tlo.methods.cervical_cancer module ================================== .. automodule:: tlo.methods.cervical_cancer .. autoclass:: CervicalCancer Bases: :class:`tlo.core.Module`, :class:`tlo.methods.hsi_generic_first_appts.GenericFirstAppointmentsMixin` **PARAMETERS:** .. list-table:: :widths: 25 25 50 :header-rows: 1 * - Item - Type - Description * - init_prev_cin_hpv_cc_stage_hiv - LIST - initial proportions in hpv cancer categories in women with hiv * - init_prev_cin_hpv_cc_stage_nhiv - LIST - initial proportions in hpv cancer categories in women without hiv * - r_hpv - REAL - probability per month of oncogenic hpv infection * - r_cin1_hpv - REAL - probability per month of incident cin1 amongst people with hpv * - prob_revert_from_cin1 - REAL - probability of reverting from cin1 to none * - r_cin2_cin1 - REAL - probability per month of incident cin2 amongst people with cin1 * - r_cin3_cin2 - REAL - probability per month of incident cin3 amongst people with cin2 * - r_stage1_cin3 - REAL - probability per month of incident stage1 cervical cancer amongst people with cin3 * - r_stage2a_stage1 - REAL - probability per month of incident stage2a cervical cancer amongst people with stage1 * - r_stage2b_stage2a - REAL - probability per month of incident stage2b cervical cancer amongst people with stage2a * - r_stage3_stage2b - REAL - probability per month of incident stage3 cervical cancer amongst people with stage2b * - r_stage4_stage3 - REAL - probability per month of incident stage4 cervical cancer amongst people with stage3 * - rr_progress_cc_hiv - REAL - risk ratio for progressing through cin and cervical cancer stages if have unsuppressed hiv * - rr_hpv_vaccinated - REAL - risk ratio for hpv if vaccinated - this is combined effect of probability the hpv is vaccine-preventable and vaccine efficacy against vaccine-preventable hpv * - rr_hpv_age50plus - REAL - risk ratio for hpv if age 50 plus * - prob_cure_stage1 - REAL - probability of cure if treated in stage 1 cervical cancer * - prob_cure_stage2a - REAL - probability of cure if treated in stage 2a cervical cancer * - prob_cure_stage2b - REAL - probability of cure if treated in stage 2b cervical cancer * - prob_cure_stage3 - REAL - probability of cure if treated in stage 3 cervical cancer * - r_death_cervical_cancer - REAL - probability per month of death from cervical cancer amongst people with stage 4 cervical cancer * - p_vaginal_bleeding_if_no_cc - REAL - Probability of vaginal bleeding onset if not in stage 1/2/3/4 * - r_vaginal_bleeding_cc_stage1 - REAL - probability of vaginal bleeding if have stage 1 cervical cancer * - rr_vaginal_bleeding_cc_stage2a - REAL - risk ratio for vaginal bleeding if have stage 2a cervical cancer * - rr_vaginal_bleeding_cc_stage2b - REAL - risk ratio for vaginal bleeding if have stage 2b cervical cancer * - rr_vaginal_bleeding_cc_stage3 - REAL - risk ratio for vaginal bleeding if have stage 3 cervical cancer * - rr_vaginal_bleeding_cc_stage4 - REAL - risk ratio for vaginal bleeding if have stage 4 cervical cancer * - prob_referral_biopsy_given_vaginal_bleeding - REAL - probability of being referred for a biopsy if presenting with vaginal bleeding * - sensitivity_of_biopsy_for_cervical_cancer - REAL - sensitivity of biopsy for diagnosis of cervical cancer * - sensitivity_of_xpert_for_hpv_cin_cc - REAL - sensitivity of xpert for presence of hpv, cin or cervical cancer * - sensitivity_of_via_for_cin_cc - REAL - sensitivity of via for cin and cervical cancer * - prob_xpert_screen - REAL - probability of xpert screening * - prob_via_screen - REAL - probability of via screening * - prob_thermoabl_successful - REAL - probability of thermoablation treatment successful in removing CIN (ce_hpv_cc_status set to none) * - prob_cryotherapy_successful - REAL - probability of cryotherapy treatment successful in removing CIN (ce_hpv_cc_status set to none) * - transition_screening_method_year - REAL - year screening method switches from VIA to Xpert * - transition_to_thermo_year - REAL - year CIN removal method switches from Cryo to Thermo * - screening_min_age_hv_neg - REAL - minimum age individual to be screened if HIV negative * - screening_max_age_hv_neg - REAL - maximum age individual to be screened if HIV negative * - screening_min_age_hv_pos - REAL - minimum age individual to be screened if HIV positive * - screening_max_age_hv_pos - REAL - maximum age individual to be screened if HIV positive * - yrs_between_screen_hv_pos - REAL - minimum years between screening if HIV positive * - yrs_between_screen_hv_neg - REAL - minimum years between screening if HIV negative * - palliative_care_bed_days - REAL - palliative_care_bed_days * - stage_1_3_daly_wt - REAL - GBD sequalae code corresponding to stage_1_3_daly_wt * - stage_1_3_treated_daly_wt - REAL - GBD sequalae code corresponding to stage_1_3_treated_daly_wt * - stage4_daly_wt - REAL - GBD sequalae code corresponding tostage4_daly_wt * - min_yrs_between_screening_if_cin_treated - REAL - minimum