generated from opensafely/research-template
/
project.yaml
4155 lines (3827 loc) · 186 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 100000
actions:
## # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml DIRECTLY
## This file is created by create-project.R
## Edit and run create-project.R to update the project.yaml
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Pre-server scripts
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Extract and tidy
## # # # # # # # # # # # # # # # # # # #
extract:
run: cohortextractor:latest generate_cohort --study-definition study_definition
--output-format feather
needs: []
outputs:
highly_sensitive:
cohort: output/input.feather
extract_report:
run: cohort-report:v3.0.0 output/input.feather
needs:
- extract
outputs:
moderately_sensitive:
html: output/data/reports/extract/*.html
png: output/data/reports/extract/*.png
config:
output_path: output/data/reports/extract/
data_process:
run: r:latest analysis/data_process.R
needs:
- extract
outputs:
highly_sensitive:
rds: output/data/data_processed.rds
vaxlong: output/data/data_vaxlong.rds
skim_process:
run: r:latest analysis/data_skim.R output/data/data_processed.rds output/data_properties
needs:
- data_process
outputs:
moderately_sensitive:
cohort: output/data_properties/data_processed*.txt
data_process_long:
run: r:latest analysis/data_process_long.R
needs:
- data_process
outputs:
highly_sensitive:
processed: output/data/data_long*.rds
data_selection:
run: r:latest analysis/data_selection.R
needs:
- data_process
outputs:
highly_sensitive:
data: output/data/data_cohort.rds
feather: output/data/data_cohort.feather
moderately_sensitive:
flow: output/data/flowchart.csv
skim_selection:
run: r:latest analysis/data_skim.R output/data/data_cohort.rds output/data_properties
needs:
- data_selection
outputs:
moderately_sensitive:
cohort: output/data_properties/data_cohort*.txt
cohort_report:
run: cohort-report:v3.0.0 output/data/data_cohort.feather
needs:
- data_selection
outputs:
moderately_sensitive:
html: output/data/reports/cohort/*.html
png: output/data/reports/cohort/*.png
config:
output_path: output/data/reports/cohort/
## # # # # # # # # # # # # # # # # # # #
## Descriptive stats
## # # # # # # # # # # # # # # # # # # #
descriptive_table1:
run: r:latest analysis/table1.R
needs:
- data_selection
outputs:
moderately_sensitive:
html: output/descriptive/table1/*.html
csv: output/descriptive/table1/*.csv
descriptive_vaxdate:
run: r:latest analysis/vax_date.R
needs:
- data_selection
outputs:
moderately_sensitive:
png: output/descriptive/vaxdate/*.png
pdf: output/descriptive/vaxdate/*.pdf
svg: output/descriptive/vaxdate/*.svg
## # # # # # # # # # # # # # # # # # # #
## Matching
## # # # # # # # # # # # # # # # # # # #
match_seqtrialcox_pfizer:
run: r:latest analysis/match_seqtrialcox.R pfizer
needs:
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/match/pfizer/match_*.rds
moderately_sensitive:
txt: output/match/pfizer/match_*.txt
merge_seqtrialcox_pfizer:
run: r:latest analysis/merge_seqtrialcox.R pfizer
needs:
- data_process
- data_process_long
- data_selection
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
txt: output/match/pfizer/merge_*.txt
csv: output/match/pfizer/merge_*.csv
png: output/match/pfizer/merge_*.png
pdf: output/match/pfizer/merge_*.pdf
html: output/match/pfizer/merge_*.html
match_seqtrialcox_moderna:
run: r:latest analysis/match_seqtrialcox.R moderna
needs:
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/match/moderna/match_*.rds
moderately_sensitive:
txt: output/match/moderna/match_*.txt
merge_seqtrialcox_moderna:
run: r:latest analysis/merge_seqtrialcox.R moderna
needs:
- data_process
- data_process_long
- data_selection
- match_seqtrialcox_moderna
outputs:
moderately_sensitive:
txt: output/match/moderna/merge_*.txt
csv: output/match/moderna/merge_*.csv
png: output/match/moderna/merge_*.png
pdf: output/match/moderna/merge_*.pdf
html: output/match/moderna/merge_*.html
