Vidigi vs BupaR

Tip

Switch this page to the light mode using the toggle at the top of the navigation sidebar on the left of this page.

I have not yet worked out how to change the colour of the text on the resulting process maps, so using light mode is currently the only way to see it.

The title of this section is perhaps misleading! As the author of the package, I think the visuals produced by the two packages occupy slightly different niches, and the use of both can benefit your project.

As an additional bonus, the process of creating the logs you require for a vidigi project give you the perfect dataset for your bupaR visuals too!

bupaR outputs could form part of a verification and validation strategy. They can also perform part of your communications strategy, helping to provide a talking point for meetings with stakeholders in much the same way as a screenshot of your Simul8 or Anylogic model would. In the absence of a graphical interface for building a model, the bupar outputs can help you - and your stakeholders - to ensure that linkages between different model steps are sensible and appropriate.

We will begin in Python, working to add a couple of columns to our vidigi event log to prepare it for use in bupaR.

from examples.example_2_branching_multistep.ex_2_model_classes import Trial, g
import pandas as pd
import os

g.sim_duration = 3000
g.number_of_runs = 1

View Imported Code, which has had logging steps added at the appropriate points in the ‘model’ class

import random
import numpy as np
import pandas as pd
import simpy
from sim_tools.distributions import Exponential, Lognormal, Uniform, Normal, Bernoulli
from vidigi.utils import populate_store
from examples.simulation_utility_functions import trace


# Class to store global parameter values.  We don't create an instance of this
# class - we just refer to the class blueprint itself to access the numbers
# inside.
class g:
    '''
    Create a scenario to parameterise the simulation model

    Parameters:
    -----------
    random_number_set: int, optional (default=DEFAULT_RNG_SET)
        Set to control the initial seeds of each stream of pseudo
        random numbers used in the model.

    n_triage: int
        The number of triage cubicles

    n_reg: int
        The number of registration clerks

    n_exam: int
        The number of examination rooms

    n_trauma: int
        The number of trauma bays for stablisation

    n_cubicles_non_trauma_treat: int
        The number of non-trauma treatment cubicles

    n_cubicles_trauma_treat: int
        The number of trauma treatment cubicles

    triage_mean: float
        Mean duration of the triage distribution (Exponential)

    reg_mean: float
        Mean duration of the registration distribution (Lognormal)

    reg_var: float
        Variance of the registration distribution (Lognormal)

    exam_mean: float
        Mean of the examination distribution (Normal)

    exam_var: float
        Variance of the examination distribution (Normal)

    trauma_mean: float
        Mean of the trauma stabilisation distribution (Exponential)

    trauma_treat_mean: float
        Mean of the trauma cubicle treatment distribution (Lognormal)

    trauma_treat_var: float
        Variance of the trauma cubicle treatment distribution (Lognormal)

    non_trauma_treat_mean: float
        Mean of the non trauma treatment distribution

    non_trauma_treat_var: float
        Variance of the non trauma treatment distribution

    non_trauma_treat_p: float
        Probability non trauma patient requires treatment

    prob_trauma: float
        probability that a new arrival is a trauma patient.
    '''
    random_number_set = 42

    n_triage=2
    n_reg=2
    n_exam=3
    n_trauma=4
    n_cubicles_non_trauma_treat=4
    n_cubicles_trauma_treat=5

    triage_mean=6
    reg_mean=8
    reg_var=2
    exam_mean=16
    exam_var=3
    trauma_mean=90
    trauma_treat_mean=30
    trauma_treat_var=4
    non_trauma_treat_mean=13.3
    non_trauma_treat_var=2

    non_trauma_treat_p=0.6
    prob_trauma=0.12

    arrival_df="ed_arrivals.csv"

    sim_duration = 600
    number_of_runs = 100

# Class representing patients coming in to the clinic.
class Patient:
    '''
    Class defining details for a patient entity
    '''
    def __init__(self, p_id):
        '''
        Constructor method

        Params:
        -----
        identifier: int
            a numeric identifier for the patient.
        '''
        self.identifier = p_id

        # Time of arrival in model/at centre
        self.arrival = -np.inf
        # Total time in pathway
        self.total_time = -np.inf

        # Shared waits
        self.wait_triage = -np.inf
        self.wait_reg = -np.inf
        self.wait_treat = -np.inf
        # Non-trauma pathway - examination wait
        self.wait_exam = -np.inf
        # Trauma pathway - stabilisation wait
        self.wait_trauma = -np.inf

        # Shared durations
        self.triage_duration = -np.inf
        self.reg_duration = -np.inf
        self.treat_duration = -np.inf

        # Non-trauma pathway - examination duration
        self.exam_duration = -np.inf
        # Trauma pathway - stabilisation duration
        self.trauma_duration = -np.inf


# Class representing our model of the clinic.
class Model:
    '''
    Simulates the simplest minor treatment process for a patient

    1. Arrive
    2. Examined/treated by nurse when one available
    3. Discharged
    '''
    # Constructor to set up the model for a run.  We pass in a run number when
    # we create a new model.
    def __init__(self, run_number):
        # Create a SimPy environment in which everything will live
        self.env = simpy.Environment()

        self.event_log = []

        # Create a patient counter (which we'll use as a patient ID)
        self.patient_counter = 0

        self.trauma_patients = []
        self.non_trauma_patients = []

        # Create our resources
        self.init_resources()

        # Store the passed in run number
        self.run_number = run_number

        # Create a new Pandas DataFrame that will store some results against
        # the patient ID (which we'll use as the index).
        self.results_df = pd.DataFrame()
        self.results_df["Patient ID"] = [1]
        self.results_df["Queue Time Cubicle"] = [0.0]
        self.results_df["Time with Nurse"] = [0.0]
        self.results_df.set_index("Patient ID", inplace=True)

        # Create an attribute to store the mean queuing times across this run of
        # the model
        self.mean_q_time_cubicle = 0

        # create distributions

        # Triage duration
        self.triage_dist = Exponential(g.triage_mean,
                                       random_seed=self.run_number*g.random_number_set)

        # Registration duration (non-trauma only)
        self.reg_dist = Lognormal(g.reg_mean,
                                  np.sqrt(g.reg_var),
                                  random_seed=self.run_number*g.random_number_set)

        # Evaluation (non-trauma only)
        self.exam_dist = Normal(g.exam_mean,
                                np.sqrt(g.exam_var),
                                random_seed=self.run_number*g.random_number_set)

        # Trauma/stablisation duration (trauma only)
        self.trauma_dist = Exponential(g.trauma_mean,
                                       random_seed=self.run_number*g.random_number_set)

        # Non-trauma treatment
        self.nt_treat_dist = Lognormal(g.non_trauma_treat_mean,
                                       np.sqrt(g.non_trauma_treat_var),
                                       random_seed=self.run_number*g.random_number_set)

        # treatment of trauma patients
        self.treat_dist = Lognormal(g.trauma_treat_mean,
                                    np.sqrt(g.non_trauma_treat_var),
                                    random_seed=self.run_number*g.random_number_set)

        # probability of non-trauma patient requiring treatment
        self.nt_p_treat_dist = Bernoulli(g.non_trauma_treat_p,
                                         random_seed=self.run_number*g.random_number_set)

        # probability of non-trauma versus trauma patient
        self.p_trauma_dist = Bernoulli(g.prob_trauma,
                                       random_seed=self.run_number*g.random_number_set)

