lossfunction=LossLikelihood)
    # try:

    #     model_fit = fit_adjust_model(sample=sample, model=model, lossfunction=LossLikelihoodGonogo, fitting_method="differential_evolution")

    #     # print('model: {}'.format(model_fit.solve({'stimulus':0}).prob_correct()))
    #     # print('data: {}'.format(df.loc[df['stimulus']==0, 'response'].mean()))
    #     # print()
    #     # print('model: {}'.format(model_fit.solve({'stimulus':1}).prob_correct()))
    #     # print('data: {}'.format(df.loc[df['stimulus']==1, 'response'].mean()))

    #     # # plot:
    #     # ddm.plot.plot_fit_diagnostics(model=model_fit, sample=sample)

    #     # get params:
    #     params = pd.DataFrame(np.atleast_2d([p.real for p in model_fit.get_model_parameters()]), columns=model_fit.get_model_parameter_names())
    #     params['bic'] = model_fit.fitresult.value()
    # except Exception as e:

    #     print(e)
    #     params = pd.DataFrame(np.atleast_2d([np.nan, np.nan, np.nan, np.nan]), columns=model.get_model_parameter_names())
    return model
コード例 #8
0
            wves = sqrt(
                float(self.kves)**2 /
                (float(self.kvis)**2 + float(self.kves)**2))
            wvis = sqrt(
                float(self.kvis)**2 /
                (float(self.kvis)**2 + float(self.kves)**2))

            return wves * mu_ves + wvis * mu_vis


from ddm import Model, Fittable
from ddm.functions import fit_adjust_model
from ddm.models import NoiseConstant, BoundConstant, OverlayNonDecision

model = Model(
    name="3DMP Kiani09 Sim",
    drift=DriftRate(kves=Fittable(minval=0, maxval=3),
                    kvis=Fittable(minval=3, maxval=6),
                    acc=acc,
                    vel=vel),
    bound=BoundConstant(B=Fittable(minval=50, maxval=90)),
    noise=NoiseConstant(noise=1),
    overlay=OverlayNonDecision(nondectime=Fittable(minval=.1, maxval=.4)),
    dx=.01,
    dt=.001,
    T_dur=2.0)

fit_model = fit_adjust_model(sample=sample, model=model)

#model_gui(model=model, sample=sample)
コード例 #9
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        model_ic = ICPoint(x0=x0)

        _overlay_map = OverlayMappingError(mappingcoef=mappingcoef)
        _overlay_nondecision = OverlayNonDecision(nondectime=nondectime)

        _overlay_mix = OverlayExponentialRewardMixture(
            pmixturecoef=pmixturecoef, ratehr=ratehr, ratelr=ratelr)

        model_overlay = OverlayChain(
            overlays=[_overlay_nondecision, _overlay_map, _overlay_mix])

        modelparams = {"dx": 0.005, "dt": 0.002, "T_dur": 3.0}

        modelname = "Shinn et al (2020) model (%s)" % (
            "gain function" if URGENCY == "gain" else "collapsing bounds")
        model = Model(name=modelname,
                      **modelparams,
                      drift=model_drift,
                      noise=model_noise,
                      bound=model_bounds,
                      IC=model_ic,
                      overlay=model_overlay)

        ddm.plot.model_gui(model,
                           conditions={
                               "coherence": [50, 53, 60, 70],
                               "presample": [0, 400, 800],
                               "highreward": [0, 1]
                           })
        # END demo
コード例 #10
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ファイル: SmithFood1.py プロジェクト: tianqimark/DDM_fitting
        # This is just a temorary solution
        if noise != 0:
            return noise
        else:
            return noise + 0.001


from ddm import Model, Fittable
from ddm.functions import fit_adjust_model, display_model
from ddm.models import NoiseConstant, BoundConstant, OverlayChain, OverlayNonDecision, OverlayPoissonMixture
model_foodc = Model(
    name='Data from Smith 2018 two food choice. Fit a regular DDM to it',
    drift=DriftFoodc(d=Fittable(minval=0, maxval=0.001)),
    noise=NoiseFoodc(sigma=Fittable(minval=0, maxval=0.05)),
    bound=BoundConstant(B=1),
    overlay=OverlayChain(overlays=[
        OverlayNonDecision(nondectime=Fittable(minval=0, maxval=1)),
        OverlayPoissonMixture(pmixturecoef=.02, rate=1)
    ]),
    dx=.001,
    dt=.01,
    T_dur=10)

