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Cervical cancer #1287

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Cervical cancer #1287

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4299067
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andrew-phillips-1 Oct 16, 2023
d6bdece
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andrew-phillips-1 Oct 16, 2023
533357a
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andrew-phillips-1 Oct 16, 2023
116f241
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andrew-phillips-1 Oct 16, 2023
4bc722b
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andrew-phillips-1 Oct 16, 2023
9a3b48a
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andrew-phillips-1 Oct 16, 2023
0393e17
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andrew-phillips-1 Oct 16, 2023
bc1ac59
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andrew-phillips-1 Oct 17, 2023
5a66e5d
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Oct 17, 2023
b24c6bd
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Oct 17, 2023
cc488bd
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Oct 18, 2023
144644a
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Oct 18, 2023
f1015b5
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Oct 18, 2023
f2b44b0
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Oct 19, 2023
0d06e44
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Oct 19, 2023
c964058
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Oct 19, 2023
1b0226b
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Oct 19, 2023
fdcea86
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Oct 20, 2023
7f13653
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Oct 21, 2023
356973c
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Oct 21, 2023
91efced
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Oct 23, 2023
443401b
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Nov 4, 2023
9e60e5c
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Nov 13, 2023
8f5e8f0
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Nov 26, 2023
5464169
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Nov 28, 2023
86a503f
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Dec 3, 2023
242de2c
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Dec 4, 2023
77a2808
first pass at cervical cancer module based on editing breast cancer m…
andrew-phillips-1 Dec 4, 2023
41b9743
HSIs
andrew-phillips-1 Dec 6, 2023
0fe0ee1
HSIs
andrew-phillips-1 Dec 6, 2023
b3d77af
HSIs
andrew-phillips-1 Dec 7, 2023
b242de7
HSIs
andrew-phillips-1 Dec 10, 2023
9ed44ac
HSIs
andrew-phillips-1 Dec 10, 2023
41d1152
HSIs
andrew-phillips-1 Dec 10, 2023
fdbd1ac
HSIs
andrew-phillips-1 Dec 24, 2023
38e34e3
HSIs
andrew-phillips-1 Dec 30, 2023
c665214
HSIs
andrew-phillips-1 Jan 1, 2024
4470892
HSIs
andrew-phillips-1 Jan 2, 2024
e6008cf
Merge branch 'master' into cervical_cancer_
andrew-phillips-1 Jan 3, 2024
90bbbb9
HSIs
andrew-phillips-1 Jan 3, 2024
7beb619
Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel in…
andrew-phillips-1 Jan 3, 2024
b42dea3
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andrew-phillips-1 Jan 4, 2024
0a3f2d6
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andrew-phillips-1 Jan 4, 2024
ee6e3c1
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andrew-phillips-1 Feb 24, 2024
12f312f
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andrew-phillips-1 Feb 24, 2024
a4cfcc8
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andrew-phillips-1 Feb 26, 2024
e30fa14
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andrew-phillips-1 Mar 4, 2024
28ffe64
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andrew-phillips-1 Mar 4, 2024
416027c
Merge remote-tracking branch 'origin/master'
andrew-phillips-1 Mar 4, 2024
cae6c2c
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andrew-phillips-1 Jun 10, 2024
6007b2a
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andrew-phillips-1 Jun 13, 2024
5b67b62
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andrew-phillips-1 Jun 13, 2024
68f14cc
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andrew-phillips-1 Jun 13, 2024
de34cc5
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andrew-phillips-1 Jun 18, 2024
6a27f52
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andrew-phillips-1 Jun 18, 2024
ca8a1f5
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andrew-phillips-1 Jun 19, 2024
01398e9
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andrew-phillips-1 Jun 20, 2024
3e4508b
Merge branch 'refs/heads/master' into cervical_cancer_
tbhallett Jun 20, 2024
e30044f
refactor to use `do_at_generic_first_appt` on the module
tbhallett Jun 20, 2024
2c53eb2
roll back changes to healthsystem.py
tbhallett Jun 20, 2024
9138a01
roll back changes to hiv.py
tbhallett Jun 20, 2024
73682ea
cleaning up files
tbhallett Jun 20, 2024
445b6b3
cleaning up files
tbhallett Jun 20, 2024
d727856
.
andrew-phillips-1 Jun 20, 2024
8dcc0e6
Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_…
andrew-phillips-1 Jun 20, 2024
6f25468
Merge remote-tracking branch 'origin/master' into cervical_cancer_
andrew-phillips-1 Jun 21, 2024
910a080
HSIs restructured with Screening HSI
thewati Jun 21, 2024
e81857e
HSIs restructured with Screening HSI
thewati Jun 21, 2024
890b245
.
andrew-phillips-1 Jun 21, 2024
eef200f
Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel in…
andrew-phillips-1 Jun 21, 2024
00b5944
.
andrew-phillips-1 Jun 24, 2024
381a307
Merge branch 'master' into cervical_cancer_
thewati Jun 24, 2024
23724e8
restructured HSIs again within module
thewati Jun 24, 2024
5373f3a
.
