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update yaml
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@emprestige
emprestige committed Sep 24, 2024
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8 changes: 4 additions & 4 deletions actions.txt
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Expand Up @@ -15,10 +15,10 @@ generate_dataset_older_adults_s1_specific_secondary process_dataset_older_adults
generate_dataset_adults_s1_specific_secondary process_dataset_adults_s1_specific_secondary describe_dataset_adults_s1_specific_secondary analyse_dataset_adults_rsv_s1_specific_secondary analyse_dataset_adults_rsv_further_s1_specific_secondary analyse_dataset_adults_flu_s1_specific_secondary analyse_dataset_adults_flu_further_s1_specific_secondary analyse_dataset_adults_overall_and_all_cause_s1_specific_secondary analyse_dataset_adults_overall_and_all_cause_further_s1_specific_secondary generate_dataset_adults_s2_specific_secondary process_dataset_adults_s2_specific_secondary describe_dataset_adults_s2_specific_secondary analyse_dataset_adults_rsv_s2_specific_secondary analyse_dataset_adults_rsv_further_s2_specific_secondary analyse_dataset_adults_flu_s2_specific_secondary analyse_dataset_adults_flu_further_s2_specific_secondary analyse_dataset_adults_overall_and_all_cause_s2_specific_secondary analyse_dataset_adults_overall_and_all_cause_further_s2_specific_secondary generate_dataset_adults_s3_specific_secondary process_dataset_adults_s3_specific_secondary describe_dataset_adults_s3_specific_secondary analyse_dataset_adults_rsv_s3_specific_secondary analyse_dataset_adults_rsv_further_s3_specific_secondary analyse_dataset_adults_flu_s3_specific_secondary analyse_dataset_adults_flu_further_s3_specific_secondary analyse_dataset_adults_overall_and_all_cause_s3_specific_secondary analyse_dataset_adults_overall_and_all_cause_further_s3_specific_secondary generate_dataset_adults_s4_specific_secondary process_dataset_adults_s4_specific_secondary describe_dataset_adults_s4_specific_secondary analyse_dataset_adults_rsv_s4_specific_secondary analyse_dataset_adults_rsv_further_s4_specific_secondary analyse_dataset_adults_flu_s4_specific_secondary analyse_dataset_adults_flu_further_s4_specific_secondary analyse_dataset_adults_overall_and_all_cause_s4_specific_secondary analyse_dataset_adults_overall_and_all_cause_further_s4_specific_secondary analyse_dataset_adults_covid_s4_specific_secondary analyse_dataset_adults_covid_further_s4_specific_secondary generate_dataset_adults_s5_specific_secondary process_dataset_adults_s5_specific_secondary describe_dataset_adults_s5_specific_secondary analyse_dataset_adults_rsv_s5_specific_secondary analyse_dataset_adults_rsv_further_s5_specific_secondary analyse_dataset_adults_flu_s5_specific_secondary analyse_dataset_adults_flu_further_s5_specific_secondary analyse_dataset_adults_overall_and_all_cause_s5_specific_secondary analyse_dataset_adults_overall_and_all_cause_further_s5_specific_secondary analyse_dataset_adults_covid_s5_specific_secondary analyse_dataset_adults_covid_further_s5_specific_secondary generate_dataset_adults_s6_specific_secondary process_dataset_adults_s6_specific_secondary describe_dataset_adults_s6_specific_secondary analyse_dataset_adults_rsv_s6_specific_secondary analyse_dataset_adults_rsv_further_s6_specific_secondary analyse_dataset_adults_flu_s6_specific_secondary analyse_dataset_adults_flu_further_s6_specific_secondary analyse_dataset_adults_overall_and_all_cause_s6_specific_secondary analyse_dataset_adults_overall_and_all_cause_further_s6_specific_secondary analyse_dataset_adults_covid_s6_specific_secondary analyse_dataset_adults_covid_further_s6_specific_secondary generate_dataset_adults_s7_specific_secondary process_dataset_adults_s7_specific_secondary describe_dataset_adults_s7_specific_secondary analyse_dataset_adults_rsv_s7_specific_secondary analyse_dataset_adults_rsv_further_s7_specific_secondary analyse_dataset_adults_flu_s7_specific_secondary analyse_dataset_adults_flu_further_s7_specific_secondary analyse_dataset_adults_overall_and_all_cause_s7_specific_secondary analyse_dataset_adults_overall_and_all_cause_further_s7_specific_secondary analyse_dataset_adults_covid_s7_specific_secondary analyse_dataset_adults_covid_further_s7_specific_secondary
