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Updates/fixes to MNH modules following on from Joe's PhD #1251

Merged
merged 166 commits into from
Feb 14, 2024
Merged

Updates/fixes to MNH modules following on from Joe's PhD #1251

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7a1ef6f
prepare HIV and TB modules for PR
tdm32 Nov 11, 2022
6375729
merge in edited hiv and tb files
tdm32 Nov 11, 2022
249d917
remove hv_vmmc_counter property
tdm32 Nov 11, 2022
3fbb17d
check tb and hiv tests
tdm32 Nov 11, 2022
9830a43
flake8 checks
tdm32 Nov 11, 2022
997b3f5
Change clustering of tb in hiv+
tdm32 Nov 21, 2022
76545d2
use parameter for importation rate not value
tdm32 Nov 21, 2022
560fff0
HIV infant NVP - cap repeat visits at 5
tdm32 Nov 28, 2022
8901991
test runs
tdm32 Nov 28, 2022
e554e9a
cap repeat infant NVP appts at 5
tdm32 Nov 28, 2022
bf92082
add referred_from and repeat_visits arguments to HSI_Hiv_StartInfantP…
tdm32 Nov 28, 2022
cf55a19
edit infant NVP follow-up date
tdm32 Nov 29, 2022
bf2c483
fixes to failing tests
tdm32 Nov 29, 2022
b562202
fixes to failing tests
tdm32 Nov 30, 2022
9587d8f
Updates to resource files with amended parameter values and new param…
joehcollins Dec 1, 2022
838efe8
Edits to antenatal healthcare code to ensure that coverage of inpatie…
joehcollins Dec 1, 2022
0466bb5
edit ipt coverage rates to ensure sims can run to 2099
tdm32 Dec 1, 2022
b318cc1
edit test_hiv_tb_scenarios.py to get correct IPT coverage for children
tdm32 Dec 1, 2022
add9a56
refer ART to level 2 if unsuccessful at level 1a
tdm32 Dec 1, 2022
3b6e5dc
change importation rate to 10/100,000
tdm32 Dec 1, 2022
317b075
add fix to test_hiv_tb_scenarios.py
tdm32 Dec 1, 2022
a4a9e87
edits to pregnancy_supervisor.py in order to conduct sensitivity anal…
joehcollins Dec 1, 2022
03ce3dd
fix error caused by resetting ps_antepartum_haem
joehcollins Dec 1, 2022
6f1deef
updating pregnancy_helper_functions.py. Fixes to repeat risk of death…
joehcollins Dec 1, 2022
e63cf66
added updated call to check_if_delayed_careseeking
joehcollins Dec 1, 2022
68c877f
update labour.py analysis event and analysis parameters
joehcollins Dec 1, 2022
af2ae7a
update labour.py logging and remove redundant parameters
joehcollins Dec 1, 2022
f3f11e7
final labour.py updates
joehcollins Dec 1, 2022
96b71c2
fix error in labour_lm.py
joehcollins Dec 1, 2022
7cf2952
small updates in postnatal_supervisor.py including removing redundant…
joehcollins Dec 1, 2022
00b9515
removing redundant properties
joehcollins Dec 1, 2022
325832f
removing redundant properties
joehcollins Dec 1, 2022
69c27cb
Adding sensitivity scenario scripts
joehcollins Dec 1, 2022
9f71279
updating analysis scripts
joehcollins Dec 1, 2022
2e6fb54
updates to met_need.py
joehcollins Dec 1, 2022
46579e3
fixes to analysis_utility_functions.py to produce required outputs
joehcollins Dec 1, 2022
089e0cb
finalising calibration analysis scripts
joehcollins Dec 1, 2022
6ee2f2f
updating scenario files params
joehcollins Dec 1, 2022
b01722e
Merge branch 'master' into jcollins_thesis_analaysis_final_dec2022
joehcollins Dec 1, 2022
c7b8f9c
Merge branch 'tara_TbHivUpdates_Nov2022' into jcollins_thesis_analays…
joehcollins Dec 1, 2022
7eee27c
increased CFR for uterine rupture as MMR for that comp is low
joehcollins Dec 1, 2022
a6e6a7b
Merge branch 'master' into jcollins_thesis_analaysis_final_dec2022
joehcollins Dec 2, 2022
869c1b4
fixes to paed continual ART referrals