        # init sampling for non-stationary poisson process
        self.init_nspp()

    def init_nspp(self):

        # read arrival profile
        self.arrivals = pd.read_csv(g.arrival_df)  # pylint: disable=attribute-defined-outside-init
        self.arrivals['mean_iat'] = 60 / self.arrivals['arrival_rate']

        # maximum arrival rate (smallest time between arrivals)
        self.lambda_max = self.arrivals['arrival_rate'].max()  # pylint: disable=attribute-defined-outside-init

        # thinning exponential
        self.arrival_dist = Exponential(60.0 / self.lambda_max,  # pylint: disable=attribute-defined-outside-init
                                            random_seed=self.run_number*g.random_number_set)

        # thinning uniform rng
        self.thinning_rng = Uniform(low=0.0, high=1.0,  # pylint: disable=attribute-defined-outside-init
                                    random_seed=self.run_number*g.random_number_set)


    def init_resources(self):
        '''
        Init the number of resources
        and store in the arguments container object

        Resource list:
            1. Nurses/treatment bays (same thing in this model)

        '''
        # Shared Resources
        self.triage_cubicles = simpy.Store(self.env)
        populate_store(num_resources=g.n_triage,
                simpy_store=self.triage_cubicles,
                sim_env=self.env)

        self.registration_cubicles = simpy.Store(self.env)
        populate_store(num_resources=g.n_reg,
                       simpy_store=self.registration_cubicles,
                       sim_env=self.env)

        # Non-trauma
        self.exam_cubicles = simpy.Store(self.env)
        populate_store(num_resources=g.n_exam,
                       simpy_store=self.exam_cubicles,
                       sim_env=self.env)

        self.non_trauma_treatment_cubicles = simpy.Store(self.env)
        populate_store(num_resources=g.n_cubicles_non_trauma_treat,
                       simpy_store=self.non_trauma_treatment_cubicles,
                       sim_env=self.env)

        # Trauma
        self.trauma_stabilisation_bays = simpy.Store(self.env)
        populate_store(num_resources=g.n_trauma,
                       simpy_store=self.trauma_stabilisation_bays,
                       sim_env=self.env)

        self.trauma_treatment_cubicles = simpy.Store(self.env)
        populate_store(num_resources=g.n_cubicles_trauma_treat,
                       simpy_store=self.trauma_treatment_cubicles,
                       sim_env=self.env)

    # A generator function that represents the DES generator for patient
    # arrivals
    def generator_patient_arrivals(self):
        # We use an infinite loop here to keep doing this indefinitely whilst
        # the simulation runs
        while True:
            t = int(self.env.now // 60) % self.arrivals.shape[0]
            lambda_t = self.arrivals['arrival_rate'].iloc[t]

            # set to a large number so that at least 1 sample taken!
            u = np.Inf

            interarrival_time = 0.0
            # reject samples if u >= lambda_t / lambda_max
            while u >= (lambda_t / self.lambda_max):
                interarrival_time += self.arrival_dist.sample()
                u = self.thinning_rng.sample()

            # Freeze this instance of this function in place until the
            # inter-arrival time we sampled above has elapsed.  Note - time in
            # SimPy progresses in "Time Units", which can represent anything
            # you like (just make sure you're consistent within the model)
            yield self.env.timeout(interarrival_time)

            # Increment the patient counter by 1 (this means our first patient
            # will have an ID of 1)
            self.patient_counter += 1

            # Create a new patient - an instance of the Patient Class we
            # defined above.  Remember, we pass in the ID when creating a
            # patient - so here we pass the patient counter to use as the ID.
            p = Patient(self.patient_counter)

            trace(f'patient {self.patient_counter} arrives at: {self.env.now:.3f}')
            self.event_log.append(
                {'patient': self.patient_counter,
                 'pathway': 'Shared',
                 'event': 'arrival',
                 'event_type': 'arrival_departure',
                 'time': self.env.now}
            )

            # sample if the patient is trauma or non-trauma
            trauma = self.p_trauma_dist.sample()

            # Tell SimPy to start up the attend_clinic generator function with
            # this patient (the generator function that will model the
            # patient's journey through the system)
            # and store patient in list for later easy access
            if trauma:
                # create and store a trauma patient to update KPIs.
                self.trauma_patients.append(p)
                self.env.process(self.attend_trauma_pathway(p))

            else:
                # create and store a non-trauma patient to update KPIs.
                self.non_trauma_patients.append(p)
                self.env.process(self.attend_non_trauma_pathway(p))

    # A generator function that represents the pathway for a patient going
    # through the clinic.
    # The patient object is passed in to the generator function so we can
    # extract information from / record information to it
    def attend_non_trauma_pathway(self, patient):
        '''
        simulates the non-trauma/minor treatment process for a patient

        1. request and wait for sign-in/triage
        2. patient registration
        3. examination
        4a. percentage discharged
        4b. remaining percentage treatment then discharge
        '''
        # record the time of arrival and entered the triage queue
        patient.arrival = self.env.now
        self.event_log.append(
            {'patient': patient.identifier,
             'pathway': 'Non-Trauma',
             'event_type': 'queue',
             'event': 'triage_wait_begins',
             'time': self.env.now}
        )

        ###################################################
        # request sign-in/triage
        triage_resource = yield self.triage_cubicles.get()

        # record the waiting time for triage
        patient.wait_triage = self.env.now - patient.arrival
        trace(f'patient {patient.identifier} triaged to minors '
                f'{self.env.now:.3f}')
        self.event_log.append(
            {'patient': patient.identifier,
                'pathway': 'Non-Trauma',
                'event_type': 'resource_use',
                'event': 'triage_begins',
                'time': self.env.now,
                'resource_id': triage_resource.id_attribute
                }
        )

        # sample triage duration.
        patient.triage_duration = self.triage_dist.sample()
        yield self.env.timeout(patient.triage_duration)

        trace(f'triage {patient.identifier} complete {self.env.now:.3f}; '
                f'waiting time was {patient.wait_triage:.3f}')
        self.event_log.append(
            {'patient': patient.identifier,
                'pathway': 'Non-Trauma',
                'event_type': 'resource_use_end',
                'event': 'triage_complete',
                'time': self.env.now,
                'resource_id': triage_resource.id_attribute}
        )

        # Resource is no longer in use, so put it back in the store
        self.triage_cubicles.put(triage_resource)
        #########################################################

        # record the time that entered the registration queue
        start_wait = self.env.now
        self.event_log.append(
            {'patient': patient.identifier,
             'pathway': 'Non-Trauma',
             'event_type': 'queue',
             'event': 'MINORS_registration_wait_begins',
             'time': self.env.now}
        )

        #########################################################
        # request registration clerk
        registration_resource = yield self.registration_cubicles.get()

        # record the waiting time for registration
        patient.wait_reg = self.env.now - start_wait
        trace(f'registration of patient {patient.identifier} at '
                f'{self.env.now:.3f}')
        self.event_log.append(
            {'patient': patient.identifier,
                'pathway': 'Non-Trauma',
                'event_type': 'resource_use',
                'event': 'MINORS_registration_begins',
                'time': self.env.now,
                'resource_id': registration_resource.id_attribute
                }
        )

