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dvc.lock
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schema: '2.0'
stages:
filter:
cmd: "lyscripts data filter data/joined.csv data/filtered.csv --include-subsites
C01 C02 C03 C04 C05 C06 C09 C10\n"
deps:
- path: data/joined.csv
hash: md5
md5: 711468c4027e6221a49568d80635e260
size: 934594
outs:
- path: data/filtered.csv
hash: md5
md5: 611103c49a8a482b7302339fdebf0173
size: 823891
join:
cmd: "lyscripts data join --inputs data/2021-usz-oropharynx.csv data/2021-clb-oropharynx.csv
data/2023-clb-multisite.csv data/2023-isb-multisite.csv data/2023-hvh-oropharynx.csv
--output data/joined.csv\n"
deps:
- path: data/2021-clb-oropharynx.csv
hash: md5
md5: d40c0a1ae967a6983d60a0a809cf3972
size: 92742
- path: data/2021-usz-oropharynx.csv
hash: md5
md5: 1b949c74081ac4b6224186ebbb9c90df
size: 159482
- path: data/2023-clb-multisite.csv
hash: md5
md5: 9d72ee96af2c51033a2fb0bb8551e318
size: 123938
- path: data/2023-hvh-oropharynx.csv
hash: md5
md5: a5be2bcb32619f901c48bd1d8a7bae8d
size: 82567
- path: data/2023-isb-multisite.csv
hash: md5
md5: 6135ac91c08b7518372488fb2e0f9b69
size: 204322
outs:
- path: data/joined.csv
hash: md5
md5: 711468c4027e6221a49568d80635e260
size: 934594
enhance:
cmd: "lyscripts data enhance data/filtered.csv data/enhanced.csv --params _variables.yml\n"
deps:
- path: data/filtered.csv
hash: md5
md5: 611103c49a8a482b7302339fdebf0173
size: 823891
params:
_variables.yml:
modalities:
CT:
- 0.76
- 0.81
FNA:
- 0.98
- 0.8
MRI:
- 0.63
- 0.81
PET:
- 0.86
- 0.79
diagnostic_consensus:
- 0.86
- 0.81
max_llh:
- 1.0
- 1.0
pCT:
- 0.86
- 0.81
pathology:
- 1.0
- 1.0
outs:
- path: data/enhanced.csv
hash: md5
md5: 8ed98ad0206f0114124a8b7da30961c5
size: 997595
plot_prevalence_by_subsite:
cmd: "python scripts/prevalence_by_subsite.py --input data/enhanced.csv --params
_variables.yml --output figures/prevalence_by_subsite.svg\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 8ed98ad0206f0114124a8b7da30961c5
size: 997595
- path: scripts/prevalence_by_subsite.py
hash: md5
md5: 1b27b6ac6a904a6dab72e1ffa82444d2
size: 2637
params:
_variables.yml:
barplot_kwargs:
width: 0.9
zorder: 2
icd_code_map:
C01: base of tongue
C02: tongue, other
C03: gum
C04: floor of mouth
C05: palate
C06: mouth, other
C09: tonsil
C10: oropharynx, other
outs:
- path: figures/prevalence_by_subsite.svg
hash: md5
md5: 980152f2795f8696679dec1f99b68c85
size: 47152
write_num_patients:
cmd: "python scripts/write_num_patients.py --input data/enhanced.csv --output
_variables.yml\n"
deps:
- path: scripts/write_num_patients.py
hash: md5
md5: 344f827d3bd6d36a4f3f38f8b3d3f79f
size: 1413
params:
_variables.yml:
icd_code_map:
C01: base of tongue
C02: tongue, other
C03: gum
C04: floor of mouth
C05: palate
C06: mouth, other
C09: tonsil
C10: oropharynx, other
filter_oropharynx_and_oral_cavity:
cmd: "lyscripts data filter data/joined.csv data/filtered.csv --include-subsites
C01 C02 C03 C04 C05 C06 C09 C10\n"
deps:
- path: data/joined.csv
hash: md5
md5: 711468c4027e6221a49568d80635e260
size: 934594
outs:
- path: data/filtered.csv
hash: md5
md5: 611103c49a8a482b7302339fdebf0173
size: 823891
filter_oropharynx:
cmd: "lyscripts data filter data/enhanced.csv data/oropharynx.csv --include-subsites
C01 C09 C10\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 8ed98ad0206f0114124a8b7da30961c5
size: 997595
outs:
- path: data/oropharynx.csv
hash: md5