combine_match:
run: r:latest analysis/combine_match.R
needs:
- match_seqtrialcox_pfizer
- match_seqtrialcox_moderna
- merge_seqtrialcox_pfizer
- merge_seqtrialcox_moderna
outputs:
moderately_sensitive:
csv: output/match/combined/*.csv
## # # # # # # # # # # # # # # # # # # #
## Pfizer models
## # # # # # # # # # # # # # # # # # # #
## ### Overall models (''none'')
model_seqtrialcox_pfizer_postest_none:
run: r:latest analysis/model_seqtrialcox.R pfizer postest none
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/postest/none/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/postest/none/model_*.txt
csv: output/models/seqtrialcox/pfizer/postest/none/model_*.csv
report_seqtrialcox_pfizer_postest_none:
run: r:latest analysis/report_seqtrialcox.R pfizer postest none
needs:
- data_selection
- model_seqtrialcox_pfizer_postest_none
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/postest/none/report_*.csv
svg: output/models/seqtrialcox/pfizer/postest/none/report_*.svg
png: output/models/seqtrialcox/pfizer/postest/none/report_*.png
model_seqtrialcox_pfizer_covidemergency_none:
run: r:latest analysis/model_seqtrialcox.R pfizer covidemergency none
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidemergency/none/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidemergency/none/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidemergency/none/model_*.csv
report_seqtrialcox_pfizer_covidemergency_none:
run: r:latest analysis/report_seqtrialcox.R pfizer covidemergency none
needs:
- data_selection
- model_seqtrialcox_pfizer_covidemergency_none
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidemergency/none/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidemergency/none/report_*.svg
png: output/models/seqtrialcox/pfizer/covidemergency/none/report_*.png
model_seqtrialcox_pfizer_covidadmittedproxy1_none:
run: r:latest analysis/model_seqtrialcox.R pfizer covidadmittedproxy1 none
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidadmittedproxy1/none/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidadmittedproxy1/none/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidadmittedproxy1/none/model_*.csv
report_seqtrialcox_pfizer_covidadmittedproxy1_none:
run: r:latest analysis/report_seqtrialcox.R pfizer covidadmittedproxy1 none
needs:
- data_selection
- model_seqtrialcox_pfizer_covidadmittedproxy1_none
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidadmittedproxy1/none/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidadmittedproxy1/none/report_*.svg
png: output/models/seqtrialcox/pfizer/covidadmittedproxy1/none/report_*.png
model_seqtrialcox_pfizer_covidadmitted_none:
run: r:latest analysis/model_seqtrialcox.R pfizer covidadmitted none
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidadmitted/none/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidadmitted/none/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidadmitted/none/model_*.csv
report_seqtrialcox_pfizer_covidadmitted_none:
run: r:latest analysis/report_seqtrialcox.R pfizer covidadmitted none
needs:
- data_selection
- model_seqtrialcox_pfizer_covidadmitted_none
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidadmitted/none/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidadmitted/none/report_*.svg
png: output/models/seqtrialcox/pfizer/covidadmitted/none/report_*.png
model_seqtrialcox_pfizer_noncovidadmitted_none:
run: r:latest analysis/model_seqtrialcox.R pfizer noncovidadmitted none
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/noncovidadmitted/none/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/noncovidadmitted/none/model_*.txt
csv: output/models/seqtrialcox/pfizer/noncovidadmitted/none/model_*.csv
report_seqtrialcox_pfizer_noncovidadmitted_none:
run: r:latest analysis/report_seqtrialcox.R pfizer noncovidadmitted none
needs:
- data_selection
- model_seqtrialcox_pfizer_noncovidadmitted_none
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/noncovidadmitted/none/report_*.csv