        # sample registration duration.
        patient.reg_duration = self.reg_dist.sample()
        yield self.env.timeout(patient.reg_duration)

        trace(f'patient {patient.identifier} registered at'
                f'{self.env.now:.3f}; '
                f'waiting time was {patient.wait_reg:.3f}')
        self.event_log.append(
            {'patient': patient.identifier,
                'pathway': 'Non-Trauma',
                'event': 'MINORS_registration_complete',
                'event_type': 'resource_use_end',
                'time': self.env.now,
                'resource_id': registration_resource.id_attribute}
        )
        # Resource is no longer in use, so put it back in the store
        self.registration_cubicles.put(registration_resource)
        ########################################################

        # record the time that entered the evaluation queue
        start_wait = self.env.now

        self.event_log.append(
            {'patient': patient.identifier,
             'pathway': 'Non-Trauma',
             'event': 'MINORS_examination_wait_begins',
             'event_type': 'queue',
             'time': self.env.now}
        )

        #########################################################
        # request examination resource
        examination_resource = yield self.exam_cubicles.get()

        # record the waiting time for examination to begin
        patient.wait_exam = self.env.now - start_wait
        trace(f'examination of patient {patient.identifier} begins '
                f'{self.env.now:.3f}')
        self.event_log.append(
            {'patient': patient.identifier,
                'pathway': 'Non-Trauma',
                'event': 'MINORS_examination_begins',
                'event_type': 'resource_use',
                'time': self.env.now,
                'resource_id': examination_resource.id_attribute
                }
        )

        # sample examination duration.
        patient.exam_duration = self.exam_dist.sample()
        yield self.env.timeout(patient.exam_duration)

        trace(f'patient {patient.identifier} examination complete '
                f'at {self.env.now:.3f};'
                f'waiting time was {patient.wait_exam:.3f}')
        self.event_log.append(
            {'patient': patient.identifier,
                'pathway': 'Non-Trauma',
                'event': 'MINORS_examination_complete',
                'event_type': 'resource_use_end',
                'time': self.env.now,
                'resource_id': examination_resource.id_attribute}
        )
        # Resource is no longer in use, so put it back in
        self.exam_cubicles.put(examination_resource)
        ############################################################################

        # sample if patient requires treatment?
        patient.require_treat = self.nt_p_treat_dist.sample()  #pylint: disable=attribute-defined-outside-init

        if patient.require_treat:

            self.event_log.append(
                {'patient': patient.identifier,
                 'pathway': 'Non-Trauma',
                 'event': 'requires_treatment',
                 'event_type': 'attribute_assigned',
                 'time': self.env.now}
            )

            # record the time that entered the treatment queue
            start_wait = self.env.now
            self.event_log.append(
                {'patient': patient.identifier,
                 'pathway': 'Non-Trauma',
                 'event': 'MINORS_treatment_wait_begins',
                 'event_type': 'queue',
                 'time': self.env.now}
            )
            ###################################################
            # request treatment cubicle

            non_trauma_treatment_resource = yield self.non_trauma_treatment_cubicles.get()

            # record the waiting time for treatment
            patient.wait_treat = self.env.now - start_wait
            trace(f'treatment of patient {patient.identifier} begins '
                    f'{self.env.now:.3f}')
            self.event_log.append(
                {'patient': patient.identifier,
                    'pathway': 'Non-Trauma',
                    'event': 'MINORS_treatment_begins',
                    'event_type': 'resource_use',
                    'time': self.env.now,
                    'resource_id': non_trauma_treatment_resource.id_attribute
                }
            )

            # sample treatment duration.
            patient.treat_duration = self.nt_treat_dist.sample()
            yield self.env.timeout(patient.treat_duration)

            trace(f'patient {patient.identifier} treatment complete '
                    f'at {self.env.now:.3f};'
                    f'waiting time was {patient.wait_treat:.3f}')
            self.event_log.append(
                {'patient': patient.identifier,
                    'pathway': 'Non-Trauma',
                    'event': 'MINORS_treatment_complete',
                    'event_type': 'resource_use_end',
                    'time': self.env.now,
                    'resource_id': non_trauma_treatment_resource.id_attribute}
            )

            # Resource is no longer in use, so put it back in the store
            self.non_trauma_treatment_cubicles.put(non_trauma_treatment_resource)
        ##########################################################################

        # Return to what happens to all patients, regardless of whether they were sampled as needing treatment
        self.event_log.append(
            {'patient': patient.identifier,
            'pathway': 'Shared',
            'event': 'depart',
            'event_type': 'arrival_departure',
            'time': self.env.now}
        )

        # total time in system
        patient.total_time = self.env.now - patient.arrival

    def attend_trauma_pathway(self, patient):
        '''
        simulates the major treatment process for a patient

        1. request and wait for sign-in/triage
        2. trauma
        3. treatment
        '''
        # record the time of arrival and entered the triage queue
        patient.arrival = self.env.now
        self.event_log.append(
            {'patient': patient.identifier,
             'pathway': 'Trauma',
             'event_type': 'queue',
             'event': 'triage_wait_begins',
             'time': self.env.now}
        )

        ###################################################
        # request sign-in/triage
        triage_resource = yield self.triage_cubicles.get()

        # record the waiting time for triage
        patient.wait_triage = self.env.now - patient.arrival

        trace(f'patient {patient.identifier} triaged to trauma '
                f'{self.env.now:.3f}')
        self.event_log.append(
            {'patient': patient.identifier,
             'pathway': 'Trauma',
             'event_type': 'resource_use',
             'event': 'triage_begins',
             'time': self.env.now,
             'resource_id': triage_resource.id_attribute
            }
        )

        # sample triage duration.
        patient.triage_duration = self.triage_dist.sample()
        yield self.env.timeout(patient.triage_duration)

        trace(f'triage {patient.identifier} complete {self.env.now:.3f}; '
              f'waiting time was {patient.wait_triage:.3f}')
        self.event_log.append(
            {'patient': patient.identifier,
             'pathway': 'Trauma',
             'event_type': 'resource_use_end',
             'event': 'triage_complete',
             'time': self.env.now,
             'resource_id': triage_resource.id_attribute}
        )

        # Resource is no longer in use, so put it back in the store
        self.triage_cubicles.put(triage_resource)
        ###################################################

        # record the time that entered the trauma queue
        start_wait = self.env.now
        self.event_log.append(
            {'patient': patient.identifier,
             'pathway': 'Trauma',
             'event_type': 'queue',
             'event': 'TRAUMA_stabilisation_wait_begins',
             'time': self.env.now}
        )

        ###################################################
        # request trauma room
        trauma_resource = yield self.trauma_stabilisation_bays.get()

        self.event_log.append(
            {'patient': patient.identifier,
                'pathway': 'Trauma',
                'event_type': 'resource_use',
                'event': 'TRAUMA_stabilisation_begins',
                'time': self.env.now,
                'resource_id': trauma_resource.id_attribute
                }
        )

        # record the waiting time for trauma
        patient.wait_trauma = self.env.now - start_wait

        # sample stablisation duration.
        patient.trauma_duration = self.trauma_dist.sample()
        yield self.env.timeout(patient.trauma_duration)

        trace(f'stabilisation of patient {patient.identifier} at '
              f'{self.env.now:.3f}')
        self.event_log.append(
            {'patient': patient.identifier,
             'pathway': 'Trauma',
             'event_type': 'resource_use_end',
             'event': 'TRAUMA_stabilisation_complete',
             'time': self.env.now,
             'resource_id': trauma_resource.id_attribute
            }
        )
        # Resource is no longer in use, so put it back in the store
        self.trauma_stabilisation_bays.put(trauma_resource)

