time_to_background_HIVtestNOW |
3.0 |
Legacy parameter for different background testing function |
cascade |
- |
time_to_background_HIVtest_maxval |
8.0 |
Legacy parameter for different background testing function |
cascade |
- |
time_to_background_HIVtest_exponent |
6.0 |
Legacy parameter for different background testing function |
cascade |
- |
time_to_background_HIVtest_midpoint |
6.5 |
Legacy parameter for different background testing function |
cascade |
- |
p_HIV_background_testing_female_pre2006 |
0.5 |
Baseline probability of a female having an HIV test in period from when HIV tests were first offered until 2006 in the background cascade |
cascade |
- |
p_HIV_background_testing_female_current |
0.5 |
Annual baseline probability of a female having an HIV test from 2006 onwards in the background cascade |
cascade |
- |
RR_HIV_background_testing_male |
0.5 |
Relative probability of a man having a HIV test in the background cascade compared to a woman |
cascade |
- |
HIV_rapid_test_sensitivity_CHIPS |
1.0 |
Sensitivity of the rapid HIV test used by CHiPs |
cascade |
- |
p_collect_hiv_test_results_cd4_over200 |
0.97 |
Probability collect background HIV test results when CD4>200 or HIV-negative |
cascade |
- |
p_collect_hiv_test_results_cd4_under200 |
1.0 |
Probability collect background HIV test results when HIV positive with CD4<=200 |
cascade |
- |
p_collect_cd4_test_results_cd4_nonpopart |
0.85 |
Probability collect background CD4 test results |
cascade |
- |
p_collect_cd4_test_results_cd4_popartYEAR1 |
1.0 |
Probability collect CD4 test results following CHiPs HIV test for CHiPs round 1 |
cascade |
- |
p_collect_cd4_test_results_cd4_popartYEAR2onwards |
1.0 |
Probability collect CD4 test results following CHiPs HIV test for CHiPs round 2 onwards |
cascade |
- |
p_dies_earlyart_cd4_over500 |
0.0 |
Probability die while on early ART and CD4>500 |
cascade |
- |
p_dies_earlyart_cd4_350_500 |
0.0 |
Probability die while on early ART and CD4 350-500 |
cascade |
- |
p_dies_earlyart_cd4_200_350 |
0.0 |
Probability die while on early ART and CD4 200-350 |
cascade |
- |
p_dies_earlyart_cd4_under200 |
0.08 |
Probability die while on early ART and CD4<=200 |
cascade |
- |
p_leaves_earlyart_cd4_over200_if_not_die_early |
0.0 |
Probability drop out from early ART if CD4>200, given that do not die on early ART |
cascade |
- |
p_leaves_earlyart_cd4_under200_if_not_die_early |
0.0 |
Probability drop out from early ART if CD4<=200, given that do not die on early ART |
cascade |
- |
p_becomes_vs_after_earlyart_if_not_die_early_or_leave |
0.9 |
Probability become virally suppressed after early ART, given that do not die on early ART |
cascade |
- |
p_stays_virally_suppressed |
0.6 |
Probability that a woman who becomes virally suppressed remains virally suppressed for life |
cascade |
- |
p_stays_virally_suppressed_male |
0.5 |
Relative probability of a man who becomes virally suppressed remaining virally suppressed for life (compared to a woman) |
cascade |
- |
p_stops_virally_suppressed |
0.1 |
Probability that someone who becomes virally suppressed will eventually become virally unsuppressed (but remains on ART) |
cascade |
- |
p_vu_becomes_virally_suppressed |
0.0 |
Probability that someone who becomes virally unsuppressed after early ART eventually becomes virally suppressed |
cascade |
- |
t_earlyart_dropout_nonpopart_min |
0.0 |
Minimum time (in years) from starting early ART (from background HIV test) to dropping out, for those who drop out |
cascade |
- |
t_earlyart_dropout_nonpopart_max |
0.17 |
Maximum time (in years) from starting early ART (from background HIV test) to dropping out, for those who drop out |
cascade |
- |
t_earlyart_dropout_popart_min |
0.0 |
Minimum time (in years) from starting early ART (from CHiPs HIV test) to dropping out, for those who drop out |
cascade |
- |
t_earlyart_dropout_popart_max |
0.17 |
Maximum time (in years) from starting early ART (from CHiPs HIV test) to dropping out, for those who drop out |
cascade |
- |
t_dies_earlyart_nonpopart_min |
0.0 |
Minimum time (in years) from starting early ART (from background HIV test) to dying, for those who die during early ART |
cascade |
- |
t_dies_earlyart_nonpopart_max |
0.17 |
Maximum time (in years) from starting early ART (from background HIV test) to dying, for those who die during early ART |
cascade |
- |
t_dies_earlyart_popart_min |
0.0 |
Minimum time (in years) from starting early ART (from CHiPs HIV test) to dying, for those who die during early ART |
cascade |
- |
t_dies_earlyart_popart_max |
0.17 |
Maximum time (in years) from starting early ART (from CHiPs HIV test) to dying, for those who die during early ART |
cascade |
- |
t_end_early_art |
0.17 |
Maximum duration (in years) of early ART stage (for those who will remain on ART (whether virally suppressed or unsuppressed) |
cascade |
- |
t_cd4_retest_nonpopart_min |