svg: output/models/seqtrialcox/pfizer/noncovidadmitted/none/report_*.svg
png: output/models/seqtrialcox/pfizer/noncovidadmitted/none/report_*.png
model_seqtrialcox_pfizer_covidcc_none:
run: r:latest analysis/model_seqtrialcox.R pfizer covidcc none
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidcc/none/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidcc/none/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidcc/none/model_*.csv
report_seqtrialcox_pfizer_covidcc_none:
run: r:latest analysis/report_seqtrialcox.R pfizer covidcc none
needs:
- data_selection
- model_seqtrialcox_pfizer_covidcc_none
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidcc/none/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidcc/none/report_*.svg
png: output/models/seqtrialcox/pfizer/covidcc/none/report_*.png
model_seqtrialcox_pfizer_coviddeath_none:
run: r:latest analysis/model_seqtrialcox.R pfizer coviddeath none
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/coviddeath/none/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/coviddeath/none/model_*.txt
csv: output/models/seqtrialcox/pfizer/coviddeath/none/model_*.csv
report_seqtrialcox_pfizer_coviddeath_none:
run: r:latest analysis/report_seqtrialcox.R pfizer coviddeath none
needs:
- data_selection
- model_seqtrialcox_pfizer_coviddeath_none
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/coviddeath/none/report_*.csv
svg: output/models/seqtrialcox/pfizer/coviddeath/none/report_*.svg
png: output/models/seqtrialcox/pfizer/coviddeath/none/report_*.png
model_seqtrialcox_pfizer_noncoviddeath_none:
run: r:latest analysis/model_seqtrialcox.R pfizer noncoviddeath none
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/noncoviddeath/none/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/noncoviddeath/none/model_*.txt
csv: output/models/seqtrialcox/pfizer/noncoviddeath/none/model_*.csv
report_seqtrialcox_pfizer_noncoviddeath_none:
run: r:latest analysis/report_seqtrialcox.R pfizer noncoviddeath none
needs:
- data_selection
- model_seqtrialcox_pfizer_noncoviddeath_none
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/noncoviddeath/none/report_*.csv
svg: output/models/seqtrialcox/pfizer/noncoviddeath/none/report_*.svg
png: output/models/seqtrialcox/pfizer/noncoviddeath/none/report_*.png
## ### Models by primary course (''vax12_type'')
model_seqtrialcox_pfizer_postest_vax12_type-az-az:
run: r:latest analysis/model_seqtrialcox.R pfizer postest vax12_type-az-az
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/postest/vax12_type-az-az/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/postest/vax12_type-az-az/model_*.txt
csv: output/models/seqtrialcox/pfizer/postest/vax12_type-az-az/model_*.csv
report_seqtrialcox_pfizer_postest_vax12_type-az-az:
run: r:latest analysis/report_seqtrialcox.R pfizer postest vax12_type-az-az
needs:
- data_selection
- model_seqtrialcox_pfizer_postest_vax12_type-az-az
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/postest/vax12_type-az-az/report_*.csv
svg: output/models/seqtrialcox/pfizer/postest/vax12_type-az-az/report_*.svg
png: output/models/seqtrialcox/pfizer/postest/vax12_type-az-az/report_*.png
model_seqtrialcox_pfizer_postest_vax12_type-pfizer-pfizer:
run: r:latest analysis/model_seqtrialcox.R pfizer postest vax12_type-pfizer-pfizer
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/postest/vax12_type-pfizer-pfizer/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/postest/vax12_type-pfizer-pfizer/model_*.txt
csv: output/models/seqtrialcox/pfizer/postest/vax12_type-pfizer-pfizer/model_*.csv
report_seqtrialcox_pfizer_postest_vax12_type-pfizer-pfizer:
run: r:latest analysis/report_seqtrialcox.R pfizer postest vax12_type-pfizer-pfizer
needs:
- data_selection
- model_seqtrialcox_pfizer_postest_vax12_type-pfizer-pfizer
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/postest/vax12_type-pfizer-pfizer/report_*.csv