        #######################################################

        # record the time that patient entered the treatment queue
        start_wait = self.env.now
        self.event_log.append(
            {'patient': patient.identifier,
             'pathway': 'Trauma',
             'event_type': 'queue',
             'event': 'TRAUMA_treatment_wait_begins',
             'time': self.env.now}
        )

        ########################################################
        # request treatment cubicle
        trauma_treatment_resource = yield self.trauma_treatment_cubicles.get()

        # record the waiting time for trauma
        patient.wait_treat = self.env.now - start_wait
        trace(f'treatment of patient {patient.identifier} at '
                f'{self.env.now:.3f}')
        self.event_log.append(
            {'patient': patient.identifier,
                'pathway': 'Trauma',
                'event_type': 'resource_use',
                'event': 'TRAUMA_treatment_begins',
                'time': self.env.now,
                'resource_id': trauma_treatment_resource.id_attribute
                }
        )

        # sample treatment duration.
        patient.treat_duration = self.trauma_dist.sample()
        yield self.env.timeout(patient.treat_duration)

        trace(f'patient {patient.identifier} treatment complete {self.env.now:.3f}; '
              f'waiting time was {patient.wait_treat:.3f}')
        self.event_log.append(
            {'patient': patient.identifier,
             'pathway': 'Trauma',
             'event_type': 'resource_use_end',
             'event': 'TRAUMA_treatment_complete',
             'time': self.env.now,
             'resource_id': trauma_treatment_resource.id_attribute}
        )
        self.event_log.append(
            {'patient': patient.identifier,
            'pathway': 'Shared',
            'event': 'depart',
            'event_type': 'arrival_departure',
            'time': self.env.now}
        )

        # Resource is no longer in use, so put it back in the store
        self.trauma_treatment_cubicles.put(trauma_treatment_resource)

        #########################################################

        # total time in system
        patient.total_time = self.env.now - patient.arrival


    # This method calculates results over a single run.  Here we just calculate
    # a mean, but in real world models you'd probably want to calculate more.
    def calculate_run_results(self):
        # Take the mean of the queuing times across patients in this run of the
        # model.
        self.mean_q_time_cubicle = self.results_df["Queue Time Cubicle"].mean()

    # The run method starts up the DES entity generators, runs the simulation,
    # and in turns calls anything we need to generate results for the run
    def run(self):
        # Start up our DES entity generators that create new patients.  We've
        # only got one in this model, but we'd need to do this for each one if
        # we had multiple generators.
        self.env.process(self.generator_patient_arrivals())

        # Run the model for the duration specified in g class
        self.env.run(until=g.sim_duration)

        # Now the simulation run has finished, call the method that calculates
        # run results
        self.calculate_run_results()

        self.event_log = pd.DataFrame(self.event_log)

        self.event_log["run"] = self.run_number

        return {'results': self.results_df, 'event_log': self.event_log}

# Class representing a Trial for our simulation - a batch of simulation runs.
class Trial:
    # The constructor sets up a pandas dataframe that will store the key
    # results from each run against run number, with run number as the index.
    def  __init__(self):
        self.df_trial_results = pd.DataFrame()
        self.df_trial_results["Run Number"] = [0]
        self.df_trial_results["Arrivals"] = [0]
        self.df_trial_results["Mean Queue Time Cubicle"] = [0.0]
        self.df_trial_results.set_index("Run Number", inplace=True)

        self.all_event_logs = []

    # Method to run a trial
    def run_trial(self):
        # Run the simulation for the number of runs specified in g class.
        # For each run, we create a new instance of the Model class and call its
        # run method, which sets everything else in motion.  Once the run has
        # completed, we grab out the stored run results (just mean queuing time
        # here) and store it against the run number in the trial results
        # dataframe.
        for run in range(g.number_of_runs):
            random.seed(run)

            my_model = Model(run)
            model_outputs = my_model.run()
            patient_level_results = model_outputs["results"]
            event_log = model_outputs["event_log"]

            self.df_trial_results.loc[run] = [
                len(patient_level_results),
                my_model.mean_q_time_cubicle,
            ]

            # print(event_log)

            self.all_event_logs.append(event_log)

        self.all_event_logs = pd.concat(self.all_event_logs)

my_trial = Trial()

my_trial.run_trial()

my_trial.all_event_logs.head(10)

	patient	pathway	event	event_type	time	resource_id	run
0	1	Shared	arrival	arrival_departure	3.285355	NaN	0
1	1	Non-Trauma	triage_wait_begins	queue	3.285355	NaN	0
2	1	Non-Trauma	triage_begins	resource_use	3.285355	1.0	0
3	2	Shared	arrival	arrival_departure	3.289691	NaN	0
4	2	Non-Trauma	triage_wait_begins	queue	3.289691	NaN	0
5	2	Non-Trauma	triage_begins	resource_use	3.289691	2.0	0
6	1	Non-Trauma	triage_complete	resource_use_end	7.364946	1.0	0
7	1	Non-Trauma	MINORS_registration_wait_begins	queue	7.364946	NaN	0
8	1	Non-Trauma	MINORS_registration_begins	resource_use	7.364946	1.0	0
9	2	Non-Trauma	triage_complete	resource_use_end	9.407274	2.0	0

my_trial.all_event_logs.event_type.value_counts()

event_type
queue                 2100
resource_use          2035
resource_use_end      2021
arrival_departure     1167
attribute_assigned     264
Name: count, dtype: int64

my_trial.all_event_logs.event.value_counts()

event
arrival                             623
triage_wait_begins                  623
triage_begins                       622
triage_complete                     620
depart                              544
MINORS_registration_wait_begins     539
MINORS_registration_begins          514
MINORS_registration_complete        512
MINORS_examination_wait_begins      512
MINORS_examination_begins           475
MINORS_examination_complete         472
requires_treatment                  264
MINORS_treatment_wait_begins        264
MINORS_treatment_begins             264
MINORS_treatment_complete           262
TRAUMA_stabilisation_wait_begins     81
TRAUMA_stabilisation_begins          81
TRAUMA_stabilisation_complete        81
TRAUMA_treatment_wait_begins         81
TRAUMA_treatment_begins              79
TRAUMA_treatment_complete            74
Name: count, dtype: int64

# First, identify all patients who have a 'depart' event
# patients_with_depart = my_trial.all_event_logs[my_trial.all_event_logs['event'].str.contains('depart')]['patient'].unique()

# Then filter the original DataFrame to only include those patients
# filtered_df = my_trial.all_event_logs[my_trial.all_event_logs['patient'].isin(patients_with_depart)]

logs_transformed = my_trial.all_event_logs[~my_trial.all_event_logs['event'].str.contains('wait')].copy()
# logs_transformed = filtered_df[~filtered_df['event'].str.contains('wait')].copy()
logs_transformed = logs_transformed[logs_transformed['event_type'].isin(['resource_use', 'resource_use_end'])].copy()
logs_transformed['event_stage'] = logs_transformed['event_type'].apply(lambda x: 'complete' if 'end' in x else 'start')
logs_transformed['event_name'] = logs_transformed['event'].str.replace('_begins|_complete', '', regex=True)
logs_transformed['resource_id_full'] = logs_transformed.apply(lambda x: f"{x['event_name']}_{x['resource_id']:.0f}", axis=1)
logs_transformed = logs_transformed.sort_values(['run', 'time'], ascending=True)
# logs_transformed["activity_id"] = (
#     logs_transformed.groupby(["run", "patient", "event_name"]).ngroup() + 1
# )