0.9 |
Minimum time between successive CD4 tests when not initially eligible for ART following positive background HIV test result |
cascade |
- |
t_cd4_retest_nonpopart_max |
1.1 |
Maximum time between successive CD4 tests when not initially eligible for ART following positive background HIV test result |
cascade |
- |
t_cd4_retest_popart_min |
0.9 |
Minimum time between successive CD4 tests when not initially eligible for ART following positive CHiPs HIV test result (arm B) |
cascade |
- |
t_cd4_retest_popart_max |
1.1 |
Maximum time between successive CD4 tests when not initially eligible for ART following positive CHiPs HIV test result (arm B) |
cascade |
- |
t_cd4_whenartfirstavail_min |
0.0 |
Minimum time (in years) until someone who is HIV-positive aware (and wants to start ART) has a CD4 test to determine eligibility for ART, when ART first becomes available |
cascade |
- |
t_cd4_whenartfirstavail_max |
2.0 |
Maximum time (in years) until someone who is HIV-positive aware (and wants to start ART) has a CD4 test to determine eligibility for ART, when ART first becomes available |
cascade |
- |
t_delay_hivtest_to_cd4test_nonpopart_min |
0.02083333 |
Minimum time in years from (positive) background HIV test to CD4 test |
cascade |
- |
t_delay_hivtest_to_cd4test_nonpopart_max |
0.5 |
Maximum time in years from (positive) background HIV test to CD4 test |
cascade |
- |
t_delay_hivtest_to_cd4test_popart_min |
0.0208333 |
Minimum time in years from (positive) CHiPs HIV test to CD4 test |
cascade |
- |
t_delay_hivtest_to_cd4test_popart_max |
0.08 |
Maximum time in years from (positive) CHiPs HIV test to CD4 test |
cascade |
- |
t_start_art_nonpopart_mean |
0.55 |
Mean time in years to start ART through background HIV testing (of those who decide to start ART) |
cascade |
- |
n_time_periods_art_popart_round_1 |
6.0 |
Number of time periods in R1 with different distributions of time to start ART following a positive CHiPs test (see Supplement Table S4.5) |
cascade |
- |
n_time_periods_art_popart_round_2 |
1.0 |
Number of time periods in R2 with different distributions of time to start ART following a positive CHiPs test |
cascade |
- |
n_time_periods_art_popart_round_3 |
1.0 |
Number of time periods in R3 with different distributions of time to start ART following a positive CHiPs test |
cascade |
- |
t_start_art_popart_round1_mean_fast_1 |
0.198 |
Mean time to start ART fast (years) in Round 1 Period 1 |
cascade |
- |
t_start_art_popart_round1_mean_fast_2 |
0.161 |
Mean time to start ART fast (years) in Round 1 Period 2 |
cascade |
- |
t_start_art_popart_round1_mean_fast_3 |
0.11800000000000001 |
Mean time to start ART fast (years) in Round 1 Period 3 |
cascade |
- |
t_start_art_popart_round1_mean_fast_4 |
0.135 |
Mean time to start ART fast (years) in Round 1 Period 4 |
cascade |
- |
t_start_art_popart_round1_mean_fast_5 |
0.081 |
Mean time to start ART fast (years) in Round 1 Period 5 |
cascade |
- |
t_start_art_popart_round1_mean_fast_6 |
0.027999999999999997 |
Mean time to start ART fast (years) in Round 1 Period 6 |
cascade |
- |
t_start_art_popart_round1_mean_slow_1 |
2.7110000000000003 |
Mean time to start ART slow (years) in Round 1 Period 1 |
cascade |
- |
t_start_art_popart_round1_mean_slow_2 |
2.378 |
Mean time to start ART slow (years) in Round 1 Period 2 |
cascade |
- |
t_start_art_popart_round1_mean_slow_3 |
2.086 |
Mean time to start ART slow (years) in Round 1 Period 3 |
cascade |
- |
t_start_art_popart_round1_mean_slow_4 |
1.62 |
Mean time to start ART slow (years) in Round 1 Period 4 |
cascade |
- |
t_start_art_popart_round1_mean_slow_5 |
1.2819999999999998 |
Mean time to start ART slow (years) in Round 1 Period 5 |
cascade |
- |
t_start_art_popart_round1_mean_slow_6 |
0.8540000000000001 |
Mean time to start ART slow (years) in Round 1 Period 6 |
cascade |
- |
p_start_art_popart_round1_mean_fast_1 |
0.215 |
Probability of being a fast starter in Round 1 Period 1 |
cascade |
- |
p_start_art_popart_round1_mean_fast_2 |
0.18600000000000003 |
Probability of being a fast starter in Round 1 Period 2 |
cascade |
- |
p_start_art_popart_round1_mean_fast_3 |
0.18 |
Probability of being a fast starter in Round 1 Period 3 |
cascade |
- |
p_start_art_popart_round1_mean_fast_4 |
0.2 |
Probability of being a fast starter in Round 1 Period 4 |
cascade |
- |
p_start_art_popart_round1_mean_fast_5 |
0.313 |
Probability of being a fast starter in Round 1 Period 5 |
cascade |
- |
p_start_art_popart_round1_mean_fast_6 |
0.175 |
Probability of being a fast starter in Round 1 Period 6 |
cascade |
- |
t_start_art_popart_round2_mean_fast |
0.075 |
Mean time to start ART fast (years) in Round 2 |
cascade |
- |
t_start_art_popart_round2_mean_slow |
1.262 |
Mean time to start ART slow (years) in Round 2 |
cascade |
- |
p_start_art_popart_round2_mean_fast |
0.226 |
Probability of being a fast starter in Round 2 |
