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9ef7c8d
fix indexing
mmsuarezcosta Oct 23, 2024
a0b2b12
fix indexing
mmsuarezcosta Oct 23, 2024
a520791
add new fts
mmsuarezcosta Oct 23, 2024
1b7016d
add variables, add prob for via
mmsuarezcosta Oct 23, 2024
e77278f
improve for readability
mmsuarezcosta Oct 23, 2024
9a57fcb
update out statement to assess entire population
mmsuarezcosta Oct 29, 2024
2a9e18c
set screening age as variable
mmsuarezcosta Oct 30, 2024
1bd4268
initialize screening to F
mmsuarezcosta Oct 30, 2024
130fee0
remove duplicate
mmsuarezcosta Oct 30, 2024
ce4fa2e
30d marker
mmsuarezcosta Oct 30, 2024
4329d8a
out updates
mmsuarezcosta Oct 30, 2024
4985355
force to be in stage4 for palliative care -- previously if 'None' was…
mmsuarezcosta Oct 30, 2024
61e537d
change from symptoms to selection in polling
thewati Oct 31, 2024
5cf3315
change to jan to avoid 2x initialization of population
mmsuarezcosta Nov 1, 2024
bc3ec13
delete HSI_CervicalCancer_Screening, not used
mmsuarezcosta Nov 1, 2024
eeefe7d
change diagnoses stages to only be stage 1 to 4
mmsuarezcosta Nov 1, 2024
2a49fcc
change diagnoses stages to only be stage 1 to 4
mmsuarezcosta Nov 1, 2024
a81d5ec
add 'none' to ce_stage_at_diagnosis
mmsuarezcosta Nov 1, 2024
201c2eb
repeated screening and cin procedure in functions
mmsuarezcosta Nov 1, 2024
13e0900
adjust biopsy logic
mmsuarezcosta Nov 1, 2024
f181070
remove hard coding, start setting parametrs
mmsuarezcosta Nov 4, 2024
dc4d263
rename for clarity
mmsuarezcosta Nov 4, 2024
7cc3342
adjust cerv cancer consumables
mmsuarezcosta Nov 4, 2024
da0ca1d
removing hard coding and adding todos
mmsuarezcosta Nov 4, 2024
02c6f53
set eligible population based on hiv criteria
mmsuarezcosta Nov 4, 2024
b6e5a49
set eligible population based on hiv criteria
mmsuarezcosta Nov 4, 2024
212bb6c
behavior based on hv diagnosis rather than inherent property
mmsuarezcosta Nov 4, 2024
a12fe17
palliative care fix
mmsuarezcosta Nov 4, 2024
ade941b
update cancer consumables
mmsuarezcosta Nov 11, 2024
9625665
remove hard coding
mmsuarezcosta Nov 11, 2024
63677bb
equipment and consumables
mmsuarezcosta Nov 11, 2024
8ee9c70
remove hard code
mmsuarezcosta Nov 11, 2024
5326af8
change screening conditions
mmsuarezcosta Nov 13, 2024
d419bd2
remove hard coding of params and move to ResourceFile_Cervical_Cancer…
mmsuarezcosta Nov 14, 2024
e7a9b9a
remove hard coding of params and move to ResourceFile_Cervical_Cancer…
mmsuarezcosta Nov 14, 2024
fea6310
remove hard coding of params and move to ResourceFile_Cervical_Cancer…
mmsuarezcosta Nov 14, 2024
8a7cf3e
.
andrew-phillips-1 Nov 15, 2024
81e1daf
Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel in…
andrew-phillips-1 Nov 15, 2024
12a308b
add comments and remove completed todos
mmsuarezcosta Dec 11, 2024
23b0240
replace min_age_hv with min_age_hpv
mmsuarezcosta Dec 11, 2024
758fa41
replace min_age_hv with min_age_hpv
mmsuarezcosta Dec 11, 2024
926633b
Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel in…
andrew-phillips-1 Dec 11, 2024
9ba2bb9
.
