parameters (.csv)

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	parameter_name	value	param_label	prior_min	prior_max	prior_note	reference	Unnamed: 7
0	beta	0.14379	undetermined	0	1	calibration		previously_0.115
1	unaids_prevalence_adjustment_factor	1.1	local	0.01	100	vague prior
2	prob_mtct_untreated	0.22	universal	0	1	vague prior	rollins
3	prob_mtct_treated	0	universal	0	1	vague prior	rollins
4	prob_mtct_incident_preg	0.3	universal	0	1	vague prior	rollins
5	monthly_prob_mtct_bf_untreated	0.01	universal	0	1	vague prior	rollins
6	monthly_prob_mtct_bf_treated	0	universal	0	1	vague prior	rollins
7	rr_fsw	7.8	universal	0.01	100	vague prior
8	rr_circumcision	0.4	local	0.01	100	vague prior	hallett2008
9	rr_rural	0.52	local	0.01	100	vague prior	wingston_dhs_analysis
10	rr_windex_poorer	0.96	local	0.01	100	vague prior	wingston_dhs_analysis
11	rr_windex_middle	1.18	local	0.01	100	vague prior	wingston_dhs_analysis
12	rr_windex_richer	1.19	local	0.01	100	vague prior	wingston_dhs_analysis
13	rr_windex_richest	1.56	local	0.01	100	vague prior	wingston_dhs_analysis
14	rr_sex_f	1.43	local	0.01	100	vague prior	wingston_dhs_analysis
15	rr_edlevel_primary	1.18	local	0.01	100	vague prior	wingston_dhs_analysis
16	rr_edlevel_secondary	1.15	local	0.01	100	vague prior	wingston_dhs_analysis
17	rr_edlevel_higher	1	local	0.01	100	vague prior	wingston_dhs_analysis
18	rr_schisto	2.3	universal	0.01	100	vague prior	Patel et al 2021
19	rr_behaviour_change	0.75	local	0.01	100	vague prior
20	proportion_reduction_in_risk_of_hiv_aq_if_on_oral_prep	0.6	universal	0	1	vague prior
21	proportion_reduction_in_risk_of_hiv_aq_if_on_inj_prep	0.95	universal	0	1	vague prior
22	mean_months_between_aids_and_death	18	universal	1	24	vague prior	Assumption
23	min_months_between_aids_and_death	0	universal	0	12	vague prior
24	mean_months_between_aids_and_death_infant	6	universal	1	24	vague prior	Assumption
25	infection_to_death_weibull_shape_1519	2	local	0.01	100	vague prior	Todd et al. 2007 & Hallett et al 2008 PLoS Med
26	infection_to_death_weibull_shape_2024	2	local	0.01	100	vague prior
27	infection_to_death_weibull_shape_2529	2	local	0.01	100	vague prior
28	infection_to_death_weibull_shape_3034	2	local	0.01	100	vague prior
29	infection_to_death_weibull_shape_3539	2	local	0.01	100	vague prior
30	infection_to_death_weibull_shape_4044	2	local	0.01	100	vague prior
31	infection_to_death_weibull_shape_4549	2	local	0.01	100	vague prior
32	infection_to_death_weibull_scale_1519	16	local	0.01	100	vague prior
33	infection_to_death_weibull_scale_2024	15.4	local	0.01	100	vague prior
34	infection_to_death_weibull_scale_2529	14.1	local	0.01	100	vague prior
35	infection_to_death_weibull_scale_3034	12.1	local	0.01	100	vague prior
36	infection_to_death_weibull_scale_3539	11	local	0.01	100	vague prior
37	infection_to_death_weibull_scale_4044	10.01	local	0.01	100	vague prior
38	infection_to_death_weibull_scale_4549	7.9	local	0.01	100	vague prior
39	art_default_to_aids_mean_years	5	universal	0.01	100	vague prior
40	prop_delayed_aids_onset	0.3	local	0	1	vague prior
41	mean_survival_for_infants_infected_prior_to_birth	1.08	local	0.01	100	vague prior	ferrand
42	infection_to_death_infant_infection_after_birth_weibull_scale	16	local	0.01	100	vague prior	ferrand
43	infection_to_death_infant_infection_after_birth_weibull_shape	2.7	local	0.01	100	vague prior	ferrand
44	rr_test_hiv_positive	1.1	local	0.01	100	vague prior
45	hiv_testing_rate_adjustment	0.75	undetermined	0.01	100	calibration
46	prob_hiv_test_at_anc_or_delivery	0.95	local	0	1	vague prior
47	prob_hiv_test_for_newborn_infant	0.95	local	0	1	vague prior
48	prob_behav_chg_after_hiv_test	0.5	local	0	1	vague prior
49	prob_prep_for_fsw_after_hiv_test	0.11	undetermined	0	1	calibration
50	prob_prep_for_agyw	0.01	undetermined	0	1	calibration
51	prob_circ_after_hiv_test	0.05	undetermined	0	1	calibration
52	increase_in_prob_circ_2019	3	undetermined	0.01	100	calibration
53	prob_circ_for_child_before_2020	0.0128	undetermined	0	1	calibration		This is estimated using DHIS2 vmmc cases and world bank population data 2015-2019.