svg: output/models/seqtrialcox/pfizer/postest/vax12_type-pfizer-pfizer/report_*.svg
png: output/models/seqtrialcox/pfizer/postest/vax12_type-pfizer-pfizer/report_*.png
model_seqtrialcox_pfizer_covidemergency_vax12_type-az-az:
run: r:latest analysis/model_seqtrialcox.R pfizer covidemergency vax12_type-az-az
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidemergency/vax12_type-az-az/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidemergency/vax12_type-az-az/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidemergency/vax12_type-az-az/model_*.csv
report_seqtrialcox_pfizer_covidemergency_vax12_type-az-az:
run: r:latest analysis/report_seqtrialcox.R pfizer covidemergency vax12_type-az-az
needs:
- data_selection
- model_seqtrialcox_pfizer_covidemergency_vax12_type-az-az
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidemergency/vax12_type-az-az/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidemergency/vax12_type-az-az/report_*.svg
png: output/models/seqtrialcox/pfizer/covidemergency/vax12_type-az-az/report_*.png
model_seqtrialcox_pfizer_covidemergency_vax12_type-pfizer-pfizer:
run: r:latest analysis/model_seqtrialcox.R pfizer covidemergency vax12_type-pfizer-pfizer
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidemergency/vax12_type-pfizer-pfizer/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidemergency/vax12_type-pfizer-pfizer/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidemergency/vax12_type-pfizer-pfizer/model_*.csv
report_seqtrialcox_pfizer_covidemergency_vax12_type-pfizer-pfizer:
run: r:latest analysis/report_seqtrialcox.R pfizer covidemergency vax12_type-pfizer-pfizer
needs:
- data_selection
- model_seqtrialcox_pfizer_covidemergency_vax12_type-pfizer-pfizer
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidemergency/vax12_type-pfizer-pfizer/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidemergency/vax12_type-pfizer-pfizer/report_*.svg
png: output/models/seqtrialcox/pfizer/covidemergency/vax12_type-pfizer-pfizer/report_*.png
model_seqtrialcox_pfizer_covidadmittedproxy1_vax12_type-az-az:
run: r:latest analysis/model_seqtrialcox.R pfizer covidadmittedproxy1 vax12_type-az-az
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidadmittedproxy1/vax12_type-az-az/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidadmittedproxy1/vax12_type-az-az/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidadmittedproxy1/vax12_type-az-az/model_*.csv
report_seqtrialcox_pfizer_covidadmittedproxy1_vax12_type-az-az:
run: r:latest analysis/report_seqtrialcox.R pfizer covidadmittedproxy1 vax12_type-az-az
needs:
- data_selection
- model_seqtrialcox_pfizer_covidadmittedproxy1_vax12_type-az-az
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidadmittedproxy1/vax12_type-az-az/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidadmittedproxy1/vax12_type-az-az/report_*.svg
png: output/models/seqtrialcox/pfizer/covidadmittedproxy1/vax12_type-az-az/report_*.png
model_seqtrialcox_pfizer_covidadmittedproxy1_vax12_type-pfizer-pfizer:
run: r:latest analysis/model_seqtrialcox.R pfizer covidadmittedproxy1 vax12_type-pfizer-pfizer
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidadmittedproxy1/vax12_type-pfizer-pfizer/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidadmittedproxy1/vax12_type-pfizer-pfizer/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidadmittedproxy1/vax12_type-pfizer-pfizer/model_*.csv
report_seqtrialcox_pfizer_covidadmittedproxy1_vax12_type-pfizer-pfizer:
run: r:latest analysis/report_seqtrialcox.R pfizer covidadmittedproxy1 vax12_type-pfizer-pfizer
needs:
- data_selection
- model_seqtrialcox_pfizer_covidadmittedproxy1_vax12_type-pfizer-pfizer
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidadmittedproxy1/vax12_type-pfizer-pfizer/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidadmittedproxy1/vax12_type-pfizer-pfizer/report_*.svg
png: output/models/seqtrialcox/pfizer/covidadmittedproxy1/vax12_type-pfizer-pfizer/report_*.png