andrew-phillips-1 Dec 11, 2024
62def2b
Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_…
mmsuarezcosta Dec 13, 2024
0e3361b
set ce_date_cin_removal if thermoablation or cryotherapy successful
mmsuarezcosta Dec 13, 2024
714f230
Merge branch 'master' into cervical_cancer_
thewati Dec 13, 2024
1f3d2d8
replace cervical_cancer file w the original one
mmsuarezcosta Dec 16, 2024
185ecde
not used
mmsuarezcosta Dec 16, 2024
4802ab9
not used
mmsuarezcosta Dec 16, 2024
012bdcd
not used
mmsuarezcosta Dec 16, 2024
b1c6db3
need to ensure treatment occurred
mmsuarezcosta Dec 16, 2024
81a0b09
add consumables for biopsy
mmsuarezcosta Dec 16, 2024
c85db36
fix to ensure CIN treatment pursued if not in Stage cancer
mmsuarezcosta Dec 16, 2024
8648c8c
do biopsy if biopsy has not been done before
mmsuarezcosta Dec 16, 2024
3971e47
do biopsy if biopsy has not been done before
mmsuarezcosta Dec 16, 2024
998c0f8
fix output file
mmsuarezcosta Dec 16, 2024
cb15ecd
additional tests
mmsuarezcosta Dec 16, 2024
ed32c08
revert resource file
mmsuarezcosta Dec 16, 2024
10c32e2
fix indenting
mmsuarezcosta Dec 16, 2024
905735e
comment out the 2024 + tests so that it runs in reasonable time
mmsuarezcosta Dec 16, 2024
c7124d5
merge
thewati Dec 17, 2024
4d19b79
remove commented out csv
thewati Dec 17, 2024
1d39d90
fix some screening logic
mmsuarezcosta Dec 17, 2024
43a21c0
Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_…
mmsuarezcosta Dec 17, 2024
58f3b7c
replace with function
mmsuarezcosta Dec 18, 2024
d50753d
biopsy only if stage 1+
mmsuarezcosta Dec 18, 2024
8a0d983
fix the tests and clean code
mmsuarezcosta Dec 18, 2024
baf4ede
update logic for min years between screening
mmsuarezcosta Dec 18, 2024
46be8d4
improved documentation
mmsuarezcosta Dec 18, 2024
2c29fa9
code clean up
mmsuarezcosta Dec 18, 2024
abbf7a1
.
andrew-phillips-1 Dec 18, 2024
9be93d2
.
andrew-phillips-1 Dec 18, 2024
f78733e
Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel in…
andrew-phillips-1 Dec 18, 2024
16e5cc7
Merge branch 'master' into cervical_cancer_
thewati Dec 18, 2024
68e87b5
comment clarity
mmsuarezcosta Dec 18, 2024
1164682
udpate cervical cancer file with parameter of minimized screening win…
mmsuarezcosta Dec 18, 2024
9ad9687
Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_…
mmsuarezcosta Dec 18, 2024
aea457f
test commit - remove space
mmsuarezcosta Dec 19, 2024
52de860
add comments
mmsuarezcosta Dec 19, 2024
bc598c1
clean code and add comments for readability
mmsuarezcosta Dec 19, 2024
f3aa9c1
Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel in…
andrew-phillips-1 Dec 19, 2024
248b468
Remove hash DF, flag that need to only plot with log and move away fr…
mmsuarezcosta Dec 20, 2024
eb59e52
improve comments/readability of tests
mmsuarezcosta Dec 20, 2024
e20be10
fix dxtest name
mmsuarezcosta Dec 20, 2024
f5a4e4e
.
andrew-phillips-1 Dec 21, 2024
1d34917
Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel in…
andrew-phillips-1 Dec 21, 2024
e0c117c
.
andrew-phillips-1 Dec 30, 2024
89b48db
.