54	prob_circ_for_child_from_2020	0.0008	undetermined	0	1	calibration		From 2020 on as indicated by DHIS2 data and PEPFAR 2020 Country Operational Plan the <15 yrs circ cases should decline dramatically. The probability derived from 2020-2022 data is 0.0008 using the same estimation method.
55	probability_of_being_retained_on_prep_every_3_months	0.9	undetermined	0	1	calibration
56	probability_of_being_retained_on_art_every_3_months	0.95	local	0	1	vague prior
57	probability_of_seeking_further_art_appointment_if_drug_not_available	0.9	local	0	1	vague prior
58	probability_of_seeking_further_art_appointment_if_appointment_not_available	0.9	local	0	1	vague prior
59	prep_start_year	2018	scenario	2010	2050	vague prior
60	ART_age_cutoff_young_child	1	local	0	20	vague prior
61	ART_age_cutoff_older_child	10	local	0	20	vague prior
62	rel_probability_art_baseline_aids	10	local	0.01	100	vague prior
63	aids_tb_death_rate_with_tb_treatment	0.15	undetermined	0.01	100	calibration
64	aids_tb_death_rate_no_tb_treatment	0.5	undetermined	0.01	100	calibration
65	hiv_healthseekingbehaviour_cap	5	local	1	10	vague prior
66	initial_dispensation_period_months	3	local	1	24	vague prior
67	dispensation_min_days	1	local	1	14	vague prior
68	length_of_inpatient_stay_if_terminal	[14,20]	local	[1,2]	[50,51]	vague prior
69	type_of_scaleup	none	scenario	NA	NA	vague prior
70	selftest_start_year	2023	local	2010	2050	vague prior
71	scaleup_start_year	2025	scenario	2010	2050	vague prior
72	interval_for_viral_load_measurement_months	24	local	1	24	vague prior
73	annual_rate_selftest	0.07	local	0	1	calibration		need 800,000 in population of 19m (0.04), half are children, lm excludes on ART
74	selftest_available	TRUE	local	NA	NA	design decision
75	young_adult_vls_factor	0.08	local	0	1	vague prior		data from MOH MW
76	proportion_young_adult_on_art	0.15	local	0	1	vague prior		mphia report
77	prob_receive_viral_load_test_result	0.6	local	0	1	vague prior		data from MOH MW
78	sensitivity_viral_load_test	0.6	local	0	1	vague prior		data from MOH MW
79	prob_of_viral_suppression_following_VL_test	0.5816	local	0	1	vague prior
80	viral_load_testing_start_year	2016	local	0	1	vague prior		data from MOH MW
81	delay_from_viral_load_to_result_months_min	3	local	0	5	vague prior
82	delay_from_viral_load_to_result_months_max	7	local	0	12	vague prior
83	tdf_test_replace_vl_test	FALSE	scenario	NA	NA	vague prior
84	targeted_adherence_monitoring	FALSE	scenario	NA	NA	vague prior
85	p_tdf_positive_given_suppressed	0.939	universal	0	1	vague prior		https://pmc.ncbi.nlm.nih.gov/articles/PMC10514373/
86	p_tdf_positive_given_not_suppressed	0.353	universal	0	1	vague prior
87	injectable_prep_allowed	FALSE	scenario	NA	NA	vague prior
88	prob_injectable_prep_vs_oral	0.7	scenario	0	1	vague prior
89	linked_to_care_after_selftest	0.563	local	0	1	vague prior		https://journals.plos.org/plosmedicine/article?id=10.1371%2Fjournal.pmed.1001873#sec019
90	selftest_sensitivity	0.9	universal	0	1	vague prior		https://gh.bmj.com/content/8/7/e012664#ref-10
91	delay_from_selftest_to_facility_weibull_shape	0.454	local	0	1	vague prior		fitted distr using data from https://peercommunityjournal.org/articles/10.24072/pcjournal.428/
92	delay_from_selftest_to_facility_weibull_scale	13	local	0	1	vague prior
93	hiv_regular_polling_event_frequency_months	12	undetermined	1	12	design decision