andrew-phillips-1 Jun 26, 2024
2d96458
.
andrew-phillips-1 Jun 26, 2024
7673ed0
Accessing consumables and analyses using logger
thewati Jun 28, 2024
1501739
.
andrew-phillips-1 Jun 29, 2024
680be51
Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_…
andrew-phillips-1 Jun 29, 2024
0e60aa3
Accessing consumables from cancer_consumables.py
thewati Jul 3, 2024
519ca33
Rollback to using csv file in analyses
thewati Jul 5, 2024
5e648e9
Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_…
andrew-phillips-1 Jul 5, 2024
b3a4202
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andrew-phillips-1 Jul 14, 2024
e574a13
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andrew-phillips-1 Jul 18, 2024
4ecf108
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andrew-phillips-1 Jul 18, 2024
e8bcffe
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andrew-phillips-1 Jul 18, 2024
ed8602d
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andrew-phillips-1 Jul 18, 2024
91475a4
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andrew-phillips-1 Jul 18, 2024
15e2df9
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andrew-phillips-1 Jul 20, 2024
ffe10d8
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andrew-phillips-1 Jul 20, 2024
c357295
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andrew-phillips-1 Jul 21, 2024
66ad5f5
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andrew-phillips-1 Jul 22, 2024
f3a9d24
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andrew-phillips-1 Jul 29, 2024
5284d9e
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andrew-phillips-1 Aug 5, 2024
3a58fa4
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andrew-phillips-1 Aug 7, 2024
563cff7
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andrew-phillips-1 Aug 8, 2024
ea1e540
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andrew-phillips-1 Aug 9, 2024
7ba6797
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andrew-phillips-1 Aug 14, 2024
f92de78
temporary rollback to using xpert and via as symptoms
thewati Aug 16, 2024
fa8ee61
Merge branch 'cervical_cancer_' of https://github.com/UCL/TLOmodel in…
andrew-phillips-1 Aug 24, 2024
4fad45a
.
andrew-phillips-1 Aug 24, 2024
8e605b8
.
andrew-phillips-1 Sep 7, 2024
1d1a19d
.
andrew-phillips-1 Oct 7, 2024
2743ade
create function for plotting
mmsuarezcosta Oct 8, 2024
402e5a1
adjust proportion plotting
mmsuarezcosta Oct 9, 2024
2299c8f
ensure original and new logging capabilities coexist in same file
mmsuarezcosta Oct 21, 2024
f7971d6
add year variation for screening and testing
mmsuarezcosta Oct 21, 2024
7bfb2ba
edit parameters
mmsuarezcosta Oct 21, 2024
7706c01
edit sign direction, should be VIA if before '24'
mmsuarezcosta Oct 21, 2024
1d8e786
remove hard coding
mmsuarezcosta Oct 22, 2024
dcd9270
add hash documentation
mmsuarezcosta Oct 22, 2024
d35718f
delete import of random
mmsuarezcosta Oct 22, 2024
0349109
delete import of random
mmsuarezcosta Oct 22, 2024
e8821b9
ensure all random instances associated with self
mmsuarezcosta Oct 22, 2024
a2dddc0
set seed non-hardcoded
mmsuarezcosta Oct 22, 2024
f244070
hash for testing
mmsuarezcosta Oct 22, 2024
c814528
merge in changes from updated cervical_cancer branch
mmsuarezcosta Oct 22, 2024
63c22e5
update variable name, improve rng
mmsuarezcosta Oct 22, 2024
d19e617
edit to ensure screening with dates for via and xpert
mmsuarezcosta Oct 22, 2024
c413fc6
Merge branch 'master' into cervical_cancer_
thewati Oct 22, 2024
9c5cf13
comment out hash
mmsuarezcosta Oct 22, 2024
bb1ddd8
Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_…
mmsuarezcosta Oct 22, 2024
3b09512
comment out hash
mmsuarezcosta Oct 22, 2024
bb2642c
remove entire df broadcasting to only alive and can't override previo…
mmsuarezcosta Oct 23, 2024
843e184
remove entire df broadcasting to only alive and can't override previo…
mmsuarezcosta Oct 23, 2024
0eb4871
revert to 2025
mmsuarezcosta Oct 23, 2024
ec94bbe
comment out hash
mmsuarezcosta Oct 23, 2024
1b705f4
comment out hash
mmsuarezcosta Oct 23, 2024
1ce601b
Rollback _initialised Simulation object
thewati Oct 23, 2024
5d69604
Merge remote-tracking branch 'origin/cervical_cancer_' into cervical_…
mmsuarezcosta Oct 23, 2024
8263482
address new stage in one line
mmsuarezcosta Oct 23, 2024
5ee1ae4
spread out death days
mmsuarezcosta Oct 23, 2024
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
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3 changes: 3 additions & 0 deletions resources/ResourceFile_Cervical_Cancer.xlsx
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