cascade |
- |
t_start_art_popart_round3_mean_fast |
0.03 |
Mean time to start ART fast (years) in Round 3 onwards |
cascade |
- |
t_start_art_popart_round3_mean_slow |
0.795 |
Mean time to start ART slow (years) in Round 3 onwards |
cascade |
- |
p_start_art_popart_round3_mean_fast |
0.284 |
Probability of being a fast starter in Round 3 onwards |
cascade |
- |
t_end_vs_becomevu_nonpopart_min |
0.01 |
Minimum time taken (in years) for someone VS and who started ART through background cascade (and who will eventually become VU) to become VU |
cascade |
- |
t_end_vs_becomevu_nonpopart_max |
6.0 |
Maximum time taken (in years) for someone VS and who started ART through background cascade (and who will eventually become VU) to become VU |
cascade |
- |
t_end_vs_becomevu_popart_min |
0.01 |
Minimum time taken (in years) for someone VS and who started ART through CHiPs testing (and who will eventually become VU) to become VU |
cascade |
- |
t_end_vs_becomevu_popart_max |
6.0 |
Maximum time taken (in years) for someone VS and who started ART through CHiPs testing (and who will eventually become VU) to become VU |
cascade |
- |
t_end_vs_dropout_nonpopart_min |
0.01 |
Minimum time taken (in years) for someone VS and who started ART through background cascade (and who will eventually drop out) to drop out |
cascade |
- |
t_end_vs_dropout_nonpopart_max |
6.0 |
Maximum time taken (in years) for someone VS and who started ART through background cascade (and who will eventually drop out) to drop out |
cascade |
- |
t_end_vs_dropout_popart_min |
0.01 |
Minimum time taken (in years) for someone VS and who started ART through CHiPs testing (and who will eventually drop out) to drop out |
cascade |
- |
t_end_vs_dropout_popart_max |
6.0 |
Maximum time taken (in years) for someone VS and who started ART through CHiPs testing (and who will eventually drop out) to drop out |
cascade |
- |
t_end_vu_becomevs_nonpopart_min |
0.01 |
Minimum time taken (in years) for someone VU and who started ART through background cascade (and who will eventually become VS) to become VS. Currently zero probability, as determined by p_vu_becomes_virally_suppressed |
cascade |
- |
t_end_vu_becomevs_nonpopart_max |
6.0 |
Maximum time taken (in years) for someone VU and who started ART through background cascade (and who will eventually become VS) to become VS. Currently zero probability, as determined by p_vu_becomes_virally_suppressed |
cascade |
- |
t_end_vu_becomevs_popart_min |
0.01 |
Minimum time taken (in years) for someone VU and who started ART through CHiPs testing (and who will eventually become VS) to become VS. Currently zero probability, as determined by p_vu_becomes_virally_suppressed |
cascade |
- |
t_end_vu_becomevs_popart_max |
6.0 |
Maximum time taken (in years) for someone VU and who started ART through CHiPs testing (and who will eventually become VS) to become VS. Currently zero probability, as determined by p_vu_becomes_virally_suppressed |
cascade |
- |
t_end_vu_dropout_nonpopart_min |
0.01 |
Minimum time taken (in years) for someone VU and who started ART through background cascade (and who does not eventually become VS) to drop out |
cascade |
- |
t_end_vu_dropout_nonpopart_max |
6.0 |
Maximum time taken (in years) for someone VU and who started ART through background cascade (and who does not eventually become VS) to drop out |
cascade |
- |
t_end_vu_dropout_popart_min |
0.01 |
Minimum time taken (in years) for someone VU and who started ART through CHiPs testing (and who does not eventually become VS) to drop out |
cascade |
- |
t_end_vu_dropout_popart_max |
6.0 |
Maximum time taken (in years) for someone VU and who started ART through CHiPs testing (and who does not eventually become VS) to drop out |
cascade |
- |
p_popart_to_cascade |
1.0 |
Probability that someone who had previously dropped out (either tested HIV+ but never linked to care, or was on ART and dropped out) will agree to PopART |
cascade |
- |
p_circ_nopopart |
0.4 |
Probability of man being circumcised following negative background HIV test result |
cascade |
- |
p_circ_popart |
0.4 |
Probability of man being circumcised following negative CHiPs HIV test result |
cascade |
- |
t_get_vmmc_nonpopart_min |
0.25 |
Minimum time (in years) between background HIV- test and getting VMMC |
cascade |
- |
t_get_vmmc_nonpopart_max |
1.0 |
Maximum time (in years) between background HIV- test and getting VMMC |
cascade |
- |
t_get_vmmc_popart_min |
0.08333 |
Minimum time (in years) between CHiPs HIV- test and getting VMMC |
cascade |
- |
t_get_vmmc_popart_max |
1.0 |
Maximum time (in years) between CHiPs HIV- test and getting VMMC |
cascade |
- |
t_vmmc_healing |
0.038 |
Time (in years) for VMMC wound to heal |
cascade |
- |
sex_ratio |
0.5073892 |
Fraction of new adults that are male |
demographics |
- |
p_child_circ |
0.0618 |
Proportion of male children who have undergone traditional circumcision |