md5: b8e927c72b59c26e0fe66022d0494a96
size: 658630
filter_oral_cavity:
cmd: "lyscripts data filter data/enhanced.csv data/oral_cavity.csv --include-subsites
C02 C03 C04 C05 C06\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 8ed98ad0206f0114124a8b7da30961c5
size: 997595
outs:
- path: data/oral_cavity.csv
hash: md5
md5: 3428c64a81e8633769c3114000a9b07b
size: 346037
sample_from_oropharynx:
cmd: "lyscripts sample data/oropharynx.csv models/oropharynx.hdf5 --params _variables.yml
--modalities max_llh --plots figures/sample_from_oropharynx --pools 0 --seed
42\n"
deps:
- path: data/oropharynx.csv
hash: md5
md5: b8e927c72b59c26e0fe66022d0494a96
size: 658630
params:
_variables.yml:
graph:
lnl:
I:
- II
II:
- III
III:
- IV
IV: []
tumor:
primary:
- I
- II
- III
- IV
model:
class: Unilateral
first_binom_prob: 0.3
kwargs:
base_symmetric: false
trans_symmetric: true
use_mixing: true
max_t: 10
t_stage_mapping:
0: all
1: all
2: all
3: all
4: all
t_stages:
- all
sampling:
burnin: 1000
kwargs:
check_interval: 50
max_steps: 20000
rel_acor_threshold: 0.075
trust_threshold: 30.0
nsteps: 20
thin_by: 10
walkers_per_dim: 20
outs:
- path: figures/sample_from_oropharynx/accept_rates.csv
hash: md5
md5: 345a4c20acbd9490bfdfbe29ef9ad8af
size: 943
- path: figures/sample_from_oropharynx/acor_times.csv
hash: md5
md5: 543ad2e8c6f4129494239bc0812abb7f
size: 932
- path: models/oropharynx.hdf5
hash: md5
md5: 23acf157edb04fc27f33f60456ac189b
size: 1454016
sample_from_oral_cavity:
cmd: "lyscripts sample data/oral_cavity.csv models/oral_cavity.hdf5 --params _variables.yml
--modalities max_llh --plots figures/sample_from_oral_cavity --pools 0 --seed
42\n"
deps:
- path: data/oral_cavity.csv
hash: md5
md5: 3428c64a81e8633769c3114000a9b07b
size: 346037
params:
_variables.yml:
graph:
lnl:
I:
- II
II:
- III
III:
- IV
IV: []
tumor:
primary:
- I
- II
- III
- IV
model:
class: Unilateral
first_binom_prob: 0.3
kwargs:
base_symmetric: false
trans_symmetric: true
use_mixing: true
max_t: 10
t_stage_mapping:
0: all
1: all
2: all
3: all
4: all
t_stages:
- all
sampling:
burnin: 1000
kwargs:
check_interval: 50
max_steps: 20000
rel_acor_threshold: 0.075
trust_threshold: 30.0
nsteps: 20
thin_by: 10
walkers_per_dim: 20
outs:
- path: figures/sample_from_oral_cavity/accept_rates.csv
hash: md5
md5: 76715bfe8f35a22dde3fa80340695c99
size: 1087
- path: figures/sample_from_oral_cavity/acor_times.csv
hash: md5
md5: 8bb9a377b2b9807586614a8d7474f97c
size: 1068
- path: models/oral_cavity.hdf5
hash: md5
md5: cc03dc96b1ac9deba1ad09a4343ae840
size: 1454016
render_pdf:
cmd: "quarto render --to iccr-pdf\n"
deps:
- path: _extensions
hash: md5
md5: 2fc478636b20635d27d084b01c3ec092.dir
size: 3885
nfiles: 9
- path: content/manuscript.qmd
hash: md5
md5: 57d9a7627e5164c560a1813394fcdf71
size: 19280
- path: figures
hash: md5
md5: d93daf3000eea2b91d606c4bc6ef7620.dir
size: 1416371
nfiles: 45
- path: models
hash: md5
md5: aacfd20d1bf7aaa820b038f6e7aecd04.dir
size: 63333481
nfiles: 4
- path: static
hash: md5
md5: 3f224fd168d985280d09aa13cb18ab7e.dir
size: 251112
nfiles: 1
params:
_variables.yml:
model.first_binom_prob: 0.3
model.max_t: 10
num_patients:
C01: 212
C02: 158
C03: 45
C04: 99
C05: 61
C06: 46
C09: 452
C10: 169
total: 1242
outs:
- path: _site/
hash: md5
md5: f20930413f3d505b56192fb6b75f91be.dir
size: 911724
nfiles: 6
mixture_model_em_sampling:
cmd: "python scripts/mixture_model_sampling.py --input data/enhanced.csv --model