andrew-phillips-1 Jan 7, 2025
ac3b861
updates to consumables and equipment
joehcollins Jan 16, 2025
10afb02
reverting to master .github
thewati Jan 17, 2025
0e9c35e
reverting to master
thewati Jan 17, 2025
b33cec9
Merge branch 'master' into cervical_cancer_
thewati Jan 17, 2025
2e2c483
Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_…
thewati Jan 17, 2025
58c3922
remove unwanted files
thewati Jan 17, 2025
bd3317e
update cancer cons
thewati Jan 17, 2025
e3a909e
remove cervical cancer from 'other' given it has its own module
mmsuarezcosta Jan 20, 2025
6e24798
cervical_cancer.py linting
mmsuarezcosta Jan 21, 2025
14a593b
cervical_cancer_analysis.py linting
mmsuarezcosta Jan 21, 2025
7cd9e79
cervical_cancer_test.py linting
mmsuarezcosta Jan 21, 2025
ead5cb7
isort
mmsuarezcosta Jan 21, 2025
32791bd
lint changes that pass tests
mmsuarezcosta Jan 22, 2025
817d15d
link changes, also comment out out_csv
mmsuarezcosta Jan 22, 2025
339c06a
add color for cervical cancer in graph
mmsuarezcosta Jan 22, 2025
243d953
add cervical cancer color
mmsuarezcosta Jan 22, 2025
ec351f2
change cervical cancer color to mediumturquoise
mmsuarezcosta Jan 22, 2025
79d7d06
add color for cervical cancer in CAUSE_OF_DEATH_OR_DALY_LABEL_TO_COLO…
mmsuarezcosta Jan 22, 2025
b18a74e
change readcsv
mmsuarezcosta Jan 22, 2025
4ce6962
remove param definition at top of file and add to resourcefile
mmsuarezcosta Jan 22, 2025
c4de745
remove screen_pop function since only used 1x
mmsuarezcosta Jan 22, 2025
26f5911
change cin procuedure to class that can be used throughout other clas…
mmsuarezcosta Jan 22, 2025
b41f0c2
added cerv cancer to bottom of each priority doc, modeled priority ba…
mmsuarezcosta Jan 22, 2025
2777ff7
del unused variables
mmsuarezcosta Jan 22, 2025
07f47b0
update consumables -- change some requirements to optional and change…
mmsuarezcosta Jan 23, 2025
9859bed
LLETZ Machines for thermoablation and Cryotherapy Unit for cryo
mmsuarezcosta Jan 27, 2025
dab92b1
LLETZ Machines for thermoablation and Cryotherapy Unit for cryo
mmsuarezcosta Jan 27, 2025
d21b9c8
update consumable chemo alternative options
mmsuarezcosta Jan 27, 2025
4fe0280
add eq. comment for future cahnge to Thermoablation Device
mmsuarezcosta Jan 27, 2025
2607b63
add cerv cancer write-up
mmsuarezcosta Jan 30, 2025
30e9cb1
Merge branch 'master' into cervical_cancer_
tbhallett Jan 30, 2025
249ffe7
definition and type changes
mmsuarezcosta Feb 24, 2025
4bdf8a8
initialize parameters related to hiv at the start
mmsuarezcosta Feb 27, 2025
1061c30
add predictors
mmsuarezcosta Feb 27, 2025
002547f
remove code duplication
mmsuarezcosta Feb 27, 2025
d073bb9
remove check_configuration_of_population because force changes for th…
mmsuarezcosta Feb 27, 2025
3512612
create batch event, fix parmeters, remove ce_date_death removed and o…
mmsuarezcosta Feb 28, 2025
2d25ff1
fix plotting from log file
mmsuarezcosta Mar 5, 2025
1516f0b
remove print statements
mmsuarezcosta Mar 5, 2025
2a03934
change the asserts to be logger warnings
mmsuarezcosta Mar 5, 2025
3ec7c1a
fix parameter and module variables
mmsuarezcosta Mar 5, 2025
9d8e721
improve format
mmsuarezcosta Mar 5, 2025
97e88af
improve format
mmsuarezcosta Mar 5, 2025
71bd056
logging every 1mo as recommended
mmsuarezcosta Mar 5, 2025
33db50a
remove unused csv import
mmsuarezcosta Mar 5, 2025
129305b
revert cervical cancer analysis parameters
mmsuarezcosta Mar 5, 2025
12b4373
move cin procedure within CervicalCancer module
mmsuarezcosta Mar 5, 2025
5d9a498
remove extra spacing
mmsuarezcosta Mar 5, 2025
f5d5b10
fix total dead count
mmsuarezcosta Mar 5, 2025
8681e2d
add equipment in function perform_cin_procedure
mmsuarezcosta Mar 10, 2025
c20d5a5
update coments and spacing
mmsuarezcosta Mar 11, 2025
a7314c0
improve coding syntax
mmsuarezcosta Mar 11, 2025
4775d38
improve coding syntax
mmsuarezcosta Mar 11, 2025
718aa59
Merge branch 'master' into cervical_cancer_
mnjowe Mar 12, 2025
4c40d31
improve coding syntax
mmsuarezcosta Mar 14, 2025
d872502
fix for no hsi running
mmsuarezcosta Mar 14, 2025
81002fe
fix vaginal bleeding check -- before vaginal bleeding symptom was not…
mmsuarezcosta Mar 17, 2025
992684f
extend simulation and remove test that is not valid in extended simul…
mmsuarezcosta Mar 17, 2025
ea2fef7
remove unused 'module'
mmsuarezcosta Mar 17, 2025
5f7c3b9
fix tox issues
mmsuarezcosta Mar 17, 2025
7a52ce8
add properties
mmsuarezcosta Mar 17, 2025
68e4389
addt test fixes
mmsuarezcosta Mar 17, 2025
594eb74
.