HIV |
- |
eff_circ_vmmc |
0.6 |
Effectiveness of voluntary male medical circumcision in reducing susceptibility to HIV infection |
HIV |
- |
eff_circ_tmc |
0.0 |
Effectiveness of traditional male circumcision in reducing susceptibility to HIV infection |
HIV |
- |
rr_circ_unhealed |
0.33 |
Relative risk (compared to uncircumcised state) of acquiring HIV during VMMC healing phase |
HIV |
- |
t0_pmtct |
1990.0 |
Legacy parameter |
HIV |
- |
t50_pmtct |
2000.0 |
Legacy parameter |
HIV |
- |
average_log_viral_load |
4.0 |
Legacy parameter |
HIV |
- |
average_annual_hazard |
0.12 |
Annual HIV female-to-male transmission hazard in individuals with maximal SPVL and in CD4 stage >500 |
HIV |
- |
RRacute_trans |
5.3 |
Relative infectivity of acute and early HIV infection (AEHI) stage (compared to chronic HIV infection with CD4>500) |
HIV |
- |
RRmale_to_female_trans |
2.0 |
Relative infectivity of male-to-female HIV transmission (compared to female-to-male) |
HIV |
- |
RRCD4_1 |
1.0 |
Relative infectivity in CD4 stage >500 (compared to chronic HIV infection with CD4>500) |
HIV |
- |
RRCD4_2 |
1.0 |
Relative infectivity in CD4 stage 350-500 (compared to chronic HIV infection with CD4>500) |
HIV |
- |
RRCD4_3 |
1.0 |
Relative infectivity in CD4 stage 200-350 (compared to chronic HIV infection with CD4>500) |
HIV |
- |
RRCD4_4 |
2.34 |
Relative infectivity in CD4 stage <=200 (compared to chronic HIV infection with CD4>500) |
HIV |
- |
SPVL_beta_k |
1.02 |
Hill coefficient (the steepness of the increase in infectiousness as a function of set-point viral load) |
HIV |
- |
SPVL_beta_50 |
13938.0 |
Set-point viral load at which infectiousness is half its maximum value |
HIV |
- |
ART_VS_INITIAL |
0.5 |
Relative infectivity of early ART stage (compared to no ART) |
HIV |
- |
ART_VS_EFFECT |
1.0 |
Relative infectivity of virally suppressed ART stage (compared to no ART) |
HIV |
- |
ART_VU_EFFECT |
0.3 |
Relative infectivity of virally unsuppressed ART stage (compared to no ART) |
HIV |
- |
Dur_acute_range_min |
0.08 |
Minimum duration of AEHI stage in years |
HIV |
- |
Dur_acute_range_max |
0.25 |
Maximum duration of AEHI stage in years |
HIV |
- |
p_initial_cd4_gt500_spvl0 |
0.8640000000000001 |
Proportion of individuals with log10 SPVL <=4.0 who have initial CD4 >500 following HIV infection |
HIV |
- |
p_initial_cd4_350_500_spvl0 |
0.113 |
Proportion of individuals with log10 SPVL <=4.0 who have initial CD4 350-500 following HIV infection |
HIV |
- |
p_initial_cd4_200_350_spvl0 |
0.023 |
Proportion of individuals with log10 SPVL <=4.0 who have initial CD4 200-350 following HIV infection |
HIV |
- |
p_initial_cd4_lt200_spvl0 |
0.0 |
Proportion of individuals with log10 SPVL <=4.0 who have initial CD4 <=200 following HIV infection |
HIV |
- |
p_initial_cd4_gt500_spvl1 |
0.78 |
Proportion of individuals with log10 SPVL 4.0-4.5 who have initial CD4 >500 following HIV infection |
HIV |
- |
p_initial_cd4_350_500_spvl1 |
0.19 |
Proportion of individuals with log10 SPVL 4.0-4.5 who have initial CD4 350-500 following HIV infection |
HIV |
- |
p_initial_cd4_200_350_spvl1 |
0.03 |
Proportion of individuals with log10 SPVL 4.0-4.5 who have initial CD4 200-350 following HIV infection |
HIV |
- |
p_initial_cd4_lt200_spvl1 |
0.0 |
Proportion of individuals with log10 SPVL 4.0-4.5 who have initial CD4 <=200 following HIV infection |
HIV |
- |
p_initial_cd4_gt500_spvl2 |
0.74 |
Proportion of individuals with log10 SPVL 4.5-5.0 who have initial CD4 >500 following HIV infection |
HIV |
- |
p_initial_cd4_350_500_spvl2 |
0.21 |
Proportion of individuals with log10 SPVL 4.5-5.0 who have initial CD4 350-500 following HIV infection |
HIV |
- |
p_initial_cd4_200_350_spvl2 |
0.05 |
Proportion of individuals with log10 SPVL 4.5-5.0 who have initial CD4 200-350 following HIV infection |
HIV |
- |
p_initial_cd4_lt200_spvl2 |
0.0 |
Proportion of individuals with log10 SPVL 4.5-5.0 who have initial CD4 <=200 following HIV infection |
HIV |
- |
p_initial_cd4_gt500_spvl3 |
0.71 |
Proportion of individuals with log10 SPVL >5.0 who have initial CD4 >500 following HIV infection |
HIV |
- |
p_initial_cd4_350_500_spvl3 |
0.25 |
Proportion of individuals with log10 SPVL >5.0 who have initial CD4 350-500 following HIV infection |
HIV |
- |
p_initial_cd4_200_350_spvl3 |
0.04 |
Proportion of individuals with log10 SPVL >5.0 who have initial CD4 200-350 following HIV infection |
HIV |
- |
p_initial_cd4_lt200_spvl3 |
0.0 |
Proportion of individuals with log10 SPVL >5.0 who have initial CD4 <=200 following HIV infection |
HIV |
- |
initial_SPVL_mu |
4.74 |
Mean SPVL in seeded HIV infections |
HIV |
- |
initial_SPVL_sigma |
0.61 |
Standard deviation of SPVL in seeded HIV infections |
HIV |
- |
SPVL_sigma_M |
0.0 |
Parameter used when SPVL inheritance is switched on (macro SPVL_INHERITANCE=1). By default SPVL inheritance is off |