model_seqtrialcox_pfizer_covidadmitted_vax12_type-az-az:
run: r:latest analysis/model_seqtrialcox.R pfizer covidadmitted vax12_type-az-az
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidadmitted/vax12_type-az-az/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidadmitted/vax12_type-az-az/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidadmitted/vax12_type-az-az/model_*.csv
report_seqtrialcox_pfizer_covidadmitted_vax12_type-az-az:
run: r:latest analysis/report_seqtrialcox.R pfizer covidadmitted vax12_type-az-az
needs:
- data_selection
- model_seqtrialcox_pfizer_covidadmitted_vax12_type-az-az
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidadmitted/vax12_type-az-az/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidadmitted/vax12_type-az-az/report_*.svg
png: output/models/seqtrialcox/pfizer/covidadmitted/vax12_type-az-az/report_*.png
model_seqtrialcox_pfizer_covidadmitted_vax12_type-pfizer-pfizer:
run: r:latest analysis/model_seqtrialcox.R pfizer covidadmitted vax12_type-pfizer-pfizer
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidadmitted/vax12_type-pfizer-pfizer/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidadmitted/vax12_type-pfizer-pfizer/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidadmitted/vax12_type-pfizer-pfizer/model_*.csv
report_seqtrialcox_pfizer_covidadmitted_vax12_type-pfizer-pfizer:
run: r:latest analysis/report_seqtrialcox.R pfizer covidadmitted vax12_type-pfizer-pfizer
needs:
- data_selection
- model_seqtrialcox_pfizer_covidadmitted_vax12_type-pfizer-pfizer
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidadmitted/vax12_type-pfizer-pfizer/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidadmitted/vax12_type-pfizer-pfizer/report_*.svg
png: output/models/seqtrialcox/pfizer/covidadmitted/vax12_type-pfizer-pfizer/report_*.png
model_seqtrialcox_pfizer_noncovidadmitted_vax12_type-az-az:
run: r:latest analysis/model_seqtrialcox.R pfizer noncovidadmitted vax12_type-az-az
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/noncovidadmitted/vax12_type-az-az/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/noncovidadmitted/vax12_type-az-az/model_*.txt
csv: output/models/seqtrialcox/pfizer/noncovidadmitted/vax12_type-az-az/model_*.csv
report_seqtrialcox_pfizer_noncovidadmitted_vax12_type-az-az:
run: r:latest analysis/report_seqtrialcox.R pfizer noncovidadmitted vax12_type-az-az
needs:
- data_selection
- model_seqtrialcox_pfizer_noncovidadmitted_vax12_type-az-az
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/noncovidadmitted/vax12_type-az-az/report_*.csv
svg: output/models/seqtrialcox/pfizer/noncovidadmitted/vax12_type-az-az/report_*.svg
png: output/models/seqtrialcox/pfizer/noncovidadmitted/vax12_type-az-az/report_*.png
model_seqtrialcox_pfizer_noncovidadmitted_vax12_type-pfizer-pfizer:
run: r:latest analysis/model_seqtrialcox.R pfizer noncovidadmitted vax12_type-pfizer-pfizer
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/noncovidadmitted/vax12_type-pfizer-pfizer/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/noncovidadmitted/vax12_type-pfizer-pfizer/model_*.txt
csv: output/models/seqtrialcox/pfizer/noncovidadmitted/vax12_type-pfizer-pfizer/model_*.csv
report_seqtrialcox_pfizer_noncovidadmitted_vax12_type-pfizer-pfizer:
run: r:latest analysis/report_seqtrialcox.R pfizer noncovidadmitted vax12_type-pfizer-pfizer
needs:
- data_selection
- model_seqtrialcox_pfizer_noncovidadmitted_vax12_type-pfizer-pfizer
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/noncovidadmitted/vax12_type-pfizer-pfizer/report_*.csv
svg: output/models/seqtrialcox/pfizer/noncovidadmitted/vax12_type-pfizer-pfizer/report_*.svg
png: output/models/seqtrialcox/pfizer/noncovidadmitted/vax12_type-pfizer-pfizer/report_*.png
model_seqtrialcox_pfizer_covidcc_vax12_type-az-az:
run: r:latest analysis/model_seqtrialcox.R pfizer covidcc vax12_type-az-az