generate_dataset_children_and_adolescents_s1_specific_secondary process_dataset_children_and_adolescents_s1_specific_secondary describe_dataset_children_and_adolescents_s1_specific_secondary analyse_dataset_children_and_adolescents_rsv_s1_specific_secondary analyse_dataset_children_and_adolescents_rsv_further_s1_specific_secondary analyse_dataset_children_and_adolescents_flu_s1_specific_secondary analyse_dataset_children_and_adolescents_flu_further_s1_specific_secondary analyse_dataset_children_and_adolescents_overall_and_all_cause_s1_specific_secondary analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s1_specific_secondary generate_dataset_children_and_adolescents_s2_specific_secondary process_dataset_children_and_adolescents_s2_specific_secondary describe_dataset_children_and_adolescents_s2_specific_secondary analyse_dataset_children_and_adolescents_rsv_s2_specific_secondary analyse_dataset_children_and_adolescents_rsv_further_s2_specific_secondary analyse_dataset_children_and_adolescents_flu_s2_specific_secondary analyse_dataset_children_and_adolescents_flu_further_s2_specific_secondary analyse_dataset_children_and_adolescents_overall_and_all_cause_s2_specific_secondary analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s2_specific_secondary generate_dataset_children_and_adolescents_s3_specific_secondary process_dataset_children_and_adolescents_s3_specific_secondary describe_dataset_children_and_adolescents_s3_specific_secondary analyse_dataset_children_and_adolescents_rsv_s3_specific_secondary analyse_dataset_children_and_adolescents_rsv_further_s3_specific_secondary analyse_dataset_children_and_adolescents_flu_s3_specific_secondary analyse_dataset_children_and_adolescents_flu_further_s3_specific_secondary analyse_dataset_children_and_adolescents_overall_and_all_cause_s3_specific_secondary analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s3_specific_secondary generate_dataset_children_and_adolescents_s4_specific_secondary process_dataset_children_and_adolescents_s4_specific_secondary describe_dataset_children_and_adolescents_s4_specific_secondary analyse_dataset_children_and_adolescents_rsv_s4_specific_secondary analyse_dataset_children_and_adolescents_rsv_further_s4_specific_secondary analyse_dataset_children_and_adolescents_flu_s4_specific_secondary analyse_dataset_children_and_adolescents_flu_further_s4_specific_secondary analyse_dataset_children_and_adolescents_overall_and_all_cause_s4_specific_secondary analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s4_specific_secondary analyse_dataset_children_and_adolescents_covid_s4_specific_secondary analyse_dataset_children_and_adolescents_covid_further_s4_specific_secondary generate_dataset_children_and_adolescents_s5_specific_secondary process_dataset_children_and_adolescents_s5_specific_secondary describe_dataset_children_and_adolescents_s5_specific_secondary analyse_dataset_children_and_adolescents_rsv_s5_specific_secondary analyse_dataset_children_and_adolescents_rsv_further_s5_specific_secondary analyse_dataset_children_and_adolescents_flu_s5_specific_secondary analyse_dataset_children_and_adolescents_flu_further_s5_specific_secondary analyse_dataset_children_and_adolescents_overall_and_all_cause_s5_specific_secondary analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s5_specific_secondary analyse_dataset_children_and_adolescents_covid_s5_specific_secondary analyse_dataset_children_and_adolescents_covid_further_s5_specific_secondary generate_dataset_children_and_adolescents_s6_specific_secondary process_dataset_children_and_adolescents_s6_specific_secondary describe_dataset_children_and_adolescents_s6_specific_secondary analyse_dataset_children_and_adolescents_rsv_s6_specific_secondary analyse_dataset_children_and_adolescents_rsv_further_s6_specific_secondary analyse_dataset_children_and_adolescents_flu_s6_specific_secondary analyse_dataset_children_and_adolescents_flu_further_s6_specific_secondary analyse_dataset_children_and_adolescents_overall_and_all_cause_s6_specific_secondary analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s6_specific_secondary analyse_dataset_children_and_adolescents_covid_s6_specific_secondary analyse_dataset_children_and_adolescents_covid_further_s6_specific_secondary generate_dataset_children_and_adolescents_s7_specific_secondary process_dataset_children_and_adolescents_s7_specific_secondary describe_dataset_children_and_adolescents_s7_specific_secondary analyse_dataset_children_and_adolescents_rsv_s7_specific_secondary analyse_dataset_children_and_adolescents_rsv_further_s7_specific_secondary analyse_dataset_children_and_adolescents_flu_s7_specific_secondary analyse_dataset_children_and_adolescents_flu_further_s7_specific_secondary analyse_dataset_children_and_adolescents_overall_and_all_cause_s7_specific_secondary analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s7_specific_secondary analyse_dataset_children_and_adolescents_covid_s7_specific_secondary analyse_dataset_children_and_adolescents_covid_further_s7_specific_secondary
generate_dataset_infants_s1_specific_secondary process_dataset_infants_s1_specific_secondary describe_dataset_infants_s1_specific_secondary analyse_dataset_infants_rsv_s1_specific_secondary analyse_dataset_infants_rsv_further_s1_specific_secondary analyse_dataset_infants_flu_s1_specific_secondary analyse_dataset_infants_flu_further_s1_specific_secondary analyse_dataset_infants_overall_and_all_cause_s1_specific_secondary analyse_dataset_infants_overall_and_all_cause_further_s1_specific_secondary generate_dataset_infants_s2_specific_secondary process_dataset_infants_s2_specific_secondary describe_dataset_infants_s2_specific_secondary analyse_dataset_infants_rsv_s2_specific_secondary analyse_dataset_infants_rsv_further_s2_specific_secondary analyse_dataset_infants_flu_s2_specific_secondary analyse_dataset_infants_flu_further_s2_specific_secondary analyse_dataset_infants_overall_and_all_cause_s2_specific_secondary analyse_dataset_infants_overall_and_all_cause_further_s2_specific_secondary generate_dataset_infants_s3_specific_secondary process_dataset_infants_s3_specific_secondary describe_dataset_infants_s3_specific_secondary analyse_dataset_infants_rsv_s3_specific_secondary analyse_dataset_infants_rsv_further_s3_specific_secondary analyse_dataset_infants_flu_s3_specific_secondary analyse_dataset_infants_flu_further_s3_specific_secondary analyse_dataset_infants_overall_and_all_cause_s3_specific_secondary analyse_dataset_infants_overall_and_all_cause_further_s3_specific_secondary generate_dataset_infants_s4_specific_secondary process_dataset_infants_s4_specific_secondary describe_dataset_infants_s4_specific_secondary analyse_dataset_infants_rsv_s4_specific_secondary analyse_dataset_infants_rsv_further_s4_specific_secondary analyse_dataset_infants_flu_s4_specific_secondary analyse_dataset_infants_flu_further_s4_specific_secondary analyse_dataset_infants_overall_and_all_cause_s4_specific_secondary analyse_dataset_infants_overall_and_all_cause_further_s4_specific_secondary