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Cervical cancer #1287

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andrew-phillips-1 wants to merge 226 commits intomasterUCL/TLOmodel:masterfrom cervical_cancer_UCL/TLOmodel:cervical_cancer_Copy head branch name to clipboard

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Commits on Oct 16, 2023

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Commits on Oct 17, 2023

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• first pass at cervical cancer module based on editing breast cancer module

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• first pass at cervical cancer module based on editing breast cancer module

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Commits on Oct 18, 2023

• first pass at cervical cancer module based on editing breast cancer module

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• first pass at cervical cancer module based on editing breast cancer module

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• first pass at cervical cancer module based on editing breast cancer module

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Commits on Oct 19, 2023

• first pass at cervical cancer module based on editing breast cancer module

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• first pass at cervical cancer module based on editing breast cancer module

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• first pass at cervical cancer module based on editing breast cancer module

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• first pass at cervical cancer module based on editing breast cancer module

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Commits on Oct 20, 2023

• first pass at cervical cancer module based on editing breast cancer module

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Commits on Oct 21, 2023

• first pass at cervical cancer module based on editing breast cancer module

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• first pass at cervical cancer module based on editing breast cancer module

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Commits on Oct 23, 2023

• first pass at cervical cancer module based on editing breast cancer module

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Commits on Nov 4, 2023

• first pass at cervical cancer module based on editing breast cancer module

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Commits on Nov 13, 2023

• first pass at cervical cancer module based on editing breast cancer module

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Commits on Nov 26, 2023

• first pass at cervical cancer module based on editing breast cancer module

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Commits on Nov 28, 2023

• first pass at cervical cancer module based on editing breast cancer module

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Commits on Dec 3, 2023

• first pass at cervical cancer module based on editing breast cancer module

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Commits on Dec 4, 2023

• first pass at cervical cancer module based on editing breast cancer module

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• first pass at cervical cancer module based on editing breast cancer module

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Commits on Dec 6, 2023

• HSIs

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• HSIs

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Commits on Dec 7, 2023

• HSIs

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Commits on Dec 10, 2023

• HSIs

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• HSIs

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• HSIs

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Commits on Dec 24, 2023

• HSIs

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Commits on Dec 30, 2023

• HSIs

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Commits on Jan 1, 2024

• HSIs

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Commits on Jan 2, 2024

• HSIs

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Commits on Jan 3, 2024

• Merge branch 'master' into cervical_cancer_

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• HSIs

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• Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel into cervical_cancer_

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Commits on Jan 4, 2024

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Commits on Feb 26, 2024

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Commits on Mar 4, 2024

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• Merge remote-tracking branch 'origin/master'

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Commits on Jun 10, 2024

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Commits on Jun 13, 2024

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Commits on Jun 18, 2024

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Commits on Jun 19, 2024

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Commits on Jun 20, 2024

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• Merge branch 'refs/heads/master' into cervical_cancer_

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• refactor to use do_at_generic_first_appt on the module

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• roll back changes to healthsystem.py

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• roll back changes to hiv.py

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• cleaning up files

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• cleaning up files

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• Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_cancer_

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Commits on Jun 21, 2024

• Merge remote-tracking branch 'origin/master' into cervical_cancer_

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• HSIs restructured with Screening HSI

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• HSIs restructured with Screening HSI

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• Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel into cervical_cancer_

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Commits on Jun 24, 2024

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• Merge branch 'master' into cervical_cancer_

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• restructured HSIs again within module

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Commits on Jun 26, 2024

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Commits on Jun 28, 2024

• Accessing consumables and analyses using logger

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Commits on Jun 29, 2024

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• Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_cancer_

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Commits on Jul 3, 2024

• Accessing consumables from cancer_consumables.py

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Commits on Jul 5, 2024

• Rollback to using csv file in analyses

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• Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_cancer_