HIV |
- |
SPVL_sigma_E |
0.61 |
Standard deviation of SPVL in non-seeded infections. |
HIV |
- |
p_misclassify_cd4_0_0 |
1.0 |
Probability of classifying actual CD4 category >500 as >500 |
HIV |
- |
p_misclassify_cd4_0_1 |
0.0 |
Probability of classifying actual CD4 category >500 as 350-500 |
HIV |
- |
p_misclassify_cd4_0_2 |
0.0 |
Probability of classifying actual CD4 category >500 as 200-350 |
HIV |
- |
p_misclassify_cd4_0_3 |
0.0 |
Probability of classifying actual CD4 category >500 as <=200 |
HIV |
- |
p_misclassify_cd4_1_0 |
0.0 |
Probability of classifying actual CD4 category 350-500 as >500 |
HIV |
- |
p_misclassify_cd4_1_1 |
1.0 |
Probability of classifying actual CD4 category 350-500 as 350-500 |
HIV |
- |
p_misclassify_cd4_1_2 |
0.0 |
Probability of classifying actual CD4 category 350-500 as 200-350 |
HIV |
- |
p_misclassify_cd4_1_3 |
0.0 |
Probability of classifying actual CD4 category 350-500 as <=200 |
HIV |
- |
p_misclassify_cd4_2_0 |
0.0 |
Probability of classifying actual CD4 category 200-350 as >500 |
HIV |
- |
p_misclassify_cd4_2_1 |
0.0 |
Probability of classifying actual CD4 category 200-350 as 350-500 |
HIV |
- |
p_misclassify_cd4_2_2 |
1.0 |
Probability of classifying actual CD4 category 200-350 as 200-350 |
HIV |
- |
p_misclassify_cd4_2_3 |
0.0 |
Probability of classifying actual CD4 category 200-350 as <=200 |
HIV |
- |
p_misclassify_cd4_3_0 |
0.0 |
Probability of classifying actual CD4 category <=200 as >500 |
HIV |
- |
p_misclassify_cd4_3_1 |
0.0 |
Probability of classifying actual CD4 category <=200 as 350-500 |
HIV |
- |
p_misclassify_cd4_3_2 |
0.0 |
Probability of classifying actual CD4 category <=200 as 200-350 |
HIV |
- |
p_misclassify_cd4_3_3 |
1.0 |
Probability of classifying actual CD4 category <=200 as <=200 |
HIV |
- |
time_gt500_to_500_spvl0 |
5.35 |
Time (in years) spent in CD4 category >500 for individuals with log10 SPVL <=4.0 when not on ART |
HIV |
- |
time_350to500_to_350_spvl0 |
3.66 |
Time (in years) spent in CD4 category 350-500 for individuals with log10 SPVL <=4.0 not on ART |
HIV |
- |
time_200to350_to_200_spvl0 |
7.62 |
Time (in years) spent in CD4 category 200-350 for individuals with log10 SPVL <=4.0 not on ART |
HIV |
- |
time_lt200_to_death_spvl0 |
2.3 |
Time (in years) spent in CD4 category <=200 until death for individuals with log10 SPVL <=4.0 not on ART |
HIV |
- |
time_gt500_to_500_spvl1 |
3.12 |
Used when macro USEFOURSPVLCATEGORIES=1 for time spent (in years) in CD4 category >500 for individuals with log10 SPVL 4-4.5 when not on ART |
HIV |
- |
time_350to500_to_350_spvl1 |
3.09 |
Used when macro USEFOURSPVLCATEGORIES=1 for time spent (in years) in CD4 category 350-500 for individuals with log10 SPVL 4-4.5 when not on ART |
HIV |
- |
time_200to350_to_200_spvl1 |
8.39 |
Used when macro USEFOURSPVLCATEGORIES=1 for time spent (in years) in CD4 category 200-350 for individuals with log10 SPVL 4-4.5 when not on ART |
HIV |
- |
time_lt200_to_death_spvl1 |
2.3 |
Used when macro USEFOURSPVLCATEGORIES=1 for time spent (in years) in CD4 category <=200 for individuals with log10 SPVL 4-4.5 when not on ART |
HIV |
- |
time_gt500_to_500_spvl2 |
2.35 |
Used when macro USEFOURSPVLCATEGORIES=1 for time spent (in years) in CD4 category >500 for individuals with log10 SPVL 4.5-5 when not on ART |
HIV |
- |
time_350to500_to_350_spvl2 |
2.32 |
Used when macro USEFOURSPVLCATEGORIES=1 for time spent (in years) in CD4 category 350-500 for individuals with log10 SPVL 4.5-5 when not on ART |
HIV |
- |
time_200to350_to_200_spvl2 |
6.57 |
Used when macro USEFOURSPVLCATEGORIES=1 for time spent (in years) in CD4 category 200-350 for individuals with log10 SPVL 4.5-5 when not on ART |
HIV |
- |
time_lt200_to_death_spvl2 |
2.3 |
Used when macro USEFOURSPVLCATEGORIES=1 for time spent (in years) in CD4 category <=200 for individuals with log10 SPVL 4.5-5 when not on ART |
HIV |
- |
time_gt500_to_500_spvl3 |
1.51 |
Used when macro USEFOURSPVLCATEGORIES=1 for time spent (in years) in CD4 category >500 for individuals with log10 SPVL >5 when not on ART |
HIV |
- |
time_350to500_to_350_spvl3 |
1.44 |
Used when macro USEFOURSPVLCATEGORIES=1 for time spent (in years) in CD4 category 350-500 for individuals with log10 SPVL >5 when not on ART |
HIV |
- |
time_200to350_to_200_spvl3 |
2.93 |
Used when macro USEFOURSPVLCATEGORIES=1 for time spent (in years) in CD4 category 200-350 for individuals with log10 SPVL >5 when not on ART |
HIV |
- |
time_lt200_to_death_spvl3 |
2.3 |
Used when macro USEFOURSPVLCATEGORIES=1 for time spent (in years) in CD4 category <=200 for individuals with log10 SPVL >5 when not on ART |
HIV |
- |
cox_RRspvl_gt500_to_500 |
2.17 |
Used when macro USEFOURSPVLCATEGORIES=0 (default setting). Factor by which time in CD4 category >500 is decreased, per 10-fold increase in SPVL |
HIV |
- |
cox_RRspvl_500_to_350 |
1.88 |
