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dvc.yaml
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dvc.yaml
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stages:
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
deps:
- 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
outs:
- data/joined.csv
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
deps:
- data/joined.csv
outs:
- data/filtered.csv
enhance:
cmd: >
lyscripts data enhance data/filtered.csv data/enhanced.csv
--params _variables.yml
deps:
- data/filtered.csv
params:
- _variables.yml:
- modalities
outs:
- data/enhanced.csv
write_num_patients:
cmd: >
python scripts/write_num_patients.py
--input data/enhanced.csv
--output _variables.yml
deps:
- scripts/write_num_patients.py
params:
- _variables.yml:
- icd_code_map
plot_prevalence_by_subsite:
cmd: >
python scripts/prevalence_by_subsite.py
--input data/enhanced.csv
--params _variables.yml
--output figures/prevalence_by_subsite.svg
deps:
- data/enhanced.csv
- scripts/prevalence_by_subsite.py
params:
- _variables.yml:
- barplot_kwargs
- icd_code_map
outs:
- figures/prevalence_by_subsite.svg:
cache: false
filter_oropharynx:
cmd: >
lyscripts data filter
data/enhanced.csv
data/oropharynx.csv
--include-subsites
C01 C09 C10
deps:
- data/enhanced.csv
outs:
- data/oropharynx.csv
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
deps:
- data/oropharynx.csv
params:
- _variables.yml:
- graph
- model
- sampling
plots:
- figures/sample_from_oropharynx/acor_times.csv
- figures/sample_from_oropharynx/accept_rates.csv
outs:
- models/oropharynx.hdf5
filter_oral_cavity:
cmd: >
lyscripts data filter
data/enhanced.csv
data/oral_cavity.csv
--include-subsites
C02 C03 C04 C05 C06
deps:
- data/enhanced.csv
outs:
- data/oral_cavity.csv
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
deps:
- data/oral_cavity.csv
params:
- _variables.yml:
- graph
- model
- sampling
plots:
- figures/sample_from_oral_cavity/acor_times.csv
- figures/sample_from_oral_cavity/accept_rates.csv
outs:
- models/oral_cavity.hdf5
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
deps:
- scripts/mixture_model_sampling.py
- data/enhanced.csv
params:
- _variables.yml:
- mixture_model
outs:
- figures/mixture_history.svg:
cache: false
- models/mixture.hdf5
plot_component_assignments:
cmd: >
python scripts/plot_component_assignments.py
--model models/mixture.hdf5
--output figures/cluster_assignments.svg
--params _variables.yml
deps:
- models/mixture.hdf5
- scripts/plot_component_assignments.py
params:
- _variables.yml:
- num_patients
outs:
- figures/cluster_assignments.svg:
cache: false
plot_predicted_prevalence:
matrix:
lnl:
- I
- II
- III
- IV
icd:
- C01
- C02
- C03
- C04
- C05
- C06
- C09
- C10
cmd: >
python scripts/prevalence_comparison.py
--mixture-model models/mixture.hdf5
--params _variables.yml
--lnl ${item.lnl}
--subsite ${item.icd}
--output figures/prevalence_${item.icd}_${item.lnl}.svg
deps:
- models/oropharynx.hdf5
- models/oral_cavity.hdf5
- models/mixture.hdf5
- scripts/prevalence_comparison.py
- data/enhanced.csv
params:
- _variables.yml:
- model
- icd_code_map
outs:
- figures/prevalence_${item.icd}_${item.lnl}.svg:
cache: false
prevalence_superplot:
cmd: >
python scripts/prevalence_superplot.py
--data data/enhanced.csv
--models models/
--output figures/prevalence_comparison.svg
--params _variables.yml
--lnls I II III
--subsites C01 C09 C05
--thin-indie 1
--thin-mixture 75
deps:
- scripts/prevalence_superplot.py
- data/enhanced.csv
- models/mixture.hdf5
- models/oropharynx.hdf5
- models/oral_cavity.hdf5
params:
- _variables.yml:
- model
- icd_code_map
outs:
- figures/prevalence_comparison.svg:
cache: false
render_pdf:
cmd: >
quarto render --to iccr-pdf
deps:
- content/manuscript.qmd
- _extensions
- static
- figures
- models
params:
- _variables.yml:
- model.first_binom_prob
- model.max_t
- num_patients
outs:
- _site/