Cervical cancer (#1287)

* fix indexing

* fix indexing

* add new fts

* add variables, add prob for via

* improve for readability

* update out statement to assess entire population

* set screening age as variable

* initialize screening to F

* remove duplicate

* 30d marker

* out updates

* force to be in stage4 for palliative care -- previously if 'None' was also eligible for palliative

* change from symptoms to selection in polling

* change to jan to avoid 2x initialization of population

* delete HSI_CervicalCancer_Screening, not used

* change diagnoses stages to only be stage 1 to 4

* change diagnoses stages to only be stage 1 to 4

* add 'none' to ce_stage_at_diagnosis

* repeated screening and cin procedure in functions

* adjust biopsy logic

* remove hard coding, start setting parametrs

* rename for clarity

* adjust cerv cancer consumables

* removing hard coding and adding todos

* set eligible population based on hiv criteria

* set eligible population based on hiv criteria

* behavior based on hv diagnosis rather than inherent property

* palliative care fix

* update cancer consumables

* remove hard coding

* equipment and consumables

* remove hard code

* change screening conditions

* remove hard coding of params and move to ResourceFile_Cervical_Cancer.xlsx

* remove hard coding of params and move to ResourceFile_Cervical_Cancer.xlsx

* remove hard coding of params and move to ResourceFile_Cervical_Cancer.xlsx

* .

* add comments and remove completed todos

* replace min_age_hv with min_age_hpv

* replace min_age_hv with min_age_hpv

* .

* set ce_date_cin_removal if thermoablation or cryotherapy successful

* replace cervical_cancer file w the original one

* not used

* not used

* not used

* need to ensure treatment occurred

* add consumables for biopsy

* fix to ensure CIN treatment pursued if not in Stage cancer

* do biopsy if biopsy has not been done before

* do biopsy if biopsy has not been done before

* fix output file

* additional tests

* revert resource file

* fix indenting

* comment out the 2024 + tests so that it runs in reasonable time

* merge

* remove commented out csv

* fix some screening logic

* replace with function

* biopsy only if stage 1+
CIN treatment only if CIN as ce_hpv_cc_status

* fix the tests and clean code

* update logic for min years between screening

* improved documentation

* code clean up

* .

* .

* comment clarity

* udpate cervical cancer file with parameter of minimized screening window if previous CIN

* test commit - remove space

* add comments

* clean code and add comments for readability

* Remove hash DF, flag that need to only plot with log and move away from CSV plots

* improve comments/readability of tests

* fix dxtest name

* .

* .

* .

* updates to consumables and equipment

* reverting to master .github

* reverting to master

* remove unwanted files

* update cancer cons

* remove cervical cancer from 'other' given it has its own module

* cervical_cancer.py linting

* cervical_cancer_analysis.py linting

* cervical_cancer_test.py linting

* isort

* lint changes that pass tests

* link changes, also comment out out_csv

* add color for cervical cancer in graph

* add cervical cancer color

* change cervical cancer color to mediumturquoise

* add color for cervical cancer in CAUSE_OF_DEATH_OR_DALY_LABEL_TO_COLOR_MAP

* change readcsv

* remove param definition at top of file and add to resourcefile

* remove screen_pop function since only used 1x

* change cin procuedure to class that can be used throughout other classes with proper structured manner as mixin, also remove unecessary input parameters other than self and person_id

* added cerv cancer to bottom of each priority doc, modeled priority based on other adult cancers

* del unused variables

* update consumables -- change some requirements to optional and change the the chemo used

* LLETZ Machines for thermoablation and Cryotherapy Unit for cryo

* LLETZ Machines for thermoablation and Cryotherapy Unit for cryo

* update consumable chemo alternative options

* add eq. comment for future cahnge to Thermoablation Device

* add cerv cancer write-up

* definition and type changes

* initialize parameters related to hiv at the start

* add predictors

* remove code duplication

* remove check_configuration_of_population because force changes for this test

* create batch event, fix parmeters, remove ce_date_death removed and only have demography death date, remove unused code, equipment documentation,

* fix plotting from log file

* remove print statements

* change the asserts to be logger warnings

* fix parameter and module variables

* improve format

* improve format

* logging every 1mo as recommended

* remove unused csv import

* revert cervical cancer analysis parameters

* move cin procedure within CervicalCancer module

* remove extra spacing

* fix total dead count

* add equipment in function perform_cin_procedure

* update coments and spacing

* improve coding syntax

* improve coding syntax

* improve coding syntax

* fix for no hsi running

* fix vaginal bleeding check -- before vaginal bleeding symptom was not subset of all diagnosed because referral rate <1, so not guaranteed that they would be diagnosed.