analyse_dataset_infants_covid_s4_specific_secondary analyse_dataset_infants_covid_further_s4_specific_secondary generate_dataset_infants_s5_specific_secondary process_dataset_infants_s5_specific_secondary describe_dataset_infants_s5_specific_secondary analyse_dataset_infants_rsv_s5_specific_secondary analyse_dataset_infants_rsv_further_s5_specific_secondary analyse_dataset_infants_flu_s5_specific_secondary analyse_dataset_infants_flu_further_s5_specific_secondary analyse_dataset_infants_overall_and_all_cause_s5_specific_secondary analyse_dataset_infants_overall_and_all_cause_further_s5_specific_secondary analyse_dataset_infants_covid_s5_specific_secondary analyse_dataset_infants_covid_further_s5_specific_secondary generate_dataset_infants_s6_specific_secondary process_dataset_infants_s6_specific_secondary describe_dataset_infants_s6_specific_secondary analyse_dataset_infants_rsv_s6_specific_secondary analyse_dataset_infants_rsv_further_s6_specific_secondary analyse_dataset_infants_flu_s6_specific_secondary analyse_dataset_infants_flu_further_s6_specific_secondary analyse_dataset_infants_overall_and_all_cause_s6_specific_secondary analyse_dataset_infants_overall_and_all_cause_further_s6_specific_secondary analyse_dataset_infants_covid_s6_specific_secondary analyse_dataset_infants_covid_further_s6_specific_secondary generate_dataset_infants_s7_specific_secondary process_dataset_infants_s7_specific_secondary describe_dataset_infants_s7_specific_secondary analyse_dataset_infants_rsv_s7_specific_secondary analyse_dataset_infants_rsv_further_s7_specific_secondary analyse_dataset_infants_flu_s7_specific_secondary analyse_dataset_infants_flu_further_s7_specific_secondary analyse_dataset_infants_overall_and_all_cause_s7_specific_secondary analyse_dataset_infants_overall_and_all_cause_further_s7_specific_secondary analyse_dataset_infants_covid_s7_specific_secondary analyse_dataset_infants_covid_further_s7_specific_secondary
process_dataset_older_adults_s1_sensitive_secondary describe_cohort_older_adults_s1 process_dataset_older_adults_s2_sensitive_secondary describe_cohort_older_adults_s2 process_dataset_older_adults_s3_sensitive_secondary describe_cohort_older_adults_s3 process_dataset_older_adults_s4_sensitive_secondary describe_cohort_older_adults_s4 process_dataset_older_adults_s5_sensitive_secondary describe_cohort_older_adults_s5 process_dataset_older_adults_s6_sensitive_secondary describe_cohort_older_adults_s6 process_dataset_older_adults_s7_sensitive_secondary describe_cohort_older_adults_s7
process_dataset_adults_s1_sensitive_secondary describe_cohort_adults_s1 process_dataset_adults_s2_sensitive_secondary describe_cohort_adults_s2 process_dataset_adults_s3_sensitive_secondary describe_cohort_adults_s3 process_dataset_adults_s4_sensitive_secondary describe_cohort_adults_s4 process_dataset_adults_s5_sensitive_secondary describe_cohort_adults_s5 process_dataset_adults_s6_sensitive_secondary describe_cohort_adults_s6 process_dataset_adults_s7_sensitive_secondary describe_cohort_adults_s7
process_dataset_children_and_adolescents_s1_sensitive_secondary describe_cohort_children_and_adolescents_s1 process_dataset_children_and_adolescents_s2_sensitive_secondary describe_cohort_children_and_adolescents_s2 process_dataset_children_and_adolescents_s3_sensitive_secondary describe_cohort_children_and_adolescents_s3 process_dataset_children_and_adolescents_s4_sensitive_secondary describe_cohort_children_and_adolescents_s4 process_dataset_children_and_adolescents_s5_sensitive_secondary describe_cohort_children_and_adolescents_s5 process_dataset_children_and_adolescents_s6_sensitive_secondary describe_cohort_children_and_adolescents_s6 process_dataset_children_and_adolescents_s7_sensitive_secondary describe_cohort_children_and_adolescents_s7