# Check if an analytical solution exists.
Model.has_analytical_solution(model_foodc)
# For the current model: True

### Fit the model to the dataset to find parameters

# Use the "differential_evolution" fitting method (default, recommanded fitting method)
fit_model_foodc = fit_adjust_model(sample=foodc_sample,
                                   model=model_foodc,
コード例 #11
0
def Fit_DDM_Group_JK_ib(domain='whole'):

    # create a df to record the output data
    column_names = ['domain', 'RS_level', 'sub_omit'] + model_rDDM.get_model_parameter_names() + \
    ['loss_func_value', 'criterion', 'sample_size', 'on_bound']
    rDDM_fitting_jk = pd.DataFrame(columns=column_names)

    # decide whether to fit rDDM on the whole dataset,
    # the advantageous trials or disadvantageous trials
    if domain == 'adv':
        data_for_fit = data[data['domain_group'] == 1]
    elif domain == 'dis':
        data_for_fit = data[data['domain_group'] == 2]
    else:
        data_for_fit = data

    # fit on groups of different RS levels
    for group in np.sort(data_for_fit['RS_level'].unique()):
        data_subgroup = data_for_fit[data_for_fit['RS_level'] == group]

        # omit subjects one at a time
        for sub_omit in np.sort(data_subgroup['subject'].unique()):

            # find the current fitting parameters in the fit_ref
            where = np.where((fit_ref['domain'] == domain)
                             & (fit_ref['RS_level'] == group)
                             & (fit_ref['sub_omit'] == str(sub_omit)))

            where = int(where[0])

            # allow for extra ranges from the best fitting results
            extra = 0.05
            extra_v_dis = 0.0005
            extra_v_els = 0.005

            if domain == 'dis':
                vg_max = fit_ref.iloc[where]['vg_best'] + extra_v_dis
                vg_min = fit_ref.iloc[where]['vg_best'] - extra_v_dis
                vl_max = fit_ref.iloc[where]['vl_best'] + extra_v_dis
                vl_min = fit_ref.iloc[where]['vl_best'] - extra_v_dis
            else:
                vg_max = fit_ref.iloc[where]['vg_best'] + extra_v_els
                vg_min = fit_ref.iloc[where]['vg_best'] - extra_v_els
                vl_max = fit_ref.iloc[where]['vl_best'] + extra_v_els
                vl_min = fit_ref.iloc[where]['vl_best'] - extra_v_els

            fixed_max = fit_ref.iloc[where]['fixed_best'] + extra
            fixed_min = fit_ref.iloc[where]['fixed_best'] - extra
            B_max = fit_ref.iloc[where]['B_best'] + extra
            B_min = fit_ref.iloc[where]['B_best'] - extra
            x0_max = fit_ref.iloc[where]['x0_best'] + extra
            x0_min = fit_ref.iloc[where]['x0_best'] - extra
            nondectime_max = fit_ref.iloc[where]['nondectime_best'] + extra
            nondectime_min = fit_ref.iloc[where]['nondectime_best'] - extra

            # create a DDM modell based on the current fitting range
            model_rDDM_ib = Model(
                name='Risk_DDM_individual_range_fit',
                drift=Risk_Drift(vg=Fittable(minval=vg_min, maxval=vg_max),
                                 vl=Fittable(minval=vl_min, maxval=vl_max),
                                 fixed=Fittable(minval=fixed_min,
                                                maxval=fixed_max)),
                IC=Biased_Start(x0=Fittable(minval=x0_min, maxval=x0_max)),
                noise=NoiseConstant(noise=1),
                bound=BoundConstant(B=Fittable(minval=B_min, maxval=B_max)),

