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update yaml
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@emprestige
emprestige committed Sep 20, 2024
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Showing 3 changed files with 16 additions and 16 deletions.
2 changes: 1 addition & 1 deletion actions.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -23,5 +23,5 @@ phenotype_sensitivity_older_adults_s1 phenotype_sensitivity_older_adults_s2 phen
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
phenotype_sensitivity_infants_s1 phenotype_sensitivity_infants_s2 phenotype_sensitivity_infants_s3 phenotype_sensitivity_infants_s4 phenotype_sensitivity_infants_s5 phenotype_sensitivity_infants_s6 phenotype_sensitivity_infants_s7
collate_flow_chart_tables_older_adults collate_table1_tables_older_adults collate_rates_tables_specific_primary_older_adults collate_rates_tables_sensitive_primary_older_adults collate_rates_tables_sensitive_secondary_older_adults collate_rsv_model_outputs_tables_older_adults collate_flu_model_outputs_tables_older_adults collate_covid_model_outputs_tables_older_adults collate_overall_and_all_cause_model_outputs_tables_older_adults collate_rsv_sensitivity_model_outputs_tables_older_adults collate_flu_sensitivity_model_outputs_tables_older_adults collate_covid_sensitivity_model_outputs_tables_older_adults collate_overall_and_all_cause_sensitivity_model_outputs_tables_older_adults collate_phenotype_sensitivity_tables_older_adults collate_flow_chart_tables_adults collate_table1_tables_adults collate_rates_tables_specific_primary_adults collate_rates_tables_sensitive_primary_adults collate_rates_tables_sensitive_secondary_adults collate_rsv_model_outputs_tables_adults collate_flu_model_outputs_tables_adults collate_covid_model_outputs_tables_adults collate_overall_and_all_cause_model_outputs_tables_adults collate_rsv_sensitivity_model_outputs_tables_adults collate_flu_sensitivity_model_outputs_tables_adults collate_covid_sensitivity_model_outputs_tables_adults collate_overall_and_all_cause_sensitivity_model_outputs_tables_adults collate_phenotype_sensitivity_tables_adults collate_flow_chart_tables_children_and_adolescents collate_table1_tables_children_and_adolescents collate_rates_tables_specific_primary_children_and_adolescents collate_rates_tables_sensitive_primary_children_and_adolescents collate_rates_tables_sensitive_secondary_children_and_adolescents collate_rsv_model_outputs_tables_children_and_adolescents collate_flu_model_outputs_tables_children_and_adolescents collate_covid_model_outputs_tables_children_and_adolescents collate_overall_and_all_cause_model_outputs_tables_children_and_adolescents collate_rsv_sensitivity_model_outputs_tables_children_and_adolescents collate_flu_sensitivity_model_outputs_tables_children_and_adolescents collate_covid_sensitivity_model_outputs_tables_children_and_adolescents collate_overall_and_all_cause_sensitivity_model_outputs_tables_children_and_adolescents collate_phenotype_sensitivity_tables_children_and_adolescents collate_flow_chart_tables_infants collate_table1_tables_infants collate_rates_tables_specific_primary_infants collate_rates_tables_sensitive_primary_infants collate_rates_tables_sensitive_secondary_infants collate_rsv_model_outputs_tables_infants collate_flu_model_outputs_tables_infants collate_covid_model_outputs_tables_infants collate_overall_and_all_cause_model_outputs_tables_infants collate_rsv_sensitivity_model_outputs_tables_infants collate_flu_sensitivity_model_outputs_tables_infants collate_covid_sensitivity_model_outputs_tables_infants collate_overall_and_all_cause_sensitivity_model_outputs_tables_infants collate_phenotype_sensitivity_tables_infants
collate_flow_chart_tables_older_adults collate_table1_tables_older_adults collate_rates_tables_specific_primary_older_adults collate_rates_tables_sensitive_primary_older_adults collate_rates_tables_sensitive_secondary_older_adults collate_rsv_model_outputs_tables_older_adults collate_flu_model_outputs_tables_older_adults collate_covid_model_outputs_tables_older_adults collate_overall_and_all_cause_model_outputs_tables_older_adults collate_rsv_sensitive_model_outputs_tables_older_adults collate_flu_sensitive_model_outputs_tables_older_adults collate_covid_sensitivity_model_outputs_tables_older_adults collate_overall_and_all_cause_sensitive_model_outputs_tables_older_adults collate_phenotype_sensitivity_tables_older_adults collate_flow_chart_tables_adults collate_table1_tables_adults collate_rates_tables_specific_primary_adults collate_rates_tables_sensitive_primary_adults collate_rates_tables_sensitive_secondary_adults collate_rsv_model_outputs_tables_adults collate_flu_model_outputs_tables_adults collate_covid_model_outputs_tables_adults collate_overall_and_all_cause_model_outputs_tables_adults collate_rsv_sensitive_model_outputs_tables_adults collate_flu_sensitive_model_outputs_tables_adults collate_covid_sensitivity_model_outputs_tables_adults collate_overall_and_all_cause_sensitive_model_outputs_tables_adults collate_phenotype_sensitivity_tables_adults collate_flow_chart_tables_children_and_adolescents collate_table1_tables_children_and_adolescents collate_rates_tables_specific_primary_children_and_adolescents collate_rates_tables_sensitive_primary_children_and_adolescents collate_rates_tables_sensitive_secondary_children_and_adolescents collate_rsv_model_outputs_tables_children_and_adolescents collate_flu_model_outputs_tables_children_and_adolescents collate_covid_model_outputs_tables_children_and_adolescents collate_overall_and_all_cause_model_outputs_tables_children_and_adolescents collate_rsv_sensitive_model_outputs_tables_children_and_adolescents collate_flu_sensitive_model_outputs_tables_children_and_adolescents collate_covid_sensitivity_model_outputs_tables_children_and_adolescents collate_overall_and_all_cause_sensitive_model_outputs_tables_children_and_adolescents collate_phenotype_sensitivity_tables_children_and_adolescents collate_flow_chart_tables_infants collate_table1_tables_infants collate_rates_tables_specific_primary_infants collate_rates_tables_sensitive_primary_infants collate_rates_tables_sensitive_secondary_infants collate_rsv_model_outputs_tables_infants collate_flu_model_outputs_tables_infants collate_covid_model_outputs_tables_infants collate_overall_and_all_cause_model_outputs_tables_infants collate_rsv_sensitive_model_outputs_tables_infants collate_flu_sensitive_model_outputs_tables_infants collate_covid_sensitivity_model_outputs_tables_infants collate_overall_and_all_cause_sensitive_model_outputs_tables_infants collate_phenotype_sensitivity_tables_infants