# logs_transformed = logs_transformed.sort_values(["run", "patient", "activity_id", "event_stage"], ascending=[True, True, True, False])

# Sort the data by run, patient, time, and event_name to handle tied start times
logs_transformed = logs_transformed.sort_values(["run", "patient", "time", "event_name"])

# Get the first occurrence of each activity (the start event)
first_occurrences = (
    logs_transformed[logs_transformed["event_stage"] == "start"]
    .drop_duplicates(["run", "patient", "event_name"])
    .copy()
)

# Sort by time within each run to determine the proper sequence
first_occurrences = first_occurrences.sort_values(["run", "time", "event_name"])

# Assign sequential activity_id within each run
first_occurrences["activity_id"] = first_occurrences.groupby("run").cumcount() + 1

# Merge the activity_id back to the main DataFrame
logs_transformed = logs_transformed.merge(
    first_occurrences[["run", "patient", "event_name", "activity_id"]],
    on=["run", "patient", "event_name"],
    how="left"
)

# Sort for final ordering
logs_transformed = logs_transformed.sort_values(
    ["run", "patient", "activity_id", "event_stage"],
    ascending=[True, True, True, False]
)
logs_transformed.head(50)

	patient	pathway	event	event_type	time	resource_id	run	event_stage	event_name	resource_id_full	activity_id
0	1	Non-Trauma	triage_begins	resource_use	3.285355	1.0	0	start	triage	triage_1	1
2	1	Non-Trauma	triage_complete	resource_use_end	7.364946	1.0	0	complete	triage	triage_1	1
1	1	Non-Trauma	MINORS_registration_begins	resource_use	7.364946	1.0	0	start	MINORS_registration	MINORS_registration_1	3
4	1	Non-Trauma	MINORS_registration_complete	resource_use_end	15.418481	1.0	0	complete	MINORS_registration	MINORS_registration_1	3
3	1	Non-Trauma	MINORS_examination_begins	resource_use	15.418481	1.0	0	start	MINORS_examination	MINORS_examination_1	5
5	1	Non-Trauma	MINORS_examination_complete	resource_use_end	31.636252	1.0	0	complete	MINORS_examination	MINORS_examination_1	5
6	2	Non-Trauma	triage_begins	resource_use	3.289691	2.0	0	start	triage	triage_2	2
8	2	Non-Trauma	triage_complete	resource_use_end	9.407274	2.0	0	complete	triage	triage_2	2
7	2	Non-Trauma	MINORS_registration_begins	resource_use	9.407274	2.0	0	start	MINORS_registration	MINORS_registration_2	4
10	2	Non-Trauma	MINORS_registration_complete	resource_use_end	17.104670	2.0	0	complete	MINORS_registration	MINORS_registration_2	4
9	2	Non-Trauma	MINORS_examination_begins	resource_use	17.104670	2.0	0	start	MINORS_examination	MINORS_examination_2	6
11	2	Non-Trauma	MINORS_examination_complete	resource_use_end	32.875857	2.0	0	complete	MINORS_examination	MINORS_examination_2	6
12	2	Non-Trauma	MINORS_treatment_begins	resource_use	32.875857	1.0	0	start	MINORS_treatment	MINORS_treatment_1	7
13	2	Non-Trauma	MINORS_treatment_complete	resource_use_end	46.278797	1.0	0	complete	MINORS_treatment	MINORS_treatment_1	7
14	3	Non-Trauma	triage_begins	resource_use	33.426168	1.0	0	start	triage	triage_1	8
16	3	Non-Trauma	triage_complete	resource_use_end	33.545008	1.0	0	complete	triage	triage_1	8
15	3	Non-Trauma	MINORS_registration_begins	resource_use	33.545008	1.0	0	start	MINORS_registration	MINORS_registration_1	9
18	3	Non-Trauma	MINORS_registration_complete	resource_use_end	42.359504	1.0	0	complete	MINORS_registration	MINORS_registration_1	9
17	3	Non-Trauma	MINORS_examination_begins	resource_use	42.359504	3.0	0	start	MINORS_examination	MINORS_examination_3	12
19	3	Non-Trauma	MINORS_examination_complete	resource_use_end	59.468749	3.0	0	complete	MINORS_examination	MINORS_examination_3	12
20	3	Non-Trauma	MINORS_treatment_begins	resource_use	59.468749	2.0	0	start	MINORS_treatment	MINORS_treatment_2	16
21	3	Non-Trauma	MINORS_treatment_complete	resource_use_end	72.510229	2.0	0	complete	MINORS_treatment	MINORS_treatment_2	16
22	4	Non-Trauma	triage_begins	resource_use	37.900548	2.0	0	start	triage	triage_2	10
24	4	Non-Trauma	triage_complete	resource_use_end	37.914164	2.0	0	complete	triage	triage_2	10
23	4	Non-Trauma	MINORS_registration_begins	resource_use	37.914164	2.0	0	start	MINORS_registration	MINORS_registration_2	11
26	4	Non-Trauma	MINORS_registration_complete	resource_use_end	45.938325	2.0	0	complete	MINORS_registration	MINORS_registration_2	11
25	4	Non-Trauma	MINORS_examination_begins	resource_use	45.938325	1.0	0	start	MINORS_examination	MINORS_examination_1	13
27	4	Non-Trauma	MINORS_examination_complete	resource_use_end	62.120017	1.0	0	complete	MINORS_examination	MINORS_examination_1	13
28	4	Non-Trauma	MINORS_treatment_begins	resource_use	62.120017	3.0	0	start	MINORS_treatment	MINORS_treatment_3	17
29	4	Non-Trauma	MINORS_treatment_complete	resource_use_end	76.274743	3.0	0	complete	MINORS_treatment	MINORS_treatment_3	17
30	5	Non-Trauma	triage_begins	resource_use	51.770459	1.0	0	start	triage	triage_1	14
32	5	Non-Trauma	triage_complete	resource_use_end	55.072516	1.0	0	complete	triage	triage_1	14
31	5	Non-Trauma	MINORS_registration_begins	resource_use	55.072516	1.0	0	start	MINORS_registration	MINORS_registration_1	15
34	5	Non-Trauma	MINORS_registration_complete	resource_use_end	62.243834	1.0	0	complete	MINORS_registration	MINORS_registration_1	15
33	5	Non-Trauma	MINORS_examination_begins	resource_use	62.243834	2.0	0	start	MINORS_examination	MINORS_examination_2	18
35	5	Non-Trauma	MINORS_examination_complete	resource_use_end	77.316027	2.0	0	complete	MINORS_examination	MINORS_examination_2	18
36	6	Trauma	triage_begins	resource_use	113.767200	2.0	0	start	triage	triage_2	19
38	6	Trauma	triage_complete	resource_use_end	123.546842	2.0	0	complete	triage	triage_2	19
37	6	Trauma	TRAUMA_stabilisation_begins	resource_use	123.546842	1.0	0	start	TRAUMA_stabilisation	TRAUMA_stabilisation_1	21
39	6	Trauma	TRAUMA_stabilisation_complete	resource_use_end	184.740714	1.0	0	complete	TRAUMA_stabilisation	TRAUMA_stabilisation_1	21
40	6	Trauma	TRAUMA_treatment_begins	resource_use	184.740714	1.0	0	start	TRAUMA_treatment	TRAUMA_treatment_1	37
41	6	Trauma	TRAUMA_treatment_complete	resource_use_end	186.523313	1.0	0	complete	TRAUMA_treatment	TRAUMA_treatment_1	37
42	7	Non-Trauma	triage_begins	resource_use	123.044756	1.0	0	start	triage	triage_1	20
44	7	Non-Trauma	triage_complete	resource_use_end	127.086253	1.0	0	complete	triage	triage_1	20
43	7	Non-Trauma	MINORS_registration_begins	resource_use	127.086253	2.0	0	start	MINORS_registration	MINORS_registration_2	23
46	7	Non-Trauma	MINORS_registration_complete	resource_use_end	135.479993	2.0	0	complete	MINORS_registration	MINORS_registration_2	23
45	7	Non-Trauma	MINORS_examination_begins	resource_use	135.479993	3.0	0	start	MINORS_examination	MINORS_examination_3	27
47	7	Non-Trauma	MINORS_examination_complete	resource_use_end	152.106294	3.0	0	complete	MINORS_examination	MINORS_examination_3	27
48	8	Non-Trauma	triage_begins	resource_use	124.735469	2.0	0	start	triage	triage_2	22
50	8	Non-Trauma	triage_complete	resource_use_end	129.267277	2.0	0	complete	triage	triage_2	22