process_dataset_infants_s1_sensitive_secondary describe_cohort_infants_s1 process_dataset_infants_s2_sensitive_secondary describe_cohort_infants_s2 process_dataset_infants_s3_sensitive_secondary describe_cohort_infants_s3 process_dataset_infants_s4_sensitive_secondary describe_cohort_infants_s4 process_dataset_infants_s5_sensitive_secondary describe_cohort_infants_s5 process_dataset_infants_s6_sensitive_secondary describe_cohort_infants_s6 process_dataset_infants_s7_sensitive_secondary describe_cohort_infants_s7
describe_cohort_older_adults_s1 describe_cohort_older_adults_s2 describe_cohort_older_adults_s3 describe_cohort_older_adults_s4 describe_cohort_older_adults_s5 describe_cohort_older_adults_s6 describe_cohort_older_adults_s7
describe_cohort_adults_s1 describe_cohort_adults_s2 describe_cohort_adults_s3 describe_cohort_adults_s4 describe_cohort_adults_s5 describe_cohort_adults_s6 describe_cohort_adults_s7
describe_cohort_children_and_adolescents_s1 describe_cohort_children_and_adolescents_s2 describe_cohort_children_and_adolescents_s3 describe_cohort_children_and_adolescents_s4 describe_cohort_children_and_adolescents_s5 describe_cohort_children_and_adolescents_s6 describe_cohort_children_and_adolescents_s7
describe_cohort_infants_s1 describe_cohort_infants_s2 describe_cohort_infants_s3 describe_cohort_infants_s4 describe_cohort_infants_s5 describe_cohort_infants_s6 describe_cohort_infants_s7
phenotype_sensitivity_older_adults_s1 phenotype_sensitivity_older_adults_s2 phenotype_sensitivity_older_adults_s3 phenotype_sensitivity_older_adults_s4 phenotype_sensitivity_older_adults_s5 phenotype_sensitivity_older_adults_s6 phenotype_sensitivity_older_adults_s7
phenotype_sensitivity_adults_s1 phenotype_sensitivity_adults_s2 phenotype_sensitivity_adults_s3 phenotype_sensitivity_adults_s4 phenotype_sensitivity_adults_s5 phenotype_sensitivity_adults_s6 phenotype_sensitivity_adults_s7
phenotype_sensitivity_children_and_adolescents_s1 phenotype_sensitivity_children_and_adolescents_s2 phenotype_sensitivity_children_and_adolescents_s3 phenotype_sensitivity_children_and_adolescents_s4 phenotype_sensitivity_children_and_adolescents_s5 phenotype_sensitivity_children_and_adolescents_s6 phenotype_sensitivity_children_and_adolescents_s7
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15 changes: 2 additions & 13 deletions create-project.R
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Expand Up @@ -884,23 +884,12 @@ action_descriptive <- function(cohort, season, dates, codelist_type,

splice(

action(
name = glue("process_dataset_{cohort}_{season}_sensitive_secondary"),
run = glue("r:latest analysis/data_processing.R {cohort} {season_start_date} {season_end_date} sensitive secondary"),
arguments = c(cohort, season, dates, codelist_type, investigation_type,
season_start_date, season_end_date),
needs = list(glue("generate_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
glue("process_household_information_{season}")),
highly_sensitive = lst(
cohort = glue("output/data/input_processed_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow"))
),

action(
name = glue("describe_cohort_{cohort}_{season}"),
run = glue("r:latest analysis/cohort_description.R {cohort} {season_start_date} {season_end_date} sensitive secondary"),
run = glue("r:latest analysis/cohort_description.R {cohort} {season_start_date} {season_end_date} specific secondary"),
arguments = c(cohort, season, dates, codelist_type, investigation_type,
season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_sensitive_secondary")),
needs = list(glue("process_dataset_{cohort}_{season}_specific_secondary")),
moderately_sensitive = lst(
csv = glue("output/table1/table1_{cohort}_{dates}.csv")),
)
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