6 changes: 3 additions & 3 deletions create-project.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1670,7 +1670,7 @@ action_finalise <- function(cohort) {
),

action(
name = glue("collate_rsv_sensitivity_model_outputs_tables_{cohort}"),
name = glue("collate_rsv_sensitive_model_outputs_tables_{cohort}"),
run = glue("r:latest analysis/collation_code/rsv_sensitivity_model_outputs_table_collation.R {cohort}"),
arguments = c(cohort),
needs = list(glue("analyse_dataset_{cohort}_rsv_ethnicity_s1_sensitive_primary"),
Expand Down Expand Up @@ -1727,7 +1727,7 @@ action_finalise <- function(cohort) {
),

action(
name = glue("collate_flu_sensitivity_model_outputs_tables_{cohort}"),
name = glue("collate_flu_sensitive_model_outputs_tables_{cohort}"),
run = glue("r:latest analysis/collation_code/flu_sensitivity_model_outputs_table_collation.R {cohort}"),
arguments = c(cohort),
needs = list(glue("analyse_dataset_{cohort}_flu_ethnicity_s1_sensitive_primary"),
Expand Down Expand Up @@ -1820,7 +1820,7 @@ action_finalise <- function(cohort) {
),

action(
name = glue("collate_overall_and_all_cause_sensitivity_model_outputs_tables_{cohort}"),
name = glue("collate_overall_and_all_cause_sensitive_model_outputs_tables_{cohort}"),
run = glue("r:latest analysis/collation_code/overall_and_all_cause_sensitivity_model_outputs_table_collation.R {cohort}"),
arguments = c(cohort),
needs = list(glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s1_sensitive_primary"),
Expand Down
24 changes: 12 additions & 12 deletions project.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -44064,7 +44064,7 @@ actions:
moderately_sensitive:
csv: output/collated/analytic/older_adults_overall_and_all_cause_model_outputs_collated.csv

collate_rsv_sensitivity_model_outputs_tables_older_adults:
collate_rsv_sensitive_model_outputs_tables_older_adults:
run: r:latest analysis/collation_code/rsv_sensitivity_model_outputs_table_collation.R
older_adults older_adults
needs:
Expand Down Expand Up @@ -44121,7 +44121,7 @@ actions:
moderately_sensitive:
csv: output/collated/analytic/older_adults_rsv_sensitivity_model_outputs_collated.csv

collate_flu_sensitivity_model_outputs_tables_older_adults:
collate_flu_sensitive_model_outputs_tables_older_adults:
run: r:latest analysis/collation_code/flu_sensitivity_model_outputs_table_collation.R
older_adults older_adults
needs:
Expand Down Expand Up @@ -44214,7 +44214,7 @@ actions:
moderately_sensitive:
csv: output/collated/analytic/older_adults_covid_sensitivity_model_outputs_collated.csv

collate_overall_and_all_cause_sensitivity_model_outputs_tables_older_adults:
collate_overall_and_all_cause_sensitive_model_outputs_tables_older_adults:
run: r:latest analysis/collation_code/overall_and_all_cause_sensitivity_model_outputs_table_collation.R
older_adults older_adults
needs:
Expand Down Expand Up @@ -44566,7 +44566,7 @@ actions:
moderately_sensitive:
csv: output/collated/analytic/adults_overall_and_all_cause_model_outputs_collated.csv

collate_rsv_sensitivity_model_outputs_tables_adults:
collate_rsv_sensitive_model_outputs_tables_adults:
run: r:latest analysis/collation_code/rsv_sensitivity_model_outputs_table_collation.R
adults adults
needs:
Expand Down Expand Up @@ -44623,7 +44623,7 @@ actions:
moderately_sensitive:
csv: output/collated/analytic/adults_rsv_sensitivity_model_outputs_collated.csv

collate_flu_sensitivity_model_outputs_tables_adults:
collate_flu_sensitive_model_outputs_tables_adults:
run: r:latest analysis/collation_code/flu_sensitivity_model_outputs_table_collation.R
adults adults
needs:
Expand Down Expand Up @@ -44716,7 +44716,7 @@ actions:
moderately_sensitive:
csv: output/collated/analytic/adults_covid_sensitivity_model_outputs_collated.csv

collate_overall_and_all_cause_sensitivity_model_outputs_tables_adults:
collate_overall_and_all_cause_sensitive_model_outputs_tables_adults:
run: r:latest analysis/collation_code/overall_and_all_cause_sensitivity_model_outputs_table_collation.R
adults adults
needs:
Expand Down Expand Up @@ -45070,7 +45070,7 @@ actions:
moderately_sensitive:
csv: output/collated/analytic/children_and_adolescents_overall_and_all_cause_model_outputs_collated.csv

collate_rsv_sensitivity_model_outputs_tables_children_and_adolescents:
collate_rsv_sensitive_model_outputs_tables_children_and_adolescents:
run: r:latest analysis/collation_code/rsv_sensitivity_model_outputs_table_collation.R
children_and_adolescents children_and_adolescents
needs:
Expand Down Expand Up @@ -45127,7 +45127,7 @@ actions:
moderately_sensitive:
csv: output/collated/analytic/children_and_adolescents_rsv_sensitivity_model_outputs_collated.csv

collate_flu_sensitivity_model_outputs_tables_children_and_adolescents:
collate_flu_sensitive_model_outputs_tables_children_and_adolescents:
run: r:latest analysis/collation_code/flu_sensitivity_model_outputs_table_collation.R
children_and_adolescents children_and_adolescents
needs:
Expand Down Expand Up @@ -45220,7 +45220,7 @@ actions:
moderately_sensitive:
csv: output/collated/analytic/children_and_adolescents_covid_sensitivity_model_outputs_collated.csv

collate_overall_and_all_cause_sensitivity_model_outputs_tables_children_and_adolescents:
collate_overall_and_all_cause_sensitive_model_outputs_tables_children_and_adolescents:
run: r:latest analysis/collation_code/overall_and_all_cause_sensitivity_model_outputs_table_collation.R
children_and_adolescents children_and_adolescents
needs:
Expand Down Expand Up @@ -45572,7 +45572,7 @@ actions:
moderately_sensitive:
csv: output/collated/analytic/infants_overall_and_all_cause_model_outputs_collated.csv

collate_rsv_sensitivity_model_outputs_tables_infants:
collate_rsv_sensitive_model_outputs_tables_infants:
run: r:latest analysis/collation_code/rsv_sensitivity_model_outputs_table_collation.R
infants infants
needs:
Expand Down Expand Up @@ -45629,7 +45629,7 @@ actions:
moderately_sensitive:
csv: output/collated/analytic/infants_rsv_sensitivity_model_outputs_collated.csv

collate_flu_sensitivity_model_outputs_tables_infants:
collate_flu_sensitive_model_outputs_tables_infants:
run: r:latest analysis/collation_code/flu_sensitivity_model_outputs_table_collation.R
infants infants
needs:
Expand Down Expand Up @@ -45722,7 +45722,7 @@ actions:
moderately_sensitive:
csv: output/collated/analytic/infants_covid_sensitivity_model_outputs_collated.csv

collate_overall_and_all_cause_sensitivity_model_outputs_tables_infants:
collate_overall_and_all_cause_sensitive_model_outputs_tables_infants:
run: r:latest analysis/collation_code/overall_and_all_cause_sensitivity_model_outputs_table_collation.R
infants infants
needs:
Expand Down

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