models/mixture.hdf5 --figure figures/mixture_history.svg --params _variables.yml
--seed 42\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 8ed98ad0206f0114124a8b7da30961c5
size: 997595
- path: scripts/mixture_model_sampling.py
hash: md5
md5: d08e1345f3a245448cf16d5d711e699f
size: 3132
params:
_variables.yml:
mixture_model:
em_config:
convergence:
criterion: default
default:
lookback_period: 4
threshold: 0.015
e_step:
nburnin: 50
nsteps: 30
sampler: SIMPLE
show_progress: true
walkers_per_dim: 20
m_step:
minimize_method: SLSQP
max_steps: 20
method: INVERTED
verbose: false
mcmc_config:
sampler: SIMPLE
sampling_params:
nburnin: 600
nsteps: 1000
walkers_per_dim: 20
num_clusters: 2
outs:
- path: figures/mixture_history.svg
hash: md5
md5: b32887c0f20ad962176a09569a34552a
size: 68772
- path: models/mixture.hdf5
hash: md5
md5: 24fc8e405444106bed654115564189c9
size: 60425400
plot_cluster_assignments:
cmd: "python scripts/plot_cluster_assignments.py --model models/mixture.hdf5 --output
figures/cluster_assignments.svg --params _variables.yml\n"
deps:
- path: models/mixture.hdf5
hash: md5
md5: ac806b9608daec34d2f2be89d675a623
size: 60425400
- path: scripts/plot_cluster_assignments.py
hash: md5
md5: 0d7327277a6784ce179a07cef06c7a53
size: 3420
params:
_variables.yml:
num_patients:
C01: 212
C02: 158
C03: 45
C04: 99
C05: 61
C06: 46
C09: 452
C10: 169
total: 1242
outs:
- path: figures/cluster_assignments.svg
hash: md5
md5: 63fae40d9dcf26cbde56bedd9cb8f0da
size: 38120
plot_predicted_prevalence@pattern0-C01:
cmd: "python scripts/prevalence_comparison.py --mixture-model models/mixture.hdf5
--params _variables.yml --involvement t n n n --subsite C01 --output figures/prevalence_C01_tnnn.svg\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 8ed98ad0206f0114124a8b7da30961c5
size: 997595
- path: models/mixture.hdf5
hash: md5
md5: ac806b9608daec34d2f2be89d675a623
size: 60425400
- path: models/oral_cavity.hdf5
hash: md5
md5: cc03dc96b1ac9deba1ad09a4343ae840
size: 1454016
- path: models/oropharynx.hdf5
hash: md5
md5: 23acf157edb04fc27f33f60456ac189b
size: 1454016
- path: scripts/prevalence_comparison.py
hash: md5
md5: 57d98686c5ecf4afad1a810888664541
size: 6158
params:
_variables.yml:
icd_code_map:
C01: base of tongue
C02: tongue, other
C03: gum
C04: floor of mouth
C05: palate
C06: mouth, other
C09: tonsil
C10: oropharynx, other
model:
class: Unilateral
first_binom_prob: 0.3
kwargs:
base_symmetric: false
trans_symmetric: true
use_mixing: true
max_t: 10
t_stage_mapping:
0: all
1: all
2: all
3: all
4: all
t_stages:
- all
outs:
- path: figures/prevalence_C01_tnnn.svg
hash: md5
md5: 1da2eb61908e20ca1fb4ab4d8ea080b6
size: 27242
plot_predicted_prevalence@pattern0-C02:
cmd: "python scripts/prevalence_comparison.py --mixture-model models/mixture.hdf5
--params _variables.yml --involvement t n n n --subsite C02 --output figures/prevalence_C02_tnnn.svg\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 8ed98ad0206f0114124a8b7da30961c5
size: 997595
- path: models/mixture.hdf5
hash: md5
md5: ac806b9608daec34d2f2be89d675a623
size: 60425400
- path: models/oral_cavity.hdf5
hash: md5
md5: cc03dc96b1ac9deba1ad09a4343ae840
size: 1454016
- path: models/oropharynx.hdf5
hash: md5
md5: 23acf157edb04fc27f33f60456ac189b
size: 1454016
- path: scripts/prevalence_comparison.py
hash: md5
md5: 57d98686c5ecf4afad1a810888664541
size: 6158
params:
_variables.yml:
icd_code_map:
C01: base of tongue
C02: tongue, other
C03: gum
C04: floor of mouth
C05: palate
C06: mouth, other
C09: tonsil
C10: oropharynx, other
model:
class: Unilateral
first_binom_prob: 0.3
kwargs:
base_symmetric: false
trans_symmetric: true
use_mixing: true
max_t: 10
t_stage_mapping:
0: all
1: all
2: all
3: all
4: all
t_stages:
- all
outs:
- path: figures/prevalence_C02_tnnn.svg
hash: md5
md5: 0f04fd78d5d39501c68b03ab7257b593
size: 30121
plot_predicted_prevalence@pattern0-C03:
cmd: "python scripts/prevalence_comparison.py --mixture-model models/mixture.hdf5
--params _variables.yml --involvement t n n n --subsite C03 --output figures/prevalence_C03_tnnn.svg\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 8ed98ad0206f0114124a8b7da30961c5
size: 997595
- path: models/mixture.hdf5
hash: md5
md5: ac806b9608daec34d2f2be89d675a623
size: 60425400
- path: models/oral_cavity.hdf5
hash: md5
md5: cc03dc96b1ac9deba1ad09a4343ae840
size: 1454016
- path: models/oropharynx.hdf5
hash: md5
md5: 23acf157edb04fc27f33f60456ac189b
size: 1454016
- path: scripts/prevalence_comparison.py
hash: md5
md5: 57d98686c5ecf4afad1a810888664541
size: 6158
params:
_variables.yml:
icd_code_map:
C01: base of tongue
C02: tongue, other
C03: gum
C04: floor of mouth
C05: palate
C06: mouth, other
C09: tonsil
C10: oropharynx, other
model:
class: Unilateral
first_binom_prob: 0.3
kwargs:
base_symmetric: false
trans_symmetric: true
use_mixing: true
max_t: 10
t_stage_mapping:
0: all
1: all
2: all
3: all
4: all
t_stages:
- all
outs:
- path: figures/prevalence_C03_tnnn.svg
hash: md5
md5: d2d6d2a69298f4d7a99a0614f3fcb0f3
size: 27247
plot_predicted_prevalence@pattern0-C04:
cmd: "python scripts/prevalence_comparison.py --mixture-model models/mixture.hdf5
--params _variables.yml --involvement t n n n --subsite C04 --output figures/prevalence_C04_tnnn.svg\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 8ed98ad0206f0114124a8b7da30961c5
size: 997595
- path: models/mixture.hdf5
hash: md5
md5: ac806b9608daec34d2f2be89d675a623
size: 60425400
- path: models/oral_cavity.hdf5
hash: md5
md5: cc03dc96b1ac9deba1ad09a4343ae840
size: 1454016
- path: models/oropharynx.hdf5
hash: md5
md5: 23acf157edb04fc27f33f60456ac189b
size: 1454016
- path: scripts/prevalence_comparison.py
hash: md5
md5: 57d98686c5ecf4afad1a810888664541
size: 6158
params:
_variables.yml:
icd_code_map:
C01: base of tongue
C02: tongue, other
C03: gum
C04: floor of mouth
C05: palate
C06: mouth, other
C09: tonsil
C10: oropharynx, other
model:
class: Unilateral
first_binom_prob: 0.3
kwargs:
base_symmetric: false
trans_symmetric: true
use_mixing: true
max_t: 10
t_stage_mapping:
0: all
1: all
2: all
3: all
4: all
t_stages:
- all
outs:
- path: figures/prevalence_C04_tnnn.svg
hash: md5
md5: dac51803d7a0d5c488c787ded658444f
size: 29472
plot_predicted_prevalence@pattern0-C05:
cmd: "python scripts/prevalence_comparison.py --mixture-model models/mixture.hdf5
--params _variables.yml --involvement t n n n --subsite C05 --output figures/prevalence_C05_tnnn.svg\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 8ed98ad0206f0114124a8b7da30961c5
size: 997595
- path: models/mixture.hdf5
hash: md5
md5: ac806b9608daec34d2f2be89d675a623
size: 60425400
- path: models/oral_cavity.hdf5
hash: md5
md5: cc03dc96b1ac9deba1ad09a4343ae840
size: 1454016
- path: models/oropharynx.hdf5
hash: md5
md5: 23acf157edb04fc27f33f60456ac189b
size: 1454016
- path: scripts/prevalence_comparison.py