Used when macro USEFOURSPVLCATEGORIES=0 (default setting). Factor by which time in CD4 category 350-500 is decreased, per 10-fold increase in SPVL |
HIV |
- |
cox_RRspvl_350_to_200 |
1.96 |
Used when macro USEFOURSPVLCATEGORIES=0 (default setting). Factor by which time in CD4 category 200-350 is decreased, per 10-fold increase in SPVL |
HIV |
- |
cox_RRspvl_200_to_death |
1.63 |
Used when macro USEFOURSPVLCATEGORIES=0 (default setting). Factor by which time in CD4 category <=200 is decreased, per 10-fold increase in SPVL |
HIV |
- |
factor_for_slower_progression_ART_VU |
1.0 |
Multiplier for increased duration in each CD4 stage when on ART but virally unsuppressed (compared to being virally suppressed) |
HIV |
- |
rng_seed |
2020.0 |
Random starting seed |
init |
- |
initial_adult_population_size |
2050.0 |
Size of the population aged 14+ at the start of the simulation |
init |
- |
initial_prop_14_17 |
0.1583 |
Proportion of the modelled population at the start of the simulation that are aged 14-17 |
init |
- |
initial_prop_18_22 |
0.1613 |
Proportion of the modelled population at the start of the simulation that are aged 18-22 |
init |
- |
initial_prop_23_30 |
0.1885 |
Proportion of the modelled population at the start of the simulation that are aged 23-30 |
init |
- |
initial_prop_31_40 |
0.1983 |
Proportion of the modelled population at the start of the simulation that are aged 31-40 |
init |
- |
initial_prop_41_50 |
0.1353 |
Proportion of the modelled population at the start of the simulation that are aged 41-50 |
init |
- |
initial_prop_51_60 |
0.0828 |
Proportion of the modelled population at the start of the simulation that are aged 51-60 |
init |
- |
initial_prop_61_and_older |
0.0755 |
Proportion of the modelled population at the start of the simulation that are aged 61+ |
init |
- |
initial_low_risk_male |
0.45 |
Proportion of men who are in the low-risk activity group when entering adult population |
init |
- |
initial_low_risk_female |
0.45 |
Proportion of women who are in the low-risk activity group when entering adult population |
init |
- |
initial_med_not_low_risk_male |
0.745 |
Of those men who did not enter the low risk group, proportion of men who are in the medium-risk activity group when entering adult population |
init |
- |
initial_med_not_low_risk_female |
0.745 |
Of those women who did not enter the low risk group, proportion of women who are in the medium-risk activity group when entering adult population |
init |
- |
initial_prop_HIV_pos_low_risk_male |
2e-05 |
Unscaled % of low activity level male population seeded HIV+ each year |
init |
- |
initial_prop_HIV_pos_low_risk_female |
2e-05 |
Unscaled % of low activity level female population seeded HIV+ each year |
init |
- |
initial_prop_HIV_pos_med_risk_male |
5e-05 |
Unscaled % of medium activity level male population seeded HIV+ each year |
init |
- |
initial_prop_HIV_pos_med_risk_female |
5e-05 |
Unscaled % of medium activity level female population seeded HIV+ each year |
init |
- |
initial_prop_HIV_pos_high_risk_male |
8e-05 |
Unscaled % of high activity level male population seeded HIV+ each year |
init |
- |
initial_prop_HIV_pos_high_risk_female |
8e-05 |
Unscaled % of high activity level female population seeded HIV+ each year |
init |
- |
log_seed_multiplier |
1.0 |
log10 of factor multiplying seeded % at the start of the HIV epidemic |
init |
- |
n_years_HIV_seeding |
5.0 |
Number of years of HIV seeding after start of HIV epidemic |
init |
- |
assortativity |
0.5 |
Risk assortativity |
partnerships |
- |
prop_compromise_from_males |
0.5 |
theta, the proportion of compromise in number of sexual partners from males |
partnerships |
- |
c_f_1 |
0.011822581 |
Within-community annual partnership formation rates for women in age group 14-17 |
partnerships |
- |
c_f_2 |
0.023645162 |
Within-community annual partnership formation rates for women in age group 18-22 |
partnerships |
- |
c_f_3 |
0.018226193 |
Within-community annual partnership formation rates for women in age group 23-30 |
partnerships |
- |
c_f_4 |
0.012009144 |
Within-community annual partnership formation rates for women in age group 31-40 |
partnerships |
- |
c_f_5 |
0.009834833000000001 |
Within-community annual partnership formation rates for women in age group 41-50 |
partnerships |
- |
c_f_6 |
0.004917416 |
Within-community annual partnership formation rates for women in age group 51-60 |
partnerships |
- |
c_f_7 |
0.002458708 |
Within-community annual partnership formation rates for women in age group 61+ |
partnerships |
- |
c_m_1 |
0.021872336000000003 |
Within-community annual partnership formation rates for men in age group 14-17 |
partnerships |
- |
c_m_2 |
0.043744672000000005 |
Within-community annual partnership formation rates for men in age group 18-22 |
partnerships |
- |
c_m_3 |
0.039466657 |
Within-community annual partnership formation rates for men in age group 23-30 |
partnerships |