tdm32 Dec 2, 2022
05bf0c9
fixes to paed continual ART referrals
tdm32 Dec 2, 2022
62dcc51
check hv_art status correctly in TestAndRefer
tdm32 Dec 2, 2022
0b1bc98
Fixes to failing tests from maternal health modules
joehcollins Dec 2, 2022
fc290c0
Merge branch 'tara_TbHivUpdates_Nov2022' into jcollins_thesis_analays…
joehcollins Dec 2, 2022
654f622
add catch if person is HIV diagnosed, do not schedule another HIV tes…
tdm32 Dec 2, 2022
d7688f2
add condition not to run TB test in HIV HSI if TB already diagnosed
tdm32 Dec 2, 2022
6946283
add condition don't run newborn testing if newborn_outcomes registered
tdm32 Dec 2, 2022
59dfce2
HIV test not repeated if last test within one week
tdm32 Dec 2, 2022
3a75e1e
test_tb.py change end-date in test_basic_run_with_default_parameters …
tdm32 Dec 2, 2022
7fb4487
test_tb.py change end-date in test_basic_run_with_default_parameters …
tdm32 Dec 2, 2022
b35a730
Merge branch 'tara_TbHivUpdates_Nov2022' into jcollins_thesis_analays…
joehcollins Dec 2, 2022
51417ea
Comments added to newborn_outcomes.py to remember to update
joehcollins Dec 2, 2022
e239b2d
Merge branch 'master' into jcollins_thesis_analaysis_final_dec2022
joehcollins Dec 2, 2022
a538c24
update to stillbirth and APH calibration
joehcollins Dec 4, 2022
946bf63
use random date scheduling for TB screening HSI
tdm32 Dec 6, 2022
ae2cbe1
updates to baseline and uhc scenarios to do analysis for abstract
joehcollins Dec 6, 2022
e7b1626
correct parameter value error for treatment effect of IFA supplementa…
joehcollins Dec 7, 2022
8abb3e9
correct parameter value error for treatment effect of blood transfusi…
joehcollins Dec 7, 2022
ea66dd1
add fix to test_tb.py to make prop_smear_positive=1 for purposes of test
tdm32 Dec 7, 2022
f059062
edits to sepsis calibration and to calibration script
joehcollins Dec 7, 2022
255c350
edits to sepsis calibration and to calibration script
joehcollins Dec 7, 2022
9e3cfcc
update calibration script seed
joehcollins Dec 11, 2022
7b2db9b
fixed error in parameters introduced during calibration. update calib…
joehcollins Dec 12, 2022
d2e8ee8
fixed error in parameters introduced during calibration. update calib…
joehcollins Dec 12, 2022
7bb4f6d
update to fix parameter calibration
joehcollins Dec 13, 2022
1080ab8
Merge branch 'master' into jcollins_thesis_analaysis_final_dec2022
joehcollins Dec 13, 2022
814d081
Merge branch 'tara_TbHivUpdates_Nov2022' into jcollins_thesis_analays…
joehcollins Dec 13, 2022
a308095
final specifications for scenario files
joehcollins Dec 13, 2022
b6bf594
Updated resource files with parameter changes
joehcollins Jan 23, 2023
423ed0d
Fix to labour.py to ensure surgery for failed RP treatment. Fix that …
joehcollins Jan 23, 2023
c6ff34a
Fixed DALY weight acquisition for newborns. Update logic for ROP
joehcollins Jan 23, 2023
cd7b89a
Small fixes and logging updates to pregnancy_supervisor.py
joehcollins Jan 23, 2023
504764c
updates to analysis scripts
joehcollins Jan 23, 2023
afce3dc
updates to calibration scripts
joehcollins Jan 23, 2023
15c2d33
fix failing newborn test relating to new retinopathy logic
joehcollins Jan 23, 2023
cf40747
updated seeds for scenario files
joehcollins Jan 23, 2023
af51223
fixed error in quantiles
joehcollins Feb 6, 2023
dafdb25
fixed error in quantiles
joehcollins Feb 14, 2023
20ef10c
fixed error in quantiles
joehcollins Feb 14, 2023
8249a4e
fixed error in quantiles
joehcollins Feb 17, 2023
1fae89c