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidcc/vax12_type-az-az/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidcc/vax12_type-az-az/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidcc/vax12_type-az-az/model_*.csv
report_seqtrialcox_pfizer_covidcc_vax12_type-az-az:
run: r:latest analysis/report_seqtrialcox.R pfizer covidcc vax12_type-az-az
needs:
- data_selection
- model_seqtrialcox_pfizer_covidcc_vax12_type-az-az
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidcc/vax12_type-az-az/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidcc/vax12_type-az-az/report_*.svg
png: output/models/seqtrialcox/pfizer/covidcc/vax12_type-az-az/report_*.png
model_seqtrialcox_pfizer_covidcc_vax12_type-pfizer-pfizer:
run: r:latest analysis/model_seqtrialcox.R pfizer covidcc vax12_type-pfizer-pfizer
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidcc/vax12_type-pfizer-pfizer/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidcc/vax12_type-pfizer-pfizer/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidcc/vax12_type-pfizer-pfizer/model_*.csv
report_seqtrialcox_pfizer_covidcc_vax12_type-pfizer-pfizer:
run: r:latest analysis/report_seqtrialcox.R pfizer covidcc vax12_type-pfizer-pfizer
needs:
- data_selection
- model_seqtrialcox_pfizer_covidcc_vax12_type-pfizer-pfizer
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidcc/vax12_type-pfizer-pfizer/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidcc/vax12_type-pfizer-pfizer/report_*.svg
png: output/models/seqtrialcox/pfizer/covidcc/vax12_type-pfizer-pfizer/report_*.png
model_seqtrialcox_pfizer_coviddeath_vax12_type-az-az:
run: r:latest analysis/model_seqtrialcox.R pfizer coviddeath vax12_type-az-az
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/coviddeath/vax12_type-az-az/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/coviddeath/vax12_type-az-az/model_*.txt
csv: output/models/seqtrialcox/pfizer/coviddeath/vax12_type-az-az/model_*.csv
report_seqtrialcox_pfizer_coviddeath_vax12_type-az-az:
run: r:latest analysis/report_seqtrialcox.R pfizer coviddeath vax12_type-az-az
needs:
- data_selection
- model_seqtrialcox_pfizer_coviddeath_vax12_type-az-az
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/coviddeath/vax12_type-az-az/report_*.csv
svg: output/models/seqtrialcox/pfizer/coviddeath/vax12_type-az-az/report_*.svg
png: output/models/seqtrialcox/pfizer/coviddeath/vax12_type-az-az/report_*.png
model_seqtrialcox_pfizer_coviddeath_vax12_type-pfizer-pfizer:
run: r:latest analysis/model_seqtrialcox.R pfizer coviddeath vax12_type-pfizer-pfizer
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/coviddeath/vax12_type-pfizer-pfizer/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/coviddeath/vax12_type-pfizer-pfizer/model_*.txt
csv: output/models/seqtrialcox/pfizer/coviddeath/vax12_type-pfizer-pfizer/model_*.csv
report_seqtrialcox_pfizer_coviddeath_vax12_type-pfizer-pfizer:
run: r:latest analysis/report_seqtrialcox.R pfizer coviddeath vax12_type-pfizer-pfizer
needs:
- data_selection
- model_seqtrialcox_pfizer_coviddeath_vax12_type-pfizer-pfizer
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/coviddeath/vax12_type-pfizer-pfizer/report_*.csv
svg: output/models/seqtrialcox/pfizer/coviddeath/vax12_type-pfizer-pfizer/report_*.svg
png: output/models/seqtrialcox/pfizer/coviddeath/vax12_type-pfizer-pfizer/report_*.png
model_seqtrialcox_pfizer_noncoviddeath_vax12_type-az-az:
run: r:latest analysis/model_seqtrialcox.R pfizer noncoviddeath vax12_type-az-az
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/noncoviddeath/vax12_type-az-az/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/noncoviddeath/vax12_type-az-az/model_*.txt
csv: output/models/seqtrialcox/pfizer/noncoviddeath/vax12_type-az-az/model_*.csv
report_seqtrialcox_pfizer_noncoviddeath_vax12_type-az-az:
run: r:latest analysis/report_seqtrialcox.R pfizer noncoviddeath vax12_type-az-az
needs:
- data_selection
- model_seqtrialcox_pfizer_noncoviddeath_vax12_type-az-az
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/noncoviddeath/vax12_type-az-az/report_*.csv