logs_transformed[(logs_transformed["run"]==1) & (logs_transformed["activity_id"]==26)]

	patient	pathway	event	event_type	time	resource_id	run	event_stage	event_name	resource_id_full	activity_id

logs_transformed[logs_transformed["activity_id"]==26].sort_values('run').head(30)

	patient	pathway	event	event_type	time	resource_id	run	event_stage	event_name	resource_id_full	activity_id
60	10	Trauma	triage_begins	resource_use	129.468902	2.0	0	start	triage	triage_2	26
62	10	Trauma	triage_complete	resource_use_end	165.815421	2.0	0	complete	triage	triage_2	26

logs_transformed.sort_values('activity_id').head(20)

	patient	pathway	event	event_type	time	resource_id	run	event_stage	event_name	resource_id_full	activity_id
0	1	Non-Trauma	triage_begins	resource_use	3.285355	1.0	0	start	triage	triage_1	1
2	1	Non-Trauma	triage_complete	resource_use_end	7.364946	1.0	0	complete	triage	triage_1	1
6	2	Non-Trauma	triage_begins	resource_use	3.289691	2.0	0	start	triage	triage_2	2
8	2	Non-Trauma	triage_complete	resource_use_end	9.407274	2.0	0	complete	triage	triage_2	2
1	1	Non-Trauma	MINORS_registration_begins	resource_use	7.364946	1.0	0	start	MINORS_registration	MINORS_registration_1	3
4	1	Non-Trauma	MINORS_registration_complete	resource_use_end	15.418481	1.0	0	complete	MINORS_registration	MINORS_registration_1	3
7	2	Non-Trauma	MINORS_registration_begins	resource_use	9.407274	2.0	0	start	MINORS_registration	MINORS_registration_2	4
10	2	Non-Trauma	MINORS_registration_complete	resource_use_end	17.104670	2.0	0	complete	MINORS_registration	MINORS_registration_2	4
3	1	Non-Trauma	MINORS_examination_begins	resource_use	15.418481	1.0	0	start	MINORS_examination	MINORS_examination_1	5
5	1	Non-Trauma	MINORS_examination_complete	resource_use_end	31.636252	1.0	0	complete	MINORS_examination	MINORS_examination_1	5
11	2	Non-Trauma	MINORS_examination_complete	resource_use_end	32.875857	2.0	0	complete	MINORS_examination	MINORS_examination_2	6
9	2	Non-Trauma	MINORS_examination_begins	resource_use	17.104670	2.0	0	start	MINORS_examination	MINORS_examination_2	6
12	2	Non-Trauma	MINORS_treatment_begins	resource_use	32.875857	1.0	0	start	MINORS_treatment	MINORS_treatment_1	7
13	2	Non-Trauma	MINORS_treatment_complete	resource_use_end	46.278797	1.0	0	complete	MINORS_treatment	MINORS_treatment_1	7
14	3	Non-Trauma	triage_begins	resource_use	33.426168	1.0	0	start	triage	triage_1	8
16	3	Non-Trauma	triage_complete	resource_use_end	33.545008	1.0	0	complete	triage	triage_1	8
15	3	Non-Trauma	MINORS_registration_begins	resource_use	33.545008	1.0	0	start	MINORS_registration	MINORS_registration_1	9
18	3	Non-Trauma	MINORS_registration_complete	resource_use_end	42.359504	1.0	0	complete	MINORS_registration	MINORS_registration_1	9
24	4	Non-Trauma	triage_complete	resource_use_end	37.914164	2.0	0	complete	triage	triage_2	10
22	4	Non-Trauma	triage_begins	resource_use	37.900548	2.0	0	start	triage	triage_2	10

logs_transformed[["event_name", "event_stage", "event_type"]].value_counts()

event_name            event_stage  event_type      
triage                start        resource_use        622
                      complete     resource_use_end    620
MINORS_registration   start        resource_use        514
                      complete     resource_use_end    512
MINORS_examination    start        resource_use        475
                      complete     resource_use_end    472
MINORS_treatment      start        resource_use        264
                      complete     resource_use_end    262
TRAUMA_stabilisation  complete     resource_use_end     81
                      start        resource_use         81
TRAUMA_treatment      start        resource_use         79
                      complete     resource_use_end     74
Name: count, dtype: int64

event
triage_begins                    622
triage_complete                  620
MINORS_registration_begins       514
MINORS_registration_complete     512
MINORS_examination_begins        475
MINORS_examination_complete      472
MINORS_treatment_begins          264
MINORS_treatment_complete        262
TRAUMA_stabilisation_begins       81
TRAUMA_stabilisation_complete     81
TRAUMA_treatment_begins           79
TRAUMA_treatment_complete         74
Name: count, dtype: int64

For ease, now let’s save these results as a file that we can load into R.

We could use a csv for easy interoperability. Alternatively, we could use something like Feather or Parquet, which are usable by both R and Python while retaining data types.

For ease of use and long-term readbility, we will use csv in this case.

Source: View Imported Code, which has had logging steps added at the appropriate points in the 'model' class

Now, it’s time to move to R (as bupaR and the bupaverse is only implemented in R).

pm4py exists as a process analytics package for Python, but the visuals of bupaR are of a high quality.