andrew-phillips-1 Mar 17, 2025
b11e02a
fix 0ing of stage progressions with hivneg
mmsuarezcosta Mar 18, 2025
715ec36
rename output file for clarity
mmsuarezcosta Mar 18, 2025
89d4538
remove ce_hiv_unsuppressed parameter and update lm and output variabl…
mmsuarezcosta Mar 19, 2025
fd78f6e
Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel in…
andrew-phillips-1 Mar 20, 2025
16c003e
.
andrew-phillips-1 Mar 22, 2025
f378b22
add n_via_cin_ever_detected
mmsuarezcosta Apr 7, 2025
043358f
merge andrew changes and removal of hiv_unsupressed
mmsuarezcosta Apr 7, 2025
0c61ede
add back cons check
mmsuarezcosta Apr 7, 2025
4ff4d83
make all graphs start in 2010, dynamic ylim setting, remove plot n_hi…
mmsuarezcosta Apr 7, 2025
83e6738
Merge branch 'master' into cervical_cancer_
tamuri May 27, 2025
fddf8a6
repair broken .docx file
tbhallett Jun 2, 2025
211c072
update write-ups page
tbhallett Jun 2, 2025
9d121bd
preserve format of HealthPolicy files
tbhallett Jun 2, 2025
7e7f56a
remove several columns added by accident in PR
tbhallett Jun 2, 2025
8de5a7b
remove cerivval cancer (commented-out) from other cancers
tbhallett Jun 2, 2025
4c1bd86
remove comment discussion in write up
tbhallett Jun 2, 2025
3243ee9
linting
tbhallett Jun 3, 2025
a80411c
linting
tbhallett Jun 3, 2025
b65afc0
linting and correct comment
tbhallett Jun 3, 2025
7d90f98
linting
tbhallett Jun 3, 2025
4aee9e0
comment and no need to define ce_hpv_cc_status_original
tbhallett Jun 3, 2025
bd827db
loc for screening should not filter for those wihtout cin
tbhallett Jun 3, 2025
056018f
linting
tbhallett Jun 3, 2025
d355aca
corrected test
tbhallett Jun 3, 2025
0b5f29a
remove in-line review comments
tbhallett Jun 3, 2025
02f14a0
strengthn test
tbhallett Jun 3, 2025
ba482ce
remove failing line
tbhallett Jun 3, 2025
615eeb1
remove symptoms not used
tbhallett Jun 3, 2025
1803e71
Merge branch 'master' into cervical_cancer_
tbhallett Jun 4, 2025
0683602
update convetnion for resourcfilepath
tbhallett Jun 4, 2025
3710830
correct test
tbhallett Jun 4, 2025
bbcd636
iterate through models in reverse order to prevent people advancing t…
tbhallett Jun 4, 2025
487485e
mock properties in HIV needed to test cervical cancer module
tbhallett Jun 4, 2025
490d093
update and strengthen tests
tbhallett Jun 4, 2025
e3e8c1d
Refactor cervical cancer treatment and death handling logic
tbhallett Jun 4, 2025
49593af
remove docstring
tbhallett Jun 4, 2025
8456498
remove erroneous declaration of TB module as a dependency?!
tbhallett Jun 4, 2025
dbca90e
update label
tbhallett Jun 4, 2025
9e77197
clarify daly weight parameters
tbhallett Jun 4, 2025
f66b3f6
add default for ce_date_cin_removal
tbhallett Jun 4, 2025
8e4d046
get rid of bitwise thing
tbhallett Jun 4, 2025
ab79e87
simplify
tbhallett Jun 4, 2025
6593506
Merge branch 'master' into cervical_cancer_
tbhallett Jun 6, 2025
b7af015
declare parameter types
tbhallett Jun 6, 2025
adcb2a1
declarae and rationalise parameters
tbhallett Jun 6, 2025
0aada98
clean up parameters
tbhallett Jun 6, 2025
c069207
make onset of vaginal bleeding limited to those who do not already ha…
tbhallett Jun 6, 2025
469f2ad
correct param description
tbhallett Jun 6, 2025
45573e2
correct property description
tbhallett Jun 6, 2025
b90aae3
control cats
tbhallett Jun 6, 2025
b038e7f
symptom and >=
tbhallett Jun 6, 2025
5f732a0
remove magic number and use parameter
tbhallett Jun 6, 2025
e064063
delete setting persons on palliative care as, by definition, none are…
tbhallett Jun 6, 2025
17da1e6
simplify syntax
tbhallett Jun 6, 2025
f699442
refactor choose_cin_procedure_and_schedule_it
tbhallett Jun 6, 2025
f135177
rollback change in cats.