years between screening if individual has been treated for CIN previously **PROPERTIES:** .. list-table:: :widths: 25 25 50 :header-rows: 1 * - Item - Type - Description * - ce_hpv_cc_status - CATEGORICAL - Current hpv / cervical cancer status - note that hpv means persistent hpv. Possible values are: [none, hpv, cin1, cin2, cin3, stage1, stage2a, stage2b, stage3, stage4, ] * - ce_date_diagnosis - DATE - the date of diagnosis of cervical cancer stage (pd.NaT if never diagnosed) * - ce_stage_at_diagnosis - CATEGORICAL - the cancer stage at which cancer diagnosis was made. Possible values are: [none, stage1, stage2a, stage2b, stage3, stage4, ] * - ce_date_cin_removal - DATE - the date of last cin removal (pd.NaT if never had cin removal) * - ce_date_treatment - DATE - date of first receiving attempted curative treatment (pd.NaT if never started treatment) * - ce_ever_screened - BOOL - whether ever been screened * - ce_ever_treated - BOOL - ever been treated for cc * - ce_cured_date_cc - DATE - ever cured of cervical cancer date * - ce_cc_ever - BOOL - ever had cc * - ce_stage_at_which_treatment_given - CATEGORICAL - the cancer stage at which treatment was given (because the treatment only has an effect during the stageat which it is given). (Note treatment only initiated in stage1/2a/2b/3. Possible values are: [none, hpv, cin1, cin2, cin3, stage1, stage2a, stage2b, stage3, stage4, ] * - ce_date_palliative_care - DATE - date of first receiving palliative care (pd.NaT is never had palliative care) * - ce_ever_diagnosed - BOOL - ever diagnosed with cervical cancer (even if now cured) * - ce_xpert_hpv_ever_pos - BOOL - hpv positive on xpert test ever * - ce_via_cin_ever_detected - BOOL - cin ever_detected on via * - ce_date_last_screened - DATE - date of last screening * - ce_date_thermoabl - DATE - date of thermoablation for CIN * - ce_date_cryotherapy - DATE - date of cryotherapy for CIN * - ce_date_via - DATE - date of VIA screening * - ce_date_xpert - DATE - date of XPERT screening * - ce_current_cc_diagnosed - BOOL - currently has diagnosed cervical cancer (which until now has not been cured) * - ce_biopsy - BOOL - ce biopsy done ever **Class attributes:** CAUSES_OF_DEATH : {'CervicalCancer': } CAUSES_OF_DISABILITY : {'CervicalCancer': } INIT_DEPENDENCIES : {'Hiv', 'Lifestyle', 'SymptomManager', 'Demography', 'HealthSystem'} METADATA : {, , , } OPTIONAL_INIT_DEPENDENCIES : {'HealthSeekingBehaviour', 'HealthBurden'} __annotations__ : {} **Functions (defined or overridden in class CervicalCancer):** .. automethod:: __init__ .. automethod:: read_parameters .. automethod:: initialise_population .. automethod:: initialise_simulation .. automethod:: build_linear_models .. automethod:: on_birth .. automethod:: report_daly_values .. automethod:: do_at_generic_first_appt .. automethod:: choose_cin_procedure_and_schedule_it .. autoclass:: CervicalCancerMainPollingEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class CervicalCancerMainPollingEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: CervicalCancer_DeathInStage4 Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class CervicalCancer_DeathInStage4):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_CervicalCancer_Screening_VIA Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HSI_CervicalCancer_Screening_VIA):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_CervicalCancer_Screening_Xpert Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HSI_CervicalCancer_Screening_Xpert):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_CervicalCancer_Presentation_WithVaginalBleeding Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HSI_CervicalCancer_Presentation_WithVaginalBleeding):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_CervicalCancer_CINRemoval_Cryotherapy Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HSI_CervicalCancer_CINRemoval_Cryotherapy):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_CervicalCancer_CINRemoval_Thermoablation Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HSI_CervicalCancer_CINRemoval_Thermoablation):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_CervicalCancer_Biopsy Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HSI_CervicalCancer_Biopsy):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_CervicalCancer_Treatment_Start Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HSI_CervicalCancer_Treatment_Start):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_CervicalCancer_Treatment_PostTreatmentCheck Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HSI_CervicalCancer_Treatment_PostTreatmentCheck):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_CervicalCancer_PalliativeCare Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HSI_CervicalCancer_PalliativeCare):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: CervicalCancerLoggingEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class CervicalCancerLoggingEvent):** .. automethod:: __init__ .. automethod:: apply