Importing the required R functions and our data

library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

library(readr)
library(bupaverse)

Warning: package 'bupaverse' was built under R version 4.3.3

.______    __    __  .______      ___   ____    ____  _______ .______          _______. _______
|   _  \  |  |  |  | |   _  \    /   \  \   \  /   / |   ____||   _  \        /       ||   ____|
|  |_)  | |  |  |  | |  |_)  |  /  ^  \  \   \/   /  |  |__   |  |_)  |      |   (----`|  |__
|   _  <  |  |  |  | |   ___/  /  /_\  \  \      /   |   __|  |      /        \   \    |   __|
|  |_)  | |  `--'  | |  |     /  _____  \  \    /    |  |____ |  |\  \----.----)   |   |  |____
|______/   \______/  | _|    /__/     \__\  \__/     |_______|| _| `._____|_______/    |_______|
                                                                                                

── Attaching packages ─────────────────────────────────────── bupaverse 0.1.0 ──
✔ bupaR         0.5.4     ✔ processcheckR 0.1.4
✔ edeaR         0.9.4     ✔ processmapR   0.5.6
✔ eventdataR    0.3.1     

Warning: package 'bupaR' was built under R version 4.3.3

Warning: package 'processcheckR' was built under R version 4.3.3

── Conflicts ────────────────────────────────────────── bupaverse_conflicts() ──
✖ processcheckR::contains() masks dplyr::contains()
✖ bupaR::filter()           masks dplyr::filter(), stats::filter()
✖ processmapR::frequency()  masks stats::frequency()
✖ edeaR::setdiff()          masks dplyr::setdiff(), base::setdiff()
✖ bupaR::timestamp()        masks utils::timestamp()
✖ processcheckR::xor()      masks base::xor()

library(processanimateR)

Warning: package 'processanimateR' was built under R version 4.3.3

library(lubridate)

Attaching package: 'lubridate'

The following objects are masked from 'package:base':

    date, intersect, setdiff, union

library(DT)

Warning: package 'DT' was built under R version 4.3.3

library(psmineR)

Warning: package 'psmineR' was built under R version 4.3.3

data <- readr::read_csv("simulation_logs_for_bupar.csv")

Rows: 4056 Columns: 11
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (6): pathway, event, event_type, event_stage, event_name, resource_id_full
dbl (5): patient, time, resource_id, run, activity_id

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

data %>% head()

# A tibble: 6 × 11
  patient pathway    event        event_type  time resource_id   run event_stage
    <dbl> <chr>      <chr>        <chr>      <dbl>       <dbl> <dbl> <chr>      
1       1 Non-Trauma triage_begi… resource_…  3.29           1     0 start      
2       1 Non-Trauma triage_comp… resource_…  7.36           1     0 complete   
3       1 Non-Trauma MINORS_regi… resource_…  7.36           1     0 start      
4       1 Non-Trauma MINORS_regi… resource_… 15.4            1     0 complete   
5       1 Non-Trauma MINORS_exam… resource_… 15.4            1     0 start      
6       1 Non-Trauma MINORS_exam… resource_… 31.6            1     0 complete   
# ℹ 3 more variables: event_name <chr>, resource_id_full <chr>,
#   activity_id <dbl>

Ensuring our data has the required time columns and is only for a single run

data_processed <- data %>%
    dplyr::filter(run == 0) %>%
    dplyr::rename(minutes_after_origin=time) %>%
    # We provide a theoretical date to act as a starting point - the date does not have to be
    # a true representation of the actual simulation, though you may wish it to be if there
    # are date elements in your simulation (e.g. within-week or within-year seasonality)
    dplyr::mutate(time = as.POSIXct("2024-01-01 00:00:00", tz = "UTC") + lubridate::dminutes(minutes_after_origin)) %>%
    bupaR::convert_timestamps("time", ymd_hms) %>%
    dplyr::mutate(patient = as.factor(patient))

DT::datatable(data_processed)

Converting to the activitylog format

activity_log <- data_processed  %>%
    bupaR::eventlog(
        case_id = "patient",
        activity_id = "event_name",
        activity_instance_id = "activity_id",
        lifecycle_id = "event_stage",
        timestamp = "time",
        resource_id = "resource_id_full"
        )

## !!!! Note that the bupaR documentation recommmends using the
## to_activitylog() function at the end of this set of steps.
## This caused significant errors in testing of this code, so
## I would not recommend following this recommendation, and instead
## you can mimic the above

activity_log

# Log of 4056 events consisting of:
6 traces 
622 cases 
2035 instances of 6 activities 
20 resources 
Events occurred from 2024-01-01 00:03:17 until 2024-01-03 01:58:40 
 
# Variables were mapped as follows:
Case identifier:        patient 
Activity identifier:        event_name 
Resource identifier:        resource_id_full 
Activity instance identifier:   activity_id 
Timestamp:          time 
Lifecycle transition:       event_stage 

# A tibble: 4,056 × 13
   patient pathway    event    event_type minutes_after_origin resource_id   run
   <fct>   <chr>      <chr>    <chr>                     <dbl>       <dbl> <dbl>
 1 1       Non-Trauma triage_… resource_…                 3.29           1     0
 2 1       Non-Trauma triage_… resource_…                 7.36           1     0
 3 1       Non-Trauma MINORS_… resource_…                 7.36           1     0
 4 1       Non-Trauma MINORS_… resource_…                15.4            1     0
 5 1       Non-Trauma MINORS_… resource_…                15.4            1     0
 6 1       Non-Trauma MINORS_… resource_…                31.6            1     0
 7 2       Non-Trauma triage_… resource_…                 3.29           2     0
 8 2       Non-Trauma triage_… resource_…                 9.41           2     0
 9 2       Non-Trauma MINORS_… resource_…                 9.41           2     0
10 2       Non-Trauma MINORS_… resource_…                17.1            2     0
# ℹ 4,046 more rows
# ℹ 6 more variables: event_stage <chr>, event_name <chr>,
#   resource_id_full <chr>, activity_id <dbl>, time <dttm>, .order <int>

Creating outputs

Process Maps

Absolute frequencies

activity_log %>%
    process_map(frequency("absolute"))

activity_log %>%
    process_map(frequency("absolute-case"))

Relative frequencies

activity_log %>%
    process_map(frequency("relative"))

activity_log %>%
    process_map(frequency("relative-case"),
              render_options = list(edge_label_color = "white"))

activity_log %>%
    process_map(frequency("relative-consequent"),
              render_options = list(edge_label_color = "white"))

Performance Maps

Mean Waits

activity_log %>%
    process_map(performance())

Max Waits

activity_log %>%
    process_map(performance(FUN = max))

Warning: There was 1 warning in `summarize()`.
ℹ In argument: `label = do.call(...)`.
ℹ In group 9: `ACTIVITY_CLASSIFIER_ = NA` and `from_id = NA`.
Caused by warning in `type()`:
! no non-missing arguments to max; returning -Inf

Warning: There were 2 warnings in `summarize()`.
The first warning was:
ℹ In argument: `value = do.call(...)`.
ℹ In group 1: `ACTIVITY_CLASSIFIER_ = "ARTIFICIAL_END"`, `next_act = NA`,
  `from_id = 1`, `to_id = NA`.
Caused by warning in `type()`:
! no non-missing arguments to max; returning -Inf
ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning.

90th percentile

p90 <- function(x, ...) {
    quantile(x, probs = 0.9, ...)
}

activity_log %>%
    process_map(performance(FUN = p90))

Analytics

Take a look at this page in the bupaR docs details of each of these plots.

