Update newborn HIV screening #732
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… diagnosed mothers receive follow up tests
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Wasnt expecting every test to fail on a one line change!! Will investigate |
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@tamuri do you think this is a github thing as I'm running the first test locally and currently no issues ? (definitely not an immediate fail like seen here) |
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@tdm32 this is the branch that newborn changes can come in on? or we can just add the change to your new branch instead? (not right now of course!!!) |
tbhallett
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May 9, 2023
…ng due to unavailable consumables (#857) * import files related to tb and hiv add deviance_measure to fullmodel.py * add fixed incidence poll add scaling factor for WHO estimates add function to calculate proportion untreated each year * add script for plotting * add diabetes as risk factor * add diabetes as risk factor * flake8 and isort * put additional logging into demography for deviance_measure: only used if calibrating HIV and TB modules * flake8 tests passing * edit warning messages in HIV if event should not be running * add referred from argument to HSI_Hiv_TestAndRefer in care_of_women_during_pregnancy.py * add argument referred_from to HIV test in newborn_outcomes.py * add argument referred_from to HIV test in hsi_generic_first_appts.py * add argument referred_from to HIV test in labour.py * remove automatic HIV testing for everyone attending hsi_generic_first_appts.py * reduce retention on ART every 3 months from 1 to 0.998 * remove unused import statements * remove unused import statements * change cause of death to TB (non-AIDS) to match utils.py mapping CAUSE_OF_DEATH_LABEL_TO_COLOR_MAP * allow HIV test for person presenting at generic first appt with aids symptoms * only allow deviance_measure.py on_sim_end function to run if sim has run past 2020 (else data and model imports fail) this fixes failing tests in module_dependencies * reduce HIV testing in care_of_women_during_pregnancy.py, labour.py and newborn_outcomes.py to match quarterly reports (all set to 95% currently) * reduce viral suppression adjustment to 1 reduce prob retention on ART to 0.98 reduce prob seeking ART if drug NA to 0.98 reduce prob seeking ART if appt NA to 0.98 * flake8 * reduce ART retention * remove immediate referral for testing for baseline AIDS cases to increase mortality in first 2 yrs of sim * add condition for infant testing: mother must be known HIV+ (confirmed with Joe) linked to PR #732 * join if statement in newborn_outcomes.py to make conditions for hiv test clearer remove todo statements in hiv if finished * flake8 * change baseline aids deaths scheduling to occur at max 18 months after sim start * in HSI_Hiv_TestAndRefer only log test and update person's properties if test result is not None * set up batch runs for test runs * flake8 and isort * set up batch runs * set up batch runs * reinstate testing for baseline aids cases * flake8 * flake8 * add script to plot outputs from batch runs * edit plots * flake8 checks * fix failing hiv tests * change demography dicts to __demog_outputs to denote dict is private (used only by deviance_measure.py move logic for newborn HIV testing to HIV module move logic for mother HIV testing during/post-labour to HIV module * tidy up HIV testing on_birth in HIV module * move HIV testing logic from care_of_women_during_pregnancy.py to HIV module * flake8 edits * fix test_hiv_initiated_for_infant * remove logger_detail * update deviance_measure.py to include data to 2021 * use default dict * refactor to let the storage for the Deviance module be in the deviance module * small changes to deviance_measure.py * remove commented-out section in hsi_generic_first_appts.py * small changes to labour * small changes to care_of_women_during_pregnancy.py * Revert "add script to plot outputs from batch runs" This partially reverts commit ded2bb1. * refactor demography slightly * use of pd.notnull rather than equation to pd.NaT (catching other forms of nulls) * edit docstring in `decide_whether_hiv_test_for_mother` for clarity: the HSI is scheudled here, not just decided upon * test runs * add deviance module to list of modules returned by fullmodel * minor edits to hiv.py * use "nice name" for a label of cause of disability * cosmetic changes to tb.py * linting * update TB notified cased by including QECH data that was previously missed * update appt footprint of TBNew if to reschedule the HSI * remove EXPECTED_APPT_FOOTPRINT from HSI base class * cherry-pick change to healthsystem from PR #826 * Update src/tlo/methods/tb.py change get_blank_appt_footprint to make_appt_footprint Co-authored-by: Tim Hallett <[email protected]> * Update src/tlo/methods/tb.py remove if clause to assign year with conditions Co-authored-by: Tim Hallett <[email protected]> * add text to explain scenario supplementary analyses * remove commented out consumables in tb.py * added fix suggested in PR #859 * change spec of lm for active tb using conditional predictors * remove hiv testing rate adjustment value and add as parameter * add to comment in test * edit deviance_measure.py * add fix to linear model spec with conditional predictors * typo correct * flake8 checks passed * create test to test appt footprint of HSI_Tb_StartTreatment * update the test to check run time of the HSI * update notes * update HIV and TB calibrated parameters * change repeat occurrences of HSI_Tb_StartTreatment to call "self" instead of new instance of event * finish the new test * fixes to failing tb tests * update hiv relevant appt footprints * update EXPECTED APPT FOOTPRINT and docstrings * update appt footprint from U5OPD to Peds for treatment on infant hiv prevention * update appt footprint from O5OPD to PharmDispensing for PrEP HSI * edit scenarios and add sheet in ResourceFile_TB.xlsx for all changed parameters * edit tests to run with updated scenarios * update the VMMC schedule logic * correct the VMMC schedule logic * set up scenarios for projections * set up scenarios for projections * add parameter to ResourceFile_HIV.xlsx * edit scenarios * schedule follow-up appts, not reschedule * rollback whitespace changes for labour modules (easier for checks and future merges) * rollback whitespace changes for labour modules (easier for checks and future merges) * add a parameter to indicate the relative probability of a male aging <15 yrs to be circumcised, compared to a male aging 15+ yrs * create the separate route of VMMC for male aging <15 yrs * re-add the parameter of relative probability of circumcision for < 15yrs, as merging in master removed that change * delete deviance_measure file * create a temporary scale run script that runs only for 10 years (shorter running time than 20 years) * update docstrings * replace the relative probability of vmmc for children by the (absolute) probability (its current value is set to 1.0 and will be calibrated) * update the route of VMMC for <15 yrs * creat test_child_circ * add one more assertion to the new test * update the test so that we can vary the probability of child circumcision * fix failing test * update prob_circ_for_child * try separate probs for child vmmc before and from 2020 * remove blank line * make the code concise * logging more circ measures * add logger of hiv module to the temporary scale run * scale run for 20 years * create temporary logger for circumcision * create temporary test process to check the proportion of circ by age group * Revert "logging more circ measures" This reverts commit a88372f. * Revert "make the code concise" This reverts commit 26ef248. * finish the temporary test * Revert "finish the temporary test" This reverts commit 71e50bb. * Revert "create temporary test process to check the proportion of circ by age group" This reverts commit 9333bf7. * Revert "create temporary logger for circumcision" This reverts commit 90cc260. * delete the temporary scale run folder * use tuple unpacking and `not` for clarity * embed function that is only used by own test * use one linear model for child circ, and use year as an external variable * typo in linear model * apply model to population rather than individual * use self rather creating new instance of HSI_Hiv_Circ * linting --------- Co-authored-by: tdm32 <[email protected]> Co-authored-by: Tim Hallett <[email protected]> Co-authored-by: Tara <[email protected]> Co-authored-by: Asif Tamuri <[email protected]>
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@tdm32 wondering if i can close this old PR now?? Or is this something that still needs fixing |
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@joehcollins --- are you still working on this> Not sure if this PR is still active and in the queue for merging or not. |
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@tbhallett actually not sure on this one - i think i commented for @tdm32 to have a look and see if she remembers what our plan was here!! |
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The function decide_whether_hiv_test_for_infant in hiv.py checks this condition. As long as this is in your branches, this issue can be closed |
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Yep thats in my current branch. Closing now. |
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Small change to scheduling of HIV screening for newborns via the newborn_outcomes module so that only newborns of mothers diagnosed with HIV receive screening (previously all newborns were being screened)