* extend simulation and remove test that is not valid in extended simulation

* remove unused 'module'

* fix tox issues

* add properties

* addt test fixes

* .

* fix 0ing of stage progressions with hivneg

* rename output file for clarity

* remove ce_hiv_unsuppressed parameter and update lm and output variables accordingly

* .

* add n_via_cin_ever_detected

* add back cons check

* make all graphs start in 2010, dynamic ylim setting, remove plot n_hivneg_diagnosed_past_year because this is not a parameter we are documenting in logger

* repair broken .docx file

* update write-ups page

* preserve format of HealthPolicy files

* remove several columns added by accident in PR

* remove cerivval cancer (commented-out) from other cancers

* remove comment discussion in write up

* linting

* linting

* linting and correct comment

* linting

* comment and no need to define ce_hpv_cc_status_original

* loc for screening should not filter for those wihtout cin

* linting

* corrected test

* remove in-line review comments

* strengthn test

* remove failing line

* remove symptoms not used

* update convetnion for resourcfilepath

* correct test

* iterate through models in reverse order to prevent people advancing through all stages

* mock properties in HIV needed to test cervical cancer module

* update and strengthen tests

* Refactor cervical cancer treatment and death handling logic

Introduced `CervicalCancer_DeathInStage4` event to streamline stage 4 deaths. Simplified treatment success calculations and follow-up scheduling logic, improving code readability and maintainability. Adjusted palliative care to reuse event scheduling and fixed consumable availability checks.

* remove docstring

* remove erroneous declaration of TB module as a dependency?!

* update label

* clarify daly weight parameters

* add default for ce_date_cin_removal

* get rid of bitwise thing

* simplify

* declare parameter types

* declarae and rationalise parameters

* clean up parameters

* make onset of vaginal bleeding limited to those who do not already have it --- and remove block on onset only for those not diagnsed.

* correct param description

* correct property description

* control cats

* symptom and >=

* remove magic number and use parameter

* delete setting persons on palliative care as, by definition, none are in palliative care from init-pop

* simplify syntax

* refactor choose_cin_procedure_and_schedule_it

* rollback change in cats.

* more cleannig

* cleaning

* clean docx

* add notes

* add parameters to RF for max health system fun / max health seeking behaviour

* min age hpv mislabelled and used inconsistently, most occrurence implicit and hard-coded; revert to hard-coded throughout.

* reduce num properties and  streamline poll

* add cc to full model officially

* avoid type mismatch error

* correct init_depn

* don't rely on model having run initialised simulation when initialising HSI

* linting

* my linting

* update analysis script

* add script for calibration figure

* add comment

* refactorig and rationalise equipment declaration

* refactorig and rationalise equipment declaration

* make checking for death be on actual death not YLL

* clean up commented-out code

* refactor

* refactor to call it VIA screening throughout

* rationalise TREATMENT_ID

* clarfy transition parameters

* refactor

* for surgery - surgical equipment essential

* strengthen test about progression and make treatment put everyone back to 'hpv' (not 'none')

* fix script

* be explicit about root to be robust to from where script is run

* further fixes

* drop men

* .

* linting

* refactor screening VIA

* refactor screening xpert

* refactor presentation

* refactor CIN

* refactor treatment

* update docstring

* align HSI names and treatment_ids

---------

Co-authored-by: mmsuarezcosta <[email protected]>
Co-authored-by: thewati <[email protected]>
Co-authored-by: joehcollins <[email protected]>
Co-authored-by: Tim Hallett <[email protected]>
Co-authored-by: Emmanuel Mnjowe <[email protected]>
Co-authored-by: Asif Tamuri <[email protected]>

Author: 7 people

docs/write-ups/CervicalCancer.docx

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docs/writeups.rst

@@ -69,6 +69,8 @@ Non-Communicable Conditions
 
     * **Breast Cancer**: Cancer of the breast and its treatment. :download:`.docx <./write-ups/BreastCancer.docx>`
 
+    * **Cervical Cancer**: Cancer of the breast and its treatment. :download:`.docx <./write-ups/CervicalCancer.docx>`
+
     * **Oesophageal Cancer**: Cancer of the oesophagus and its treatment. :download:`.docx <./write-ups/OesophagealCancer.docx>`
 
     * **Other Adult Cancer**: Summary representation of any type of cancer other those listed and their treatment. :download:`.docx <./write-ups/OtherAdultCancer.docx>`

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