Idle Time

activity_log %>%
    idle_time("resource", units = "mins")

# A tibble: 20 × 2
   resource_id_full       idle_time     
   <chr>                  <drtn>        
 1 MINORS_treatment_1     2101.6612 mins
 2 MINORS_treatment_2     2065.5869 mins
 3 MINORS_treatment_3     2043.3483 mins
 4 MINORS_treatment_4     1945.5681 mins
 5 TRAUMA_treatment_1     1415.3914 mins
 6 TRAUMA_treatment_2     1275.9829 mins
 7 TRAUMA_treatment_3     1208.0795 mins
 8 TRAUMA_treatment_5     1098.2404 mins
 9 triage_2               1043.9654 mins
10 triage_1                999.9198 mins
11 TRAUMA_treatment_4      959.1452 mins
12 MINORS_registration_2   951.0949 mins
13 MINORS_registration_1   943.0261 mins
14 TRAUMA_stabilisation_1  881.6663 mins
15 TRAUMA_stabilisation_2  714.7071 mins
16 TRAUMA_stabilisation_3  691.9842 mins
17 TRAUMA_stabilisation_4  564.1900 mins
18 MINORS_examination_2    469.1167 mins
19 MINORS_examination_1    463.9669 mins
20 MINORS_examination_3    441.1148 mins

activity_log %>%
    idle_time("resource", units = "mins") %>%
    plot()

Processing Time

activity_log %>%
    processing_time("log", units = "mins") %>%
    plot()

activity_log %>%
    processing_time("case", units = "mins") %>%
    plot()

activity_log %>%
    processing_time("activity", units = "mins") %>%
    plot()

activity_log %>%
    processing_time("resource-activity", units = "mins") %>%
    plot()

Throughput time

activity_log %>%
    throughput_time("log", units = "mins") %>%
    plot()

Activity Presence

activity_log %>%
    activity_presence() %>%
    plot()

Resource visualisations

Handover-of-work network

activity_log %>%
    resource_map()

Resource precedence matrix

activity_log %>%
    resource_matrix() %>%
    plot()

Process matrix

activity_log %>%
    process_matrix(frequency("absolute")) %>%
    plot()

Trace Explorer

This plot helps us to unerstand how often different combinations of activities occur, and whether there are any unexpected paths in our data.

activity_log %>%
    trace_explorer(n_traces = 10)

Warning: Fewer traces (6) found than specified `n_traces` (10).

Animated process map

activity_log %>%
    animate_process()

Let’s compare directly with our vidigi output.

Tip

The key difference between what is produced via bupaverse’s animate_process and what can be created via vidigi is the ability of vidigi to more clearly show the scale of queues, and the number of resources available at any given point.

Vidigi can also more clearly highlight the impact of priority on resources through the use of distinct icons, though this is not demonstrated in this example.

Click here to expand vidigi animation generation code

from examples.example_2_branching_multistep.ex_2_model_classes import Trial, g
from vidigi.animation import animate_activity_log
import pandas as pd
import plotly.io as pio
#pio.renderers.default = "notebook"
pio.renderers.default = "iframe"

g.sim_duration = 3000
g.number_of_runs = 3

my_trial = Trial()

my_trial.run_trial()

event_position_df = pd.DataFrame([
                # {'event': 'arrival', 'x':  10, 'y': 250, 'label': "Arrival" },

                # Triage - minor and trauma
                {'event': 'triage_wait_begins',
                 'x':  160, 'y': 375, 'label': "Waiting for<br>Triage"  },
                {'event': 'triage_begins',
                 'x':  160, 'y': 315, 'resource':'n_triage', 'label': "Being Triaged" },

                # Minors (non-trauma) pathway
                {'event': 'MINORS_registration_wait_begins',
                 'x':  300, 'y': 145, 'label': "Waiting for<br>Registration"  },
                {'event': 'MINORS_registration_begins',
                 'x':  300, 'y': 85, 'resource':'n_reg', 'label':'Being<br>Registered'  },

                {'event': 'MINORS_examination_wait_begins',
                 'x':  465, 'y': 145, 'label': "Waiting for<br>Examination"  },
                {'event': 'MINORS_examination_begins',
                 'x':  465, 'y': 85, 'resource':'n_exam', 'label': "Being<br>Examined" },

                {'event': 'MINORS_treatment_wait_begins',
                 'x':  630, 'y': 145, 'label': "Waiting for<br>Treatment"  },
                {'event': 'MINORS_treatment_begins',
                 'x':  630, 'y': 85, 'resource':'n_cubicles_non_trauma_treat', 'label': "Being<br>Treated" },

                # Trauma pathway
                {'event': 'TRAUMA_stabilisation_wait_begins',
                 'x': 300, 'y': 560, 'label': "Waiting for<br>Stabilisation" },
                {'event': 'TRAUMA_stabilisation_begins',
                 'x': 300, 'y': 490, 'resource':'n_trauma', 'label': "Being<br>Stabilised" },

                {'event': 'TRAUMA_treatment_wait_begins',
                 'x': 630, 'y': 560, 'label': "Waiting for<br>Treatment" },
                {'event': 'TRAUMA_treatment_begins',
                 'x': 630, 'y': 490, 'resource':'n_cubicles_trauma_treat', 'label': "Being<br>Treated" },

                 {'event': 'exit',
                 'x':  670, 'y': 330, 'label': "Exit"}
            ])

animate_activity_log(
        event_log=my_trial.all_event_logs[my_trial.all_event_logs['run']==0],
        event_position_df=event_position_df,
        scenario=g(),
        debug_mode=False,
        setup_mode=False,
        every_x_time_units=5,
        include_play_button=True,
        gap_between_entities=10,
        gap_between_rows=20,
        plotly_height=900,
        plotly_width=1600,
        override_x_max=700,
        override_y_max=675,
        icon_and_text_size=20,
        wrap_queues_at=10,
        step_snapshot_max=50,
        limit_duration=3000,
        time_display_units="dhm",
        display_stage_labels=False,
        add_background_image="https://raw.githubusercontent.com/Bergam0t/vidigi/refs/heads/main/examples/example_2_branching_multistep/Full%20Model%20Background%20Image%20-%20Horizontal%20Layout.drawio.png",
    )

Other chart types

Dotted chart

We can see the impact of the pattern of daily arrivals across the course of the model, with the waits clearing out overnight when arrivals slow down.

activity_log %>%
    dotted_chart(x = "absolute")

activity_log %>%
    dotted_chart(x = "relative", sort="start")

Breaking down dotted charts by route

Minors

activity_log %>%
    filter(event_name %in% c('MINORS_examination', 'MINORS_registration', 'MINORS_treatment', 'triage')) %>%
    dotted_chart(x = "absolute")

activity_log %>%
    filter(event_name %in% c('MINORS_examination', 'MINORS_registration', 'MINORS_treatment', 'triage')) %>%
    dotted_chart(x = "relative", sort="start")

Trauma

activity_log %>%
    filter(event_name %in% c('TRAUMA_stabilisation', 'TRAUMA_treatment', 'triage')) %>%
    dotted_chart(x = "absolute")

activity_log %>%
    filter(event_name %in% c('TRAUMA_stabilisation', 'TRAUMA_treatment', 'triage')) %>%
    dotted_chart(x = "relative", sort="start")

Conclusion

vidigi and bupaR are complementary packages to use when visualising, verifying and validating your simulation models - or working with real-world process data.