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Commits on Jul 14, 2024

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Commits on Jul 18, 2024

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Commits on Jul 20, 2024

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Commits on Jul 21, 2024

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Commits on Jul 22, 2024

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Commits on Jul 29, 2024

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Commits on Aug 5, 2024

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Commits on Aug 7, 2024

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Commits on Aug 8, 2024

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Commits on Aug 9, 2024

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Commits on Aug 14, 2024

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Commits on Aug 16, 2024

• temporary rollback to using xpert and via as symptoms

  thewati

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Commits on Aug 24, 2024

• Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel into cervical_cancer_

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Commits on Sep 7, 2024

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Commits on Oct 7, 2024

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Commits on Oct 8, 2024

• create function for plotting

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Commits on Oct 9, 2024

• adjust proportion plotting

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Commits on Oct 21, 2024

• ensure original and new logging capabilities coexist in same file

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• add year variation for screening and testing

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• edit parameters

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• edit sign direction, should be VIA if before '24'

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Commits on Oct 22, 2024

• remove hard coding

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• add hash documentation

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• delete import of random

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• delete import of random

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• ensure all random instances associated with self

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• set seed non-hardcoded

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• hash for testing

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• merge in changes from updated cervical_cancer branch

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• update variable name, improve rng

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• edit to ensure screening with dates for via and xpert

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• Merge branch 'master' into cervical_cancer_

  thewati

  authored
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• comment out hash

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• Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_cancer_

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• comment out hash

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Commits on Oct 23, 2024

• remove entire df broadcasting to only alive and can't override previous ce_cc_ever

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• remove entire df broadcasting to only alive and can't override previous ce_cc_ever

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• revert to 2025

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• comment out hash

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• comment out hash

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• Rollback _initialised Simulation object

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• Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_cancer_

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  5d69604

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• address new stage in one line

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• spread out death days

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  5ee1ae4

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• fix indexing

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• fix indexing

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• add new fts

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• add variables, add prob for via

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• improve for readability

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Commits on Oct 29, 2024

• update out statement to assess entire population

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Commits on Oct 30, 2024

• set screening age as variable

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• initialize screening to F

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• remove duplicate

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• 30d marker

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• out updates

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

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Commits on Oct 31, 2024

• change from symptoms to selection in polling

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Commits on Nov 1, 2024

• change to jan to avoid 2x initialization of population

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• delete HSI_CervicalCancer_Screening, not used

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• change diagnoses stages to only be stage 1 to 4

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• change diagnoses stages to only be stage 1 to 4

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• add 'none' to ce_stage_at_diagnosis

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• repeated screening and cin procedure in functions

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• adjust biopsy logic

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Commits on Nov 4, 2024

• remove hard coding, start setting parametrs

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• rename for clarity

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• adjust cerv cancer consumables

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• removing hard coding and adding todos

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• set eligible population based on hiv criteria

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• set eligible population based on hiv criteria

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• behavior based on hv diagnosis rather than inherent property

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• palliative care fix

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Commits on Nov 11, 2024

• update cancer consumables

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• remove hard coding

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• equipment and consumables

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• remove hard code

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Commits on Nov 13, 2024

• change screening conditions

  mmsuarezcosta

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Commits on Nov 14, 2024

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

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

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

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Commits on Nov 15, 2024

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• Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel into cervical_cancer_

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Commits on Dec 11, 2024

• add comments and remove completed todos

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• replace min_age_hv with min_age_hpv

  mmsuarezcosta

  committed
  23b0240

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• replace min_age_hv with min_age_hpv

  mmsuarezcosta

  committed
  758fa41

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• Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel into cervical_cancer_

  andrew-phillips-1

  committed
  926633b

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• .

  andrew-phillips-1

  committed
  9ba2bb9

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Commits on Dec 13, 2024

• Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_cancer_

  Show description for 62def2b
  mmsuarezcosta

  committed
  62def2b

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• set ce_date_cin_removal if thermoablation or cryotherapy successful

  mmsuarezcosta

  committed
  0e3361b

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• Merge branch 'master' into cervical_cancer_