hash: md5
md5: 57d98686c5ecf4afad1a810888664541
size: 6158
params:
_variables.yml:
icd_code_map:
C01: base of tongue
C02: tongue, other
C03: gum
C04: floor of mouth
C05: palate
C06: mouth, other
C09: tonsil
C10: oropharynx, other
model:
class: Unilateral
first_binom_prob: 0.3
kwargs:
base_symmetric: false
trans_symmetric: true
use_mixing: true
max_t: 10
t_stage_mapping:
0: all
1: all
2: all
3: all
4: all
t_stages:
- all
outs:
- path: figures/prevalence_C05_tnnn.svg
hash: md5
md5: a78d744dd2895e67e75dddd61d3a831d
size: 29875
plot_predicted_prevalence@pattern0-C06:
cmd: "python scripts/prevalence_comparison.py --mixture-model models/mixture.hdf5
--params _variables.yml --involvement t n n n --subsite C06 --output figures/prevalence_C06_tnnn.svg\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 8ed98ad0206f0114124a8b7da30961c5
size: 997595
- path: models/mixture.hdf5
hash: md5
md5: ac806b9608daec34d2f2be89d675a623
size: 60425400
- path: models/oral_cavity.hdf5
hash: md5
md5: cc03dc96b1ac9deba1ad09a4343ae840
size: 1454016
- path: models/oropharynx.hdf5
hash: md5
md5: 23acf157edb04fc27f33f60456ac189b
size: 1454016
- path: scripts/prevalence_comparison.py
hash: md5
md5: 57d98686c5ecf4afad1a810888664541
size: 6158
params:
_variables.yml:
icd_code_map:
C01: base of tongue
C02: tongue, other
C03: gum
C04: floor of mouth
C05: palate
C06: mouth, other
C09: tonsil
C10: oropharynx, other
model:
class: Unilateral
first_binom_prob: 0.3
kwargs:
base_symmetric: false
trans_symmetric: true
use_mixing: true
max_t: 10
t_stage_mapping:
0: all
1: all
2: all
3: all
4: all
t_stages:
- all
outs:
- path: figures/prevalence_C06_tnnn.svg
hash: md5
md5: e197a10e939824aae0e9ece395a73595
size: 28841
plot_predicted_prevalence@pattern0-C09:
cmd: "python scripts/prevalence_comparison.py --mixture-model models/mixture.hdf5
--params _variables.yml --involvement t n n n --subsite C09 --output figures/prevalence_C09_tnnn.svg\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 8ed98ad0206f0114124a8b7da30961c5
size: 997595
- path: models/mixture.hdf5
hash: md5
md5: ac806b9608daec34d2f2be89d675a623
size: 60425400
- path: models/oral_cavity.hdf5
hash: md5
md5: cc03dc96b1ac9deba1ad09a4343ae840
size: 1454016
- path: models/oropharynx.hdf5
hash: md5
md5: 23acf157edb04fc27f33f60456ac189b
size: 1454016
- path: scripts/prevalence_comparison.py
hash: md5
md5: 57d98686c5ecf4afad1a810888664541
size: 6158
params:
_variables.yml:
icd_code_map:
C01: base of tongue
C02: tongue, other
C03: gum
C04: floor of mouth
C05: palate
C06: mouth, other
C09: tonsil
C10: oropharynx, other
model:
class: Unilateral
first_binom_prob: 0.3
kwargs:
base_symmetric: false
trans_symmetric: true
use_mixing: true
max_t: 10
t_stage_mapping:
0: all
1: all
2: all
3: all
4: all
t_stages:
- all
outs:
- path: figures/prevalence_C09_tnnn.svg
hash: md5
md5: d9442e98f5b15ac05f8edec4d1f04258
size: 28372
plot_predicted_prevalence@pattern0-C10:
cmd: "python scripts/prevalence_comparison.py --mixture-model models/mixture.hdf5
--params _variables.yml --involvement t n n n --subsite C10 --output figures/prevalence_C10_tnnn.svg\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 8ed98ad0206f0114124a8b7da30961c5
size: 997595
- path: models/mixture.hdf5
hash: md5
md5: ac806b9608daec34d2f2be89d675a623
size: 60425400
- path: models/oral_cavity.hdf5
hash: md5
md5: cc03dc96b1ac9deba1ad09a4343ae840
size: 1454016
- path: models/oropharynx.hdf5