                # Uniform Mixture Model
                overlay=OverlayChain(overlays=[
                    OverlayNonDecision(nondectime=Fittable(
                        minval=nondectime_min, maxval=nondectime_max)),
                    OverlayUniformMixture(umixturecoef=.05)
                ]),
                dx=0.001,
                dt=0.001,
                T_dur=10)
            # dx=0.01, dt=0.01, T_dur=10)

            data_jk = data_subgroup[data_subgroup['subject'] != sub_omit]

            sample_size = data_jk.shape[0]

            # create a sample and start fitting
            data_jk_sample = Sample.from_pandas_dataframe(
                data_jk, rt_column_name="RT", correct_column_name="accept")

            fit_sample = fit_adjust_model(
                sample=data_jk_sample,
                model=model_rDDM_ib,
                fitting_method='differential_evolution')

            # sort out results
            result_list = [[domain, group, sub_omit] + fit_sample.get_model_parameters() + \
                           [fit_sample.fitresult.value(), fit_sample.fitresult.loss, sample_size, 0]]
            # 0 in the end is the place holder for the counts in the on_buond column

            result_df = pd.DataFrame(result_list, columns=column_names)

            # check whether the estimated results are on the limits of the fitting ranges
            if result_df['vg'][0] == vg_min or result_df['vg'][0] == vg_max:
                result_df['on_bound'][0] += 1

            if result_df['vl'][0] == vl_min or result_df['vl'][0] == vl_max:
                result_df['on_bound'][0] += 1

            if result_df['fixed'][0] == fixed_min or result_df['fixed'][
                    0] == fixed_max:
                result_df['on_bound'][0] += 1

            if result_df['B'][0] == B_min or result_df['B'][0] == B_max:
                result_df['on_bound'][0] += 1

            if result_df['x0'][0] == x0_min or result_df['x0'][0] == x0_max:
                result_df['on_bound'][0] += 1

            if result_df['nondectime'][0] == nondectime_min or result_df[
                    'nondectime'][0] == nondectime_max:
                result_df['on_bound'][0] += 1

            # append the results
            rDDM_fitting_jk = rDDM_fitting_jk.append(result_df,
                                                     ignore_index=True)

    return rDDM_fitting_jk
コード例 #12
0
    required_conditions = ["gain", "loss"]

    def get_drift(self, conditions, **kwargs):
        valuation = self.vg * conditions['gain'] - self.vl * conditions['loss']
        return valuation + self.fixed


model_rDDM = Model(
    name='Risk_DDM',
    drift=Risk_Drift(vg=Fittable(minval=0.001, maxval=0.06),
                     vl=Fittable(minval=0.001, maxval=0.06),
                     fixed=Fittable(minval=-1.6, maxval=0.8)),
    IC=Biased_Start(x0=Fittable(minval=-0.55, maxval=0.55)),
    noise=NoiseConstant(noise=1),
    bound=BoundConstant(B=Fittable(minval=0.5, maxval=2)),

    # Uniform Mixture Model
    overlay=OverlayChain(overlays=[
        OverlayNonDecision(nondectime=Fittable(minval=0, maxval=1.1)),
        OverlayUniformMixture(umixturecoef=.05)
    ]),
    dx=0.001,
    dt=0.001,
    T_dur=10)
# dx=0.01, dt=0.01, T_dur=10)

# Check if an analytical solution exists.
model_rDDM.has_analytical_solution()
model_rDDM.get_model_parameter_names()
model_rDDM.get_model_parameters()
コード例 #13
0
import matplotlib.pyplot as plt
from ddm import Model
m = Model()
s = m.solve()
plt.plot(s.model.t_domain(), s.pdf_corr())
plt.savefig("helloworld.png")
plt.show()