- |
c_m_4 |
0.023920296 |
Within-community annual partnership formation rates for men in age group 31-40 |
partnerships |
- |
c_m_5 |
0.018824023 |
Within-community annual partnership formation rates for men in age group 41-50 |
partnerships |
- |
c_m_6 |
0.006004572 |
Within-community annual partnership formation rates for men in age group 51-60 |
partnerships |
- |
c_m_7 |
0.003002286 |
Within-community annual partnership formation rates for men in age group 61+ |
partnerships |
- |
c_multiplier |
2.25 |
Multiplier to for mis-reporting of number of sexual partners |
partnerships |
- |
rel_rate_partnership_formation_between_patches |
0.45 |
Relative rate of formation of partnerships between patches compared to within patches |
partnerships |
- |
rr_hiv_between_vs_within_patch |
0.3 |
Relative HIV transmission risk for partnerships between patches, compared to partnerships within same patch |
partnerships |
- |
relative_number_partnerships_per_risk_low |
1.0 |
Relative number of partnerships for low activity level group (compared to low activity level group) |
partnerships |
- |
relative_number_partnerships_per_risk_med |
7.7 |
Relative number of partnerships for medium activity level group (compared to low activity level group) |
partnerships |
- |
relative_number_partnerships_per_risk_high |
18.6 |
Relative number of partnerships for high activity level group (compared to low activity level group) |
partnerships |
- |
p_age_m_1_1 |
0.935028249 |
Age mixing matrix for men |
partnerships |
- |
p_age_m_1_2 |
1.0 |
- |
partnerships |
- |
p_age_m_1_3 |
0.0 |
- |
partnerships |
- |
p_age_m_1_4 |
0.0 |
- |
partnerships |
- |
p_age_m_1_5 |
0.0 |
- |
partnerships |
- |
p_age_m_1_6 |
0.0 |
- |
partnerships |
- |
p_age_m_1_7 |
0.0 |
- |
partnerships |
- |
p_age_m_2_1 |
0.26859504100000003 |
- |
partnerships |
- |
p_age_m_2_2 |
0.935028249 |
- |
partnerships |
- |
p_age_m_2_3 |
1.0 |
- |
partnerships |
- |
p_age_m_2_4 |
0.0 |
- |
partnerships |
- |
p_age_m_2_5 |
0.0 |
- |
partnerships |
- |
p_age_m_2_6 |
0.0 |
- |
partnerships |
- |
p_age_m_2_7 |
0.0 |
- |
partnerships |
- |
p_age_m_3_1 |
0.057416268 |
- |
partnerships |
- |
p_age_m_3_2 |
0.640862944 |
- |
partnerships |
- |
p_age_m_3_3 |
0.9434628979999999 |
- |
partnerships |
- |
p_age_m_3_4 |
0.875 |
- |
partnerships |
- |
p_age_m_3_5 |
1.0 |
- |
partnerships |
- |
p_age_m_3_6 |
0.0 |
- |
partnerships |
- |
p_age_m_3_7 |
0.0 |
- |
partnerships |
- |
p_age_m_4_1 |
0.012030075 |
- |
partnerships |
- |
p_age_m_4_2 |
0.112633181 |
- |
partnerships |
- |
p_age_m_4_3 |
0.615780446 |
- |
partnerships |
- |
p_age_m_4_4 |
0.9776785709999999 |
- |
partnerships |
- |
p_age_m_4_5 |
1.0 |
- |
partnerships |
- |
p_age_m_4_6 |
0.0 |
- |
partnerships |
- |
p_age_m_4_7 |
0.0 |
- |
partnerships |
- |
p_age_m_5_1 |
0.0 |
- |
partnerships |
- |
p_age_m_5_2 |
0.023972603 |
- |
partnerships |
- |
p_age_m_5_3 |
0.09473684199999999 |
- |
partnerships |
- |
p_age_m_5_4 |
0.713178295 |
- |
partnerships |
- |
p_age_m_5_5 |
0.932432432 |
- |
partnerships |
- |
p_age_m_5_6 |
0.8 |
- |
partnerships |
- |
p_age_m_5_7 |
1.0 |
- |
partnerships |
- |
p_age_m_6_1 |
0.0 |
- |
partnerships |
- |
p_age_m_6_2 |
0.0 |
- |
partnerships |
- |
p_age_m_6_3 |
0.023972603 |
- |
partnerships |
- |
p_age_m_6_4 |
0.09473684199999999 |
- |
partnerships |
- |
p_age_m_6_5 |
0.713178295 |
- |
partnerships |
- |
p_age_m_6_6 |
0.932432432 |
- |
partnerships |
- |
p_age_m_6_7 |
1.0 |
- |
partnerships |
- |
p_age_m_7_1 |
0.0 |
- |
partnerships |
- |
p_age_m_7_2 |
0.0 |
- |
partnerships |
- |
p_age_m_7_3 |
0.0 |
- |
partnerships |
- |
p_age_m_7_4 |
0.023972603 |
- |
partnerships |
- |
p_age_m_7_5 |
0.09473684199999999 |
- |
partnerships |
- |
p_age_m_7_6 |
0.713178295 |
- |
partnerships |
- |
p_age_m_7_7 |
1.0 |
- |
partnerships |
- |
p_age_f_1_1 |
0.113636364 |
Age mixing matrix for women |
partnerships |
- |
p_age_f_1_2 |
0.778329198 |
- |
partnerships |
- |
p_age_f_1_3 |
0.891791045 |
- |
partnerships |
- |
p_age_f_1_4 |
0.931034483 |
- |
partnerships |
- |
p_age_f_1_5 |
1.0 |
- |
partnerships |
- |
p_age_f_1_6 |
0.0 |
- |
partnerships |
- |
p_age_f_1_7 |
0.0 |
- |
partnerships |
- |
p_age_f_2_1 |
0.0036523009999999997 |
- |
partnerships |
- |
p_age_f_2_2 |
0.113636364 |
- |
partnerships |
- |
p_age_f_2_3 |
0.778329198 |
- |
partnerships |
- |
p_age_f_2_4 |
0.891791045 |
- |
partnerships |
- |
p_age_f_2_5 |
0.931034483 |
- |
partnerships |
- |
p_age_f_2_6 |
1.0 |
- |
partnerships |
- |
p_age_f_2_7 |
0.0 |
- |
partnerships |
- |
p_age_f_3_1 |
0.001697073 |
- |
partnerships |
- |
p_age_f_3_2 |
0.005949851 |
- |
partnerships |
- |
p_age_f_3_3 |
0.27746900399999996 |
- |
partnerships |
- |
p_age_f_3_4 |
0.889349112 |
- |
partnerships |
- |
p_age_f_3_5 |
0.930481283 |
- |
partnerships |
- |
p_age_f_3_6 |
0.7692307690000001 |
- |
partnerships |
- |
p_age_f_3_7 |
1.0 |
- |
partnerships |
- |
p_age_f_4_1 |
0.001708672 |
- |
partnerships |
- |
p_age_f_4_2 |
0.002139495 |
- |
partnerships |
- |
p_age_f_4_3 |
0.00728988 |
- |
partnerships |
- |
p_age_f_4_4 |
0.432829374 |
- |
partnerships |
- |
p_age_f_4_5 |
0.8979436409999999 |
- |
partnerships |
- |
p_age_f_4_6 |
0.9104477609999999 |
- |
partnerships |
- |
p_age_f_4_7 |
1.0 |
- |
partnerships |
- |
p_age_f_5_1 |
0.0027662520000000003 |
- |
partnerships |
- |
p_age_f_5_2 |
0.002773925 |
- |
partnerships |
- |
p_age_f_5_3 |
0.0 |
- |
partnerships |
- |
p_age_f_5_4 |
0.015299026 |
- |
partnerships |
- |
p_age_f_5_5 |
0.535310734 |
- |
partnerships |
- |
p_age_f_5_6 |
0.8632218840000001 |
- |
partnerships |
- |
p_age_f_5_7 |
1.0 |
- |
partnerships |
- |
p_age_f_6_1 |
0.0 |
- |
partnerships |
- |
p_age_f_6_2 |
0.0027662520000000003 |
- |
partnerships |
- |
p_age_f_6_3 |
0.002773925 |
- |
partnerships |
- |
p_age_f_6_4 |
0.0 |
- |
partnerships |
- |
p_age_f_6_5 |
0.015299026 |
- |
partnerships |
- |
p_age_f_6_6 |
0.535310734 |
- |
partnerships |
- |
p_age_f_6_7 |
1.0 |
- |
partnerships |
- |
p_age_f_7_1 |
0.0 |
- |
partnerships |
- |
p_age_f_7_2 |
0.0 |
- |
partnerships |
- |
p_age_f_7_3 |
0.0027662520000000003 |
- |
partnerships |
- |
p_age_f_7_4 |
0.002773925 |
- |
partnerships |
- |
p_age_f_7_5 |
0.0 |
- |
partnerships |
- |
p_age_f_7_6 |
0.015299026 |
- |
partnerships |
- |
p_age_f_7_7 |
1.0 |
- |
partnerships |
- |
max_n_part_noage_low |
1.0 |
Maximum number of concurrent partners for individuals in low activity level |
partnerships |
- |
max_n_part_noage_med |
3.0 |
Maximum number of concurrent partners for individuals in medium activity level |
partnerships |
- |
max_n_part_noage_high |
10.0 |
Maximum number of concurrent partners for individuals in high activity level |
partnerships |
- |
breakup_scale_lambda_low_within_patch |
13.7 |
Mean duration (in years) of low activity level partnerships |
partnerships |
- |
breakup_scale_lambda_med_within_patch |
6.9 |
Mean duration (in years) of medium activity level partnerships |
partnerships |
- |
breakup_scale_lambda_high_within_patch |
4.4 |
Mean duration (in years) of high activity level partnerships |
partnerships |
- |
breakup_shape_k_low |
1.0 |
Weibull scale factor chosen to be 1 so that duration of low activity level partnerships is exponential |
partnerships |
- |
breakup_shape_k_med |
1.0 |
Weibull scale factor chosen to be 1 so that duration of medium activity level partnerships is exponential |
partnerships |
- |
breakup_shape_k_high |
1.0 |
Weibull scale factor chosen to be 1 so that duration of high activity level partnerships is exponential |
partnerships |
- |
breakup_scale_multiplier_overall |
1.5 |
Multiplier scaling duration of all partnerships |
partnerships |
- |
breakup_scale_multiplier_between_vs_within_patch |
0.4 |
Multiplier scaling duration of partnerships between patches compared to within patches |
partnerships |
- |
PC_Retention_Round1 |
1.0 |
Legacy parameter for population cohort retention at R1 (100%) |
PC |
- |
PC_Retention_Round2 |
0.9 |
Legacy parameter for population cohort retention at R2 compared to R1 |
PC |
- |
PC_Retention_Round3 |
0.9 |
Legacy parameter for population cohort retention at R3 compared to R2 |
PC |
- |
PC_Retention_Round4 |
0.9 |
Legacy parameter for population cohort retention at R4 compared to R3 |
PC |
- |
start_time_hiv |
1975.0 |
Start of the HIV epidemic in the country |
times |
- |
start_time_simul |
1900.0 |
Start of simulation |
times |
- |
end_time_simul |
2020.0 |
End of simulation |
times |
- |
COUNTRY_HIV_TEST_START |
2000.0 |
Time when background HIV testing begins |
times |
- |
COUNTRY_ART_START |
2004.0 |
Time when ART first available |
times |
- |
COUNTRY_CD4_350_START |
2011.0 |
Time when ART guidelines changed to CD4<350 |
times |
- |
COUNTRY_CD4_500_START |
2014.5 |
Time when ART guidelines changed to CD4<500 (excluding PopART arm A communities) |
times |
- |
COUNTRY_IMMEDIATE_ART_START |
2016.3333 |
Time when ART guidelines changed to immediate treatment (excluding PopART arm A communities) |
times |
- |
COUNTRY_VMMC_START |
2010.0 |
Time when VMMC first available |
times |
- |
CHIPS_YEAR1_START |
2013.9375 |
Start of CHiPs round 1 |
times |
- |
CHIPS_YEAR1_END |
2015.5 |
End of CHiPs round 1 |
times |
- |
CHIPS_YEAR2_START |
2015.5 |
Start of CHiPs round 2 |
times |
- |
CHIPS_YEAR2_END |
2016.6666670000002 |
End of CHiPs round 2 |
times |
- |
CHIPS_YEAR3_START |
2016.7083329999998 |
Start of CHiPs round 3 |
times |
- |
CHIPS_YEAR3_END |
2017.9791670000002 |
End of CHiPs round 3 |
times |
- |
DURATION_POST_TRIAL_ROUND |
48.0 |
Number of timesteps in a post-trial CHiPs round (1 year) |
times |
- |
NDHSROUNDS |
3.0 |
Number of DHS rounds conducted in country |
times |
- |
DHSROUND1 |
2002.0 |
Time of first DHS round |
times |
- |
DHSROUND2 |
2007.0 |
Time of second DHS round |
times |
- |
DHSROUND3 |
2013.0 |
Time of third DHS round |
times |
- |