tbhallett Jun 6, 2025
87789f2
more cleannig
tbhallett Jun 6, 2025
d483d1a
cleaning
tbhallett Jun 6, 2025
b3c7ed9
clean docx
tbhallett Jun 6, 2025
b97ebcc
add notes
tbhallett Jun 6, 2025
be06ca3
add parameters to RF for max health system fun / max health seeking b…
tbhallett Jun 6, 2025
1116df8
min age hpv mislabelled and used inconsistently, most occrurence impl…
tbhallett Jun 6, 2025
622bde6
reduce num properties and streamline poll
tbhallett Jun 6, 2025
5453090
add cc to full model officially
tbhallett Jun 7, 2025
e19faaa
avoid type mismatch error
tbhallett Jun 7, 2025
4b47ba4
correct init_depn
tbhallett Jun 7, 2025
b399269
don't rely on model having run initialised simulation when initialisi…
tbhallett Jun 7, 2025
fab0293
linting
tbhallett Jun 7, 2025
c03cb10
my linting
tbhallett Jun 8, 2025
861f32c
update analysis script
tbhallett Jun 9, 2025
33e98b9
add script for calibration figure
tbhallett Jun 9, 2025
d746b19
add comment
tbhallett Jun 9, 2025
30103d9
refactorig and rationalise equipment declaration
tbhallett Jun 9, 2025
396ff6c
refactorig and rationalise equipment declaration
tbhallett Jun 9, 2025
068c1ff
make checking for death be on actual death not YLL
tbhallett Jun 9, 2025
a84074a
clean up commented-out code
tbhallett Jun 9, 2025
91ea702
refactor
tbhallett Jun 9, 2025
b4d8bb3
refactor to call it VIA screening throughout
tbhallett Jun 9, 2025
ab66809
rationalise TREATMENT_ID
tbhallett Jun 9, 2025
8b85187
clarfy transition parameters
tbhallett Jun 9, 2025
ac2f15b
refactor
tbhallett Jun 9, 2025
8c1fab5
for surgery - surgical equipment essential
tbhallett Jun 9, 2025
f3b0b1c
strengthen test about progression and make treatment put everyone bac…
tbhallett Jun 9, 2025
0d80478
fix script
tbhallett Jun 9, 2025
8ed995b
be explicit about root to be robust to from where script is run
tbhallett Jun 10, 2025
703bb67
further fixes
tbhallett Jun 11, 2025
0e10e33
drop men
tbhallett Jun 11, 2025
6e3a149
Merge branch 'master' into cervical_cancer_
tbhallett Jun 28, 2025
3b74044
.
andrew-phillips-1 Jun 30, 2025
082ab54
linting
tbhallett Jun 30, 2025
fd445de
Merge branch 'master' into cervical_cancer_
tamuri Jul 8, 2025
fcd52bc
Merge branch 'master' into cervical_cancer_
tbhallett Jul 21, 2025
d58a34b
refactor screening VIA
tbhallett Jul 21, 2025
9fd0b19
refactor screening xpert
tbhallett Jul 21, 2025
f9ad3a5
refactor presentation
tbhallett Jul 21, 2025
9ad2c97
refactor CIN
tbhallett Jul 21, 2025
362f719
refactor treatment
tbhallett Jul 21, 2025
b0de328
update docstring
tbhallett Jul 21, 2025
e643e5a
align HSI names and treatment_ids
tbhallett Jul 21, 2025
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3 changes: 3 additions & 0 deletions docs/write-ups/CervicalCancer.docx
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2 changes: 2 additions & 0 deletions docs/writeups.rst
Original file line number Diff line number Diff line change
Expand Up @@ -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>`
Expand Down
3 changes: 3 additions & 0 deletions resources/ResourceFile_Cervical_Cancer/parameter_values.csv
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