fixed error in quantiles
joehcollins Mar 22, 2023
301e941
updated scenario files
joehcollins May 15, 2023
21e91fa
updated analysis scripts
joehcollins Jun 15, 2023
b990093
update prob_delay_ parameter
joehcollins Jun 30, 2023
86656c8
update rr_still_birth_ur parameter
joehcollins Jun 30, 2023
4f3069c
update retionopathy and miscarriage params
joehcollins Jun 30, 2023
d5ef807
update resus treatment effects
joehcollins Jun 30, 2023
a8c2ed8
updated mean_birth_weights params
joehcollins Jun 30, 2023
9b24f03
updates to consumables
joehcollins Jun 30, 2023
a3d915b
updates to consumables
joehcollins Jun 30, 2023
f73f4dd
update enceph_cfr_multiplier
joehcollins Jun 30, 2023
a61b52e
add in logic for the effect of obesity on potl
joehcollins Jun 30, 2023
66c5834
add in updated newborn resus logic
joehcollins Jun 30, 2023
c68020b
add in updated newborn resus logic
joehcollins Jun 30, 2023
f9980a0
add in updated newborn resus logic
joehcollins Jun 30, 2023
81f56b1
cord care provisional on birth kit consumables
joehcollins Jul 1, 2023
730446b
update KMC logic
joehcollins Jul 1, 2023
579f02b
update KMC logic
joehcollins Jul 1, 2023
9d3a1e2
update KMC logic
joehcollins Jul 1, 2023
a313a84
update neonatal pnc logic so care seeking is higher for all neonates …
joehcollins Jul 1, 2023
6692e22
update logic relating to ANC qual parameters
joehcollins Jul 1, 2023
df82ada
update so that inpatient care level corresponds with referal level
joehcollins Jul 1, 2023
18e6c31
update so that inpatient care level corresponds with referal level
joehcollins Jul 1, 2023
17d5dbe
update calibration file
joehcollins Jul 1, 2023
0f3ac2e
update analysis event in pregnancy supervisor
joehcollins Jul 1, 2023
cf2198e
fix to error in newborn outcomes
joehcollins Jul 1, 2023
4d732ac
fix to error in newborn outcomes
joehcollins Jul 1, 2023
1517fa3
fix to error in newborn outcomes
joehcollins Jul 1, 2023
c3bde7c
calibration updates
joehcollins Jul 2, 2023
e71871a
calibration updates
joehcollins Jul 2, 2023
43ff8ae
calibration updates
joehcollins Jul 2, 2023
cb3acbb
calibration updates
joehcollins Jul 2, 2023
6715fe2
calibration updates
joehcollins Jul 3, 2023
a02d8cf
calibration updates
joehcollins Jul 5, 2023
15119d5
calibration updates
joehcollins Jul 5, 2023
3ab0475
calibration updates
joehcollins Jul 5, 2023
0354fa6
calibration updates
joehcollins Jul 6, 2023
2bf9d40
calibration updates
joehcollins Jul 6, 2023
d2a0352
fixes to tests
joehcollins Jul 6, 2023
cb615e6
fixes mistake to cs baseline assumption
joehcollins Jul 7, 2023
3ecb4ae
fixing errors
joehcollins Jul 9, 2023
e21f2c7
fixing errors for pph incidence
joehcollins Jul 9, 2023
354b565
fixing errors for pph incidence
joehcollins Jul 10, 2023
6683291
fixed obstructed labour error
joehcollins Jul 11, 2023
a34e6ee
fix to cause delay in PPH treatment
joehcollins Jul 13, 2023
9d48e72
analysis script update
joehcollins Jul 17, 2023
f195767
analysis script update
joehcollins Jul 20, 2023
45c5143
flake8
joehcollins Aug 3, 2023
1cef118
remove unneeded logic from did_not_run functions
joehcollins Aug 16, 2023
bbf4b9c
fix
joehcollins Sep 6, 2023
6e0002e
tidying branch
joehcollins Sep 7, 2023
71e9923
tidying comments
joehcollins Sep 9, 2023
196d537
flake8
joehcollins Sep 10, 2023
050cfb4
update to calibration script
joehcollins Sep 11, 2023
93bfd1b
update to thesis analysis script
joehcollins Sep 12, 2023
53e284a
typo
joehcollins Sep 13, 2023
4b743f4
fixed classification of post term pregnancies
joehcollins Nov 16, 2023
c71e390
fixed application of anaemia risk
joehcollins Nov 16, 2023
2264e55
fixed effect of delays on PPH interventions
joehcollins Nov 16, 2023
083e6e7
additional fix to anaemia logic
joehcollins Nov 16, 2023
43faf4b
calibration scripts
joehcollins Nov 17, 2023
0e0d77d
calibration scripts
joehcollins Nov 28, 2023
0008f31
calibration scripts
joehcollins Dec 6, 2023
89cb05b
Merge branch 'master' into jcollins_mnh_module_updates_jan24
joehcollins Jan 2, 2024
6944cdc
fixed syntax error
joehcollins Jan 2, 2024
a679a20
removed uncalled parameters. Updated ResourceFile_Improved_Healthsyst…
joehcollins Jan 2, 2024
8ef599b
Updated ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking.xls…
joehcollins Jan 2, 2024
4ad13b1
Updated ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking.xls…
joehcollins Jan 2, 2024
bfb5e45
Fixes for failing tests
joehcollins Jan 2, 2024
3bbd9ae
Removal of all internal delay/squeeze factor logic from the MNH modules
joehcollins Jan 4, 2024
dc0cf24
removed uncalled parameter from resource file
joehcollins Jan 4, 2024
e331fea
fix MNH calibration script to meet new pandas requirements
joehcollins Jan 5, 2024
57ac0bb
fix MNH analysis script to meet new pandas requirements
joehcollins Jan 5, 2024
40dd8f2
add fix to calibration script to correctly output births
joehcollins Jan 8, 2024
033fedc
flake8
joehcollins Jan 8, 2024
afe9b5b
Merge branch 'master' into jcollins_mnh_module_updates_jan24
joehcollins Jan 8, 2024
89e7e61
update priority policy resource file to include new treatment ids
joehcollins Jan 8, 2024
55a73ba
flake8
joehcollins Jan 8, 2024
ac87ae3
flake8
joehcollins Jan 8, 2024
127d4fd
fix failing health system test
joehcollins Jan 9, 2024
f9bbbdf
Merge branch 'master' into jcollins_mnh_module_updates_jan24
tbhallett Feb 1, 2024
2474a76
Merge branch 'master' into jcollins_mnh_module_updates_jan24
joehcollins Feb 7, 2024
20935cf
Merge branch 'master' into jcollins_mnh_module_updates_jan24
tbhallett Feb 13, 2024
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4 changes: 2 additions & 2 deletions resources/ResourceFile_AntenatalCare.xlsx
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4 changes: 2 additions & 2 deletions resources/ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking.xlsx
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4 changes: 2 additions & 2 deletions resources/ResourceFile_LabourSkilledBirthAttendance.xlsx
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4 changes: 2 additions & 2 deletions resources/ResourceFile_NewbornOutcomes.xlsx
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4 changes: 2 additions & 2 deletions resources/ResourceFile_PostnatalSupervisor.xlsx
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4 changes: 2 additions & 2 deletions resources/ResourceFile_PregnancySupervisor.xlsx
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4 changes: 2 additions & 2 deletions resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES.xlsx
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730 changes: 154 additions & 576 deletions src/scripts/maternal_perinatal_analyses/analysis_scripts/analysis_utility_functions.py
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168 changes: 0 additions & 168 deletions src/scripts/maternal_perinatal_analyses/analysis_scripts/checking_dalys_output.py
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