PR to record the prevalence of disease/condition, still births, neonatal death, maternal mortality #1455
Commits on Jul 25, 2024
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Just realized that I can't access the folders
Could create it within the healthburden module, but am unable to access logs? Or what is directly produced from the modules themselves.
Commits on Jul 26, 2024
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Added function to request get_current_prevalence from each registered…
… module (Get_Current_Prevalence). Also have it so that this is run every month alongside the Get_Current_Dalys logger
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Check to see if recording the prevalence is working.
Adding in disease modules gradually
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Added function calculating the prevalence of other adult cancers over…
… all individuals
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Commits on Jul 29, 2024
Commits on Aug 1, 2024
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Changed the naming of columns so the prevalence from the labour modul…
…e is recorded as intrapartum stillbirth
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Added function calculating neonatal and maternal mortality. Neonatal …
…mortality defined as death before 29 days. Maternal mortality "to align with accepted definition of maternal mortality as "annual number of female deaths from any cause related to or aggravated by pregnancy or its management (excluding accidental or incidental causes) during pregnancy and childbirth or within 42 days of termination of pregnancy, irrespective of the duration and site of the pregnancy." So this includes direct and indirect mortality. The 30% of AIDS deaths in this population is from WHO methods of MMR estimation https://www.who.int/publications/i/item/9789240068759"
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added function to report the prevalence of depression for that month …
…across all individuals
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removed some modules from checks on prevalence as either (a) forgot t…
…o do them or (b) do not have outcomes to report
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changed how infections are calculated (based on number reporting symp…
…toms caused by schisto)
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added function to calculate monthly prevalence of bladder cancer acro…
…ss all individuals
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added function to calculate monthly prevalence of diarrhoea across al…
…l individuals. Based solely on "gi_has_diarrhoea", not dehydration, pathogen, etc.
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added function to calculate monthly prevalence of different ncds. Cal…
…culated as they are for the "proportion_of_something_in_a_groupby_ready_for_logging", but across everyone and not over age/sex
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added function to calculate monthly prevalence of different ncds. Cal…
…culated as they are for the "proportion_of_something_in_a_groupby_ready_for_logging", but across everyone and not over age/sex
Commits on Aug 2, 2024
Commits on Aug 12, 2024
Commits on Aug 13, 2024
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NOT WORKING but tried to simplify the collection process as was being…
… returned as all 0s.
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Commits on Aug 15, 2024
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Now matching up more. Have to use the second key from the function I …
…wrote, as it logs before the normal logger does
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Commits on Aug 16, 2024
Commits on Aug 18, 2024
Commits on Aug 20, 2024
Commits on Aug 21, 2024
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Aded skip over dates that go beyond when the prevalence is logged by …
…the central logger. Includes matching of dates, as logging happens at different times between each disease module and the central logger.
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Commits on Aug 29, 2024
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Changed calculation of prevalence on simple whether or not person was…
… involved in an RTI
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Changed calculation of prevalence to be the number of people who are …
…logged as non-infected
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Get_Current_Prevalence have test variable that is true/false and chan…
…ges the frequency of logging. Way to move this outside of function? Removed print statements
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Made test a parameter that is default set to False and can be modifie…
…d in the script. Then, changed the offset days to 0 and have daily logging,
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Ensured indenting was correct. Removed tolerance buffer for days and …
…%. Added function to avoid repetition
Commits on Aug 30, 2024
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Attempted to make the prevalence logging daily, for the purpose of th…
…e test. Still logging monthly
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Commits on Sep 3, 2024
Commits on Sep 4, 2024
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Allow mockitis to be read in the GetPrevalence Class.
Added report_prevalence function to the mockitis module
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Changed TB prevalence logging to only include active cases. "I think …
…here we should log only active cases, this way we can compare with WHO reports / GBD etc. Also the way that we assign latent cases is not identical to other models, we don't have infections -> latent -> active so we would under-estimate the latent infections. Best to stick to symptomatic active cases only."
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Added report_prevalence to the skeleton module so that it's formally …
…part of the definition of a disease module
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Added option between daily, monthly, and yearly logging
Added check to ensure prganancy is possible
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Tidied test to have mockitis test (to check logging structures etc) a…
…s well as initial test to see if all expected modules have logged diseases
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Commits on Sep 5, 2024
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- Remove log_line_by_line for prevalence as is contained in write_to_…
…log_prevalence function
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CardioMetabolic no longer a special case. Instead, checks to see if t…
…he output of report_prevalence is a series or a dataframe. NB kept DiseaseThatCausesA for the test_healthburden to work,
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Changing the labelling of the Intrapartum and Antenatal Stillbirths t…
…o be within labour.py and pregnancy_supervisor.py respectively.
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Changing the labelling of the Intrapartum and Antenatal Stillbirths t…
…o be within labour.py and pregnancy_supervisor.py respectively.
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Changing the labelling of the Intrapartum and Antenatal Stillbirths t…
…o be within labour.py and pregnancy_supervisor.py respectively.
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Changed the indexing of self.prevalence_of_diseases to be flexible in…
… line with the parameter logging_frequency_prevalence
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Update src/tlo/methods/healthburden.py
Co-authored-by: Tim Hallett <[email protected]>
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Merge remote-tracking branch 'origin/rmw/log_prevalence_all_disease' …
…into rmw/log_prevalence_all_disease
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In healthburden module, removed checks on what the prevalence logging…
… freuquency parameter was set as, is now just passed in as an argument
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Updated the docstring to remove references to the necessity of one da…
…ta type or another.
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Refactored the function log_df_line_by_line to be a function on this …
…module, then calling it in the write_to_log and write_to_log_prevalence functions
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- Refactored the function log_df_line_by_line to be a function on thi…
…s module, then calling it in the write_to_log and write_to_log_prevalence functions - Added logic to healthburden too to ensure that if None is returned the logging etc is skipped (in accordance with it being in the base class).
Commits on Sep 11, 2024
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- Removed report_prevalence from baseclass
- Added assertion to check if a module that uses the healthburden module has a report_prevalence function
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Merge branch 'refs/heads/master' into rmw/log_prevalence_all_disease
# Conflicts: # src/tlo/core.py
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Commits on Sep 12, 2024
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Added dummy disease module to Mockitis
Reformatted test so now they log at the same rate
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Edited so that the DiseaseThatCausesA/B etc modules from the test_hea…
…lthburden are not included
Commits on Sep 30, 2024
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Changed so that the MMR, Live Births etc returns None only if Simplified Births are used
Commits on Oct 1, 2024
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Changed prevalence calculation for RTI to ensure accident happened in…
… last month. Fixed issue so that only comparing actual times (not NaT)