svg: output/models/seqtrialcox/pfizer/noncoviddeath/vax12_type-az-az/report_*.svg
png: output/models/seqtrialcox/pfizer/noncoviddeath/vax12_type-az-az/report_*.png
model_seqtrialcox_pfizer_noncoviddeath_vax12_type-pfizer-pfizer:
run: r:latest analysis/model_seqtrialcox.R pfizer noncoviddeath vax12_type-pfizer-pfizer
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/noncoviddeath/vax12_type-pfizer-pfizer/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/noncoviddeath/vax12_type-pfizer-pfizer/model_*.txt
csv: output/models/seqtrialcox/pfizer/noncoviddeath/vax12_type-pfizer-pfizer/model_*.csv
report_seqtrialcox_pfizer_noncoviddeath_vax12_type-pfizer-pfizer:
run: r:latest analysis/report_seqtrialcox.R pfizer noncoviddeath vax12_type-pfizer-pfizer
needs:
- data_selection
- model_seqtrialcox_pfizer_noncoviddeath_vax12_type-pfizer-pfizer
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/noncoviddeath/vax12_type-pfizer-pfizer/report_*.csv
svg: output/models/seqtrialcox/pfizer/noncoviddeath/vax12_type-pfizer-pfizer/report_*.svg
png: output/models/seqtrialcox/pfizer/noncoviddeath/vax12_type-pfizer-pfizer/report_*.png
## ### Models by clinical extremely vulnerable (''cev'')
model_seqtrialcox_pfizer_postest_cev-FALSE:
run: r:latest analysis/model_seqtrialcox.R pfizer postest cev-FALSE
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/postest/cev-FALSE/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/postest/cev-FALSE/model_*.txt
csv: output/models/seqtrialcox/pfizer/postest/cev-FALSE/model_*.csv
report_seqtrialcox_pfizer_postest_cev-FALSE:
run: r:latest analysis/report_seqtrialcox.R pfizer postest cev-FALSE
needs:
- data_selection
- model_seqtrialcox_pfizer_postest_cev-FALSE
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/postest/cev-FALSE/report_*.csv
svg: output/models/seqtrialcox/pfizer/postest/cev-FALSE/report_*.svg
png: output/models/seqtrialcox/pfizer/postest/cev-FALSE/report_*.png
model_seqtrialcox_pfizer_postest_cev-TRUE:
run: r:latest analysis/model_seqtrialcox.R pfizer postest cev-TRUE
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/postest/cev-TRUE/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/postest/cev-TRUE/model_*.txt
csv: output/models/seqtrialcox/pfizer/postest/cev-TRUE/model_*.csv
report_seqtrialcox_pfizer_postest_cev-TRUE:
run: r:latest analysis/report_seqtrialcox.R pfizer postest cev-TRUE
needs:
- data_selection
- model_seqtrialcox_pfizer_postest_cev-TRUE
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/postest/cev-TRUE/report_*.csv
svg: output/models/seqtrialcox/pfizer/postest/cev-TRUE/report_*.svg
png: output/models/seqtrialcox/pfizer/postest/cev-TRUE/report_*.png
model_seqtrialcox_pfizer_covidemergency_cev-FALSE:
run: r:latest analysis/model_seqtrialcox.R pfizer covidemergency cev-FALSE
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidemergency/cev-FALSE/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidemergency/cev-FALSE/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidemergency/cev-FALSE/model_*.csv
report_seqtrialcox_pfizer_covidemergency_cev-FALSE:
run: r:latest analysis/report_seqtrialcox.R pfizer covidemergency cev-FALSE
needs:
- data_selection
- model_seqtrialcox_pfizer_covidemergency_cev-FALSE
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidemergency/cev-FALSE/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidemergency/cev-FALSE/report_*.svg
png: output/models/seqtrialcox/pfizer/covidemergency/cev-FALSE/report_*.png
model_seqtrialcox_pfizer_covidemergency_cev-TRUE:
run: r:latest analysis/model_seqtrialcox.R pfizer covidemergency cev-TRUE
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidemergency/cev-TRUE/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidemergency/cev-TRUE/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidemergency/cev-TRUE/model_*.csv
report_seqtrialcox_pfizer_covidemergency_cev-TRUE:
run: r:latest analysis/report_seqtrialcox.R pfizer covidemergency cev-TRUE
