generated from opensafely/research-template
/
project.yaml
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/
project.yaml
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version: '3.0'
expectations:
population_size: 1000000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: input.csv
# generate_coverage_population:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_coverage
# outputs:
# highly_sensitive:
# cohort: input_coverage.csv
calc_coverage:
needs: [generate_study_population]
run: r:latest analysis/calculate_tpp_coverage.R input.csv data/SAPE22DT15_mid_2019_msoa.csv
outputs:
moderately_sensitive:
log: coverage_log.txt
rds: tpp_msoa_coverage.rds
csv: tpp_msoa_coverage.csv
csv2: msoas_in_tpp.csv
csv3: msoa_gt_100_cov.csv
figure: total_vs_tpp_pop.png
prelim:
needs: [generate_study_population, calc_coverage]
# last argument relates to MSOA TPP coverage >= X%
run: r:latest analysis/prelim.R input.csv tpp_msoa_coverage.rds 80
outputs:
moderately_sensitive:
log: prelim_check_log.txt
data_clean:
needs: [generate_study_population, calc_coverage]
# last argument relates to MSOA TPP coverage >= X%
run: r:latest analysis/data_clean.R input.csv tpp_msoa_coverage.rds 80
outputs:
moderately_sensitive:
log: data_clean_log.txt
highly_sensitive:
input_clean: input_clean.rds
data_check_figs:
needs: [data_clean]
run: r:latest analysis/data_check_figs.R input_clean.rds data/msoa_shp.rds
outputs:
moderately_sensitive:
figure1: tpp_coverage_msoa.png
figure2: tpp_coverage_carehomes.png
figure3: tpp_coverage_map.pdf
figure4: age_dist.png
figure5: infection_death_delays.png
figure6: hh_size_dist.png
data_setup:
needs: [data_clean]
# last argument relates to carehome TPP coverage >= X%
run: r:latest analysis/data_setup.R input_clean.rds 90
outputs:
moderately_sensitive:
log: data_setup_log.txt
highly_sensitive:
comm_prev: community_prevalence.rds
analysisdata: analysisdata.rds
ch_linelist: ch_linelist.rds
ch_agg_long: ch_agg_long.rds
descriptive:
needs: [data_clean, data_setup]
run: r:latest analysis/descriptive.R
outputs:
moderately_sensitive:
report: descriptive.pdf
log: log_descriptive.txt
data: ch_gp_permsoa.csv
run_models:
needs: [data_setup]
#
run: r:latest analysis/run_models.R analysisdata.rds community_prevalence.rds data/msoa_shp.rds 0.4
outputs:
moderately_sensitive:
output: output_model_run.txt
log: log_model_run.txt
# figure: model_resids_map.pdf
highly_sensitive:
fit: fits.rds
data: testdata.rds
validate_models:
needs: [run_models]
run: r:latest analysis/validate_models.R fits.rds testdata.rds
outputs:
moderately_sensitive:
output: output_model_val.txt
report: test_pred_figs.pdf
run_all:
needs: [validate_models, descriptive]
# In order to be valid this action needs to define a run commmand and
# some output. We don't really care what these are but the below seems to
# do the trick.
run: cohortextractor:latest --version
outputs:
moderately_sensitive:
whatever: project.yaml