hash: md5
md5: 23acf157edb04fc27f33f60456ac189b
size: 1454016
- path: scripts/prevalence_comparison.py
hash: md5
md5: 57d98686c5ecf4afad1a810888664541
size: 6158
params:
_variables.yml:
icd_code_map:
C01: base of tongue
C02: tongue, other
C03: gum
C04: floor of mouth
C05: palate
C06: mouth, other
C09: tonsil
C10: oropharynx, other
model:
class: Unilateral
first_binom_prob: 0.3
kwargs:
base_symmetric: false
trans_symmetric: true
use_mixing: true
max_t: 10
t_stage_mapping:
0: all
1: all
2: all
3: all
4: all
t_stages:
- all
outs:
- path: figures/prevalence_C10_tnnn.svg
hash: md5
md5: 0df2b53c4ac6f285e14c31a618983326
size: 28527
plot_predicted_prevalence@pattern1-C01:
cmd: "python scripts/prevalence_comparison.py --mixture-model models/mixture.hdf5
--params _variables.yml --involvement n t n n --subsite C01 --output figures/prevalence_C01_ntnn.svg\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 8ed98ad0206f0114124a8b7da30961c5
size: 997595
- path: models/mixture.hdf5
hash: md5
md5: ac806b9608daec34d2f2be89d675a623
size: 60425400
- path: models/oral_cavity.hdf5
hash: md5
md5: cc03dc96b1ac9deba1ad09a4343ae840
size: 1454016
- path: models/oropharynx.hdf5
hash: md5
md5: 23acf157edb04fc27f33f60456ac189b
size: 1454016
- path: scripts/prevalence_comparison.py
hash: md5
md5: 57d98686c5ecf4afad1a810888664541
size: 6158
params:
_variables.yml:
icd_code_map:
C01: base of tongue
C02: tongue, other
C03: gum
C04: floor of mouth
C05: palate
C06: mouth, other
C09: tonsil
C10: oropharynx, other
model:
class: Unilateral
first_binom_prob: 0.3
kwargs:
base_symmetric: false
trans_symmetric: true
use_mixing: true
max_t: 10
t_stage_mapping:
0: all
1: all
2: all
3: all
4: all
t_stages:
- all
outs:
- path: figures/prevalence_C01_ntnn.svg
hash: md5
md5: 713fea0b60004bf1115c3581dfd1770f
size: 29931
plot_predicted_prevalence@pattern1-C02:
cmd: "python scripts/prevalence_comparison.py --mixture-model models/mixture.hdf5
--params _variables.yml --involvement n t n n --subsite C02 --output figures/prevalence_C02_ntnn.svg\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 8ed98ad0206f0114124a8b7da30961c5
size: 997595
- path: models/mixture.hdf5
hash: md5
md5: ac806b9608daec34d2f2be89d675a623
size: 60425400
- path: models/oral_cavity.hdf5
hash: md5
md5: cc03dc96b1ac9deba1ad09a4343ae840
size: 1454016
- path: models/oropharynx.hdf5
hash: md5
md5: 23acf157edb04fc27f33f60456ac189b
size: 1454016
- path: scripts/prevalence_comparison.py
hash: md5
md5: 57d98686c5ecf4afad1a810888664541
size: 6158
params:
_variables.yml:
icd_code_map:
C01: base of tongue
C02: tongue, other
C03: gum
C04: floor of mouth
C05: palate
C06: mouth, other
C09: tonsil
C10: oropharynx, other
model:
class: Unilateral
first_binom_prob: 0.3
kwargs:
base_symmetric: false
trans_symmetric: true
use_mixing: true
max_t: 10
t_stage_mapping:
0: all
1: all
2: all
3: all
4: all
t_stages:
- all
outs:
- path: figures/prevalence_C02_ntnn.svg
hash: md5
md5: 92493c864c691a785df6ce165454a872
size: 29345
plot_predicted_prevalence@pattern1-C03:
cmd: "python scripts/prevalence_comparison.py --mixture-model models/mixture.hdf5
--params _variables.yml --involvement n t n n --subsite C03 --output figures/prevalence_C03_ntnn.svg\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 8ed98ad0206f0114124a8b7da30961c5
size: 997595
- path: models/mixture.hdf5
hash: md5
md5: ac806b9608daec34d2f2be89d675a623
size: 60425400