  Show description for 714f230
  thewati

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Commits on Dec 16, 2024

• replace cervical_cancer file w the original one

  mmsuarezcosta

  committed
  1f3d2d8

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• not used

  mmsuarezcosta

  committed
  185ecde

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• not used

  mmsuarezcosta

  committed
  4802ab9

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• not used

  mmsuarezcosta

  committed
  012bdcd

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• need to ensure treatment occurred

  mmsuarezcosta

  committed
  b1c6db3

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• add consumables for biopsy

  mmsuarezcosta

  committed
  81a0b09

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

  mmsuarezcosta

  committed
  c85db36

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• do biopsy if biopsy has not been done before

  mmsuarezcosta

  committed
  8648c8c

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• do biopsy if biopsy has not been done before

  mmsuarezcosta

  committed
  3971e47

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• fix output file

  mmsuarezcosta

  committed
  998c0f8

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• additional tests

  mmsuarezcosta

  committed
  cb15ecd

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• revert resource file

  mmsuarezcosta

  committed
  ed32c08

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• fix indenting

  mmsuarezcosta

  committed
  10c32e2

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

  mmsuarezcosta

  committed
  905735e

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Commits on Dec 17, 2024

• merge

  thewati

  committed
  c7124d5

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• remove commented out csv

  thewati

  committed
  4d19b79

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• fix some screening logic

  mmsuarezcosta

  committed
  1d39d90

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• Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_cancer_

  mmsuarezcosta

  committed
  43a21c0

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Commits on Dec 18, 2024

• replace with function

  mmsuarezcosta

  committed
  58f3b7c

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• biopsy only if stage 1+

  Show description for d50753d
  mmsuarezcosta

  committed
  d50753d

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• fix the tests and clean code

  mmsuarezcosta

  committed
  8a0d983

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• update logic for min years between screening

  mmsuarezcosta

  committed
  baf4ede

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• improved documentation

  mmsuarezcosta

  committed
  46be8d4

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• code clean up

  mmsuarezcosta

  committed
  2c29fa9

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• .

  andrew-phillips-1

  committed
  abbf7a1

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• .

  andrew-phillips-1

  committed
  9be93d2

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• Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel into cervical_cancer_

  Show description for f78733e
  andrew-phillips-1

  committed
  f78733e

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• Merge branch 'master' into cervical_cancer_

  Show description for 16e5cc7
  thewati

  committed
  16e5cc7

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• comment clarity

  mmsuarezcosta

  committed
  68e87b5

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

  mmsuarezcosta

  committed
  1164682

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• Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_cancer_

  mmsuarezcosta

  committed
  9ad9687

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Commits on Dec 19, 2024

• test commit - remove space

  mmsuarezcosta

  committed
  aea457f

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• add comments

  mmsuarezcosta

  committed
  52de860

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• clean code and add comments for readability

  mmsuarezcosta

  committed
  bc598c1

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• Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel into cervical_cancer_

  andrew-phillips-1

  committed
  f3aa9c1

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Commits on Dec 20, 2024

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

  mmsuarezcosta

  committed
  248b468

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• improve comments/readability of tests

  mmsuarezcosta

  committed
  eb59e52

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• fix dxtest name

  mmsuarezcosta

  committed
  e20be10

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Commits on Dec 21, 2024

• .

  andrew-phillips-1

  committed
  f5a4e4e

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• Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel into cervical_cancer_

  Show description for 1d34917
  andrew-phillips-1

  committed
  1d34917

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Commits on Dec 30, 2024

• .

  andrew-phillips-1

  committed
  e0c117c

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Commits on Jan 7, 2025

• .

  andrew-phillips-1

  committed
  89b48db

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Commits on Jan 16, 2025

• updates to consumables and equipment

  joehcollins

  committed
  ac3b861

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Commits on Jan 17, 2025

• reverting to master .github

  thewati

  committed
  10afb02

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• reverting to master

  thewati

  committed
  0e9c35e

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• Merge branch 'master' into cervical_cancer_

  Show description for b33cec9
  thewati

  committed
  b33cec9

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• Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_cancer_

  thewati

  committed
  2e2c483

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• remove unwanted files

  thewati

  committed
  58c3922

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• update cancer cons

  thewati

  committed
  bd3317e

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