94	regular_polling_event_initialisation_delay_days	0	undetermined	0	7	design decision
95	hiv_check_properties_event_delay_months	1	undetermined	1	12	design decision
96	baseline_year	2010	undetermined	2000	2020	design decision
97	end_year_circumcision_data	2020	local	2010	2050	vague prior
98	end_year_treatment_data	2025	local	2010	2050	vague prior
99	end_year_testing_data	2020	local	2010	2050	vague prior
100	years_since_infection_threshold_for_higher_art_probability	10	local	0	100	vague prior
101	years_offset_for_dummy_test_date_at_baseline	3	local	0	100	vague prior
102	age_threshold_child_adult_distinction	15	local	0	20	vague prior
103	age_max_adult	80	local	0	100	vague prior
104	age_max_infant	5	local	0	20	vague prior
105	age_default_adult	20	local	0	100	vague prior
106	age_default_children	5	local	0	20	vague prior
107	age_min_agyw	15	local	10	20	vague prior
108	age_max_agyw	30	local	20	40	vague prior
109	age_max_prep	30	local	20	40	vague prior
110	age_max_hiv_early_infant_test_years	1	local	0	5	vague prior
111	age_max_prophylaxis_years	1.5	local	0	3	vague prior
112	hiv_infection_to_aids_untreated_threshold_years	10	universal	5	20	vague prior
113	prop_aids_death_is_tb_coinfection	0.3	universal	0	1	vague prior
114	aids_death_beddays_default	17	local	5	50	vague prior
115	hiv_early_infant_test_sensitivity	0.999999	universal	0	1	vague prior
116	hiv_early_infant_test_specificity	0.999999	universal	0	1	vague prior
117	hv_min_test_interval_days	7	local	0	14	vague prior
118	infant_hiv_test_first_weeks	6	local	1	52	vague prior
119	infant_hiv_test_second_months	9	local	1	24	vague prior
120	infant_hiv_test_third_months	18	local	1	24	vague prior
121	hiv_testing_initial_window_for_individuals_with_aids_at_init_days	60	local	1	365	vague prior
122	hiv_testing_close_window_for_individuals_with_aids_at_init_days	365	local	1	365	vague prior
123	odds_ratio_health_seeking_aids_symptoms_adults	10	local	0.01	100	vague prior
124	odds_ratio_health_seeking_aids_symptoms_children	10	local	0.01	100	vague prior
125	hiv_prep_refill_appointment_window_days	7	local	1	365	vague prior
126	prep_continuation_reevaluation_period_months	3	local	0	6	vague prior
127	prep_cons_notavailable_retry_days	7	local	0	14	vague prior
128	art_continuation_appointment_window_days	14	local	1	100	vague prior
129	art_restart_appointment_delay_months	1	local	1	12	vague prior
130	art_drug_notavailable_default_retry_months	6	local	0	12	vague prior
131	art_level1a_healthseekingbehaviour_cap	2	local	0	12	vague prior
132	art_level1a_appointment_delay_months	1	local	0	12	vague prior
133	art_level1b_appointment_delay_days	1	local	0	12	vague prior
134	seek_further_art_appointment_if_appointment_not_available_min_delay_days	14	local	0	30	vague prior
135	seek_further_art_appointment_if_appointment_not_available_max_delay_days	21	local	10	50	vague prior
136	hiv_circ_procedure_first_followup_days	3	local	0	14	vague prior
137	hiv_circ_procedure_second_followup_days	7	local	0	14	vague prior
138	hiv_circ_cons_notavailable_retry_procedure_weeks	1	local	0	14	vague prior
139	infant_prophylaxis_followup_months	3	local	0	6	vague prior
140	infant_prophylaxis_cons_notavailable_retry_days	7	local	0	14	vague prior
141	proportion_on_treatment_not_lost_to_follow_up	0.99	local	0	1	vague prior