needs:
- data_selection
- model_seqtrialcox_pfizer_covidemergency_cev-TRUE
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidemergency/cev-TRUE/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidemergency/cev-TRUE/report_*.svg
png: output/models/seqtrialcox/pfizer/covidemergency/cev-TRUE/report_*.png
model_seqtrialcox_pfizer_covidadmittedproxy1_cev-FALSE:
run: r:latest analysis/model_seqtrialcox.R pfizer covidadmittedproxy1 cev-FALSE
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidadmittedproxy1/cev-FALSE/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidadmittedproxy1/cev-FALSE/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidadmittedproxy1/cev-FALSE/model_*.csv
report_seqtrialcox_pfizer_covidadmittedproxy1_cev-FALSE:
run: r:latest analysis/report_seqtrialcox.R pfizer covidadmittedproxy1 cev-FALSE
needs:
- data_selection
- model_seqtrialcox_pfizer_covidadmittedproxy1_cev-FALSE
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidadmittedproxy1/cev-FALSE/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidadmittedproxy1/cev-FALSE/report_*.svg
png: output/models/seqtrialcox/pfizer/covidadmittedproxy1/cev-FALSE/report_*.png
model_seqtrialcox_pfizer_covidadmittedproxy1_cev-TRUE:
run: r:latest analysis/model_seqtrialcox.R pfizer covidadmittedproxy1 cev-TRUE
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidadmittedproxy1/cev-TRUE/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidadmittedproxy1/cev-TRUE/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidadmittedproxy1/cev-TRUE/model_*.csv
report_seqtrialcox_pfizer_covidadmittedproxy1_cev-TRUE:
run: r:latest analysis/report_seqtrialcox.R pfizer covidadmittedproxy1 cev-TRUE
needs:
- data_selection
- model_seqtrialcox_pfizer_covidadmittedproxy1_cev-TRUE
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidadmittedproxy1/cev-TRUE/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidadmittedproxy1/cev-TRUE/report_*.svg
png: output/models/seqtrialcox/pfizer/covidadmittedproxy1/cev-TRUE/report_*.png
model_seqtrialcox_pfizer_covidadmitted_cev-FALSE:
run: r:latest analysis/model_seqtrialcox.R pfizer covidadmitted cev-FALSE
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidadmitted/cev-FALSE/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidadmitted/cev-FALSE/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidadmitted/cev-FALSE/model_*.csv
report_seqtrialcox_pfizer_covidadmitted_cev-FALSE:
run: r:latest analysis/report_seqtrialcox.R pfizer covidadmitted cev-FALSE
needs:
- data_selection
- model_seqtrialcox_pfizer_covidadmitted_cev-FALSE
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidadmitted/cev-FALSE/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidadmitted/cev-FALSE/report_*.svg
png: output/models/seqtrialcox/pfizer/covidadmitted/cev-FALSE/report_*.png
model_seqtrialcox_pfizer_covidadmitted_cev-TRUE:
run: r:latest analysis/model_seqtrialcox.R pfizer covidadmitted cev-TRUE
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs:
highly_sensitive:
rds: output/models/seqtrialcox/pfizer/covidadmitted/cev-TRUE/model_*.rds
moderately_sensitive:
txt: output/models/seqtrialcox/pfizer/covidadmitted/cev-TRUE/model_*.txt
csv: output/models/seqtrialcox/pfizer/covidadmitted/cev-TRUE/model_*.csv
report_seqtrialcox_pfizer_covidadmitted_cev-TRUE:
run: r:latest analysis/report_seqtrialcox.R pfizer covidadmitted cev-TRUE
needs:
- data_selection
- model_seqtrialcox_pfizer_covidadmitted_cev-TRUE
- match_seqtrialcox_pfizer
outputs:
moderately_sensitive:
csv: output/models/seqtrialcox/pfizer/covidadmitted/cev-TRUE/report_*.csv
svg: output/models/seqtrialcox/pfizer/covidadmitted/cev-TRUE/report_*.svg
png: output/models/seqtrialcox/pfizer/covidadmitted/cev-TRUE/report_*.png
model_seqtrialcox_pfizer_noncovidadmitted_cev-FALSE:
run: r:latest analysis/model_seqtrialcox.R pfizer noncovidadmitted cev-FALSE
needs:
- match_seqtrialcox_pfizer
- data_selection
- data_process_long
outputs: