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create-project.R
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create-project.R
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library(tidyverse)
library(yaml)
library(here)
library(glue)
# create action functions ----
## create comment function ----
comment <- function(...){
list_comments <- list(...)
comments <- map(list_comments, ~paste0("## ", ., " ##"))
comments
}
#splice <- function(...) {list_flatten(lst(...))}
## create function to convert comment "actions" in a yaml string into proper comments
convert_comment_actions <-function(yaml.txt){
yaml.txt %>%
str_replace_all("\\\n(\\s*)\\'\\'\\:(\\s*)\\'", "\n\\1") %>%
str_replace_all("([^\\'])\\\n(\\s*)\\#\\#", "\\1\n\n\\2\\#\\#") %>%
str_replace_all("\\#\\#\\'\\\n", "\n")
}
## generic action function ----
action <- function(
name,
run,
arguments=NULL,
needs=NULL,
highly_sensitive=NULL,
moderately_sensitive=NULL,
... # other arguments / options for special action types
){
outputs <- list(
highly_sensitive = highly_sensitive,
moderately_sensitive = moderately_sensitive
)
outputs[sapply(outputs, is.null)] <- NULL
action <- list(
run = paste(c(run, arguments), collapse=" "),
needs = needs,
outputs = outputs,
... = ...
)
action[sapply(action, is.null)] <- NULL
action_list <- list(name = action)
names(action_list) <- name
action_list
}
##actions for inclusion/exclusion
action_flow <- function(cohort, season, dates, season_start_date,
season_end_date) {
splice (
action(
name = glue("generate_flow_chart_data_{cohort}_{season}"),
run = glue("ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/{cohort}_{dates}_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_{cohort}_{dates}.arrow
-- {cohort} {season_start_date} {season_end_date}"),
# arguments = c(cohort, season, dates, season_start_date, season_end_date),
needs = NULL,
highly_sensitive = lst(
dataset = glue("output/flow_chart/{cohort}_{dates}_flow_chart.arrow")
)
)
)
}
action_flow_infants_sub <- function(cohort, season, dates, season_start_date,
season_end_date) {
splice (
action(
name = glue("generate_flow_chart_data_mothers_{season}"),
run = glue("ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart_mothers.py
--output output/flow_chart/mothers_{dates}_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_{cohort}_{dates}.arrow
-- {season_start_date} {season_end_date}"),
# arguments = c(season, season_start_date, season_end_date),
needs = NULL,
highly_sensitive = lst(
dataset = glue("output/flow_chart/mothers_{dates}_flow_chart.arrow"))
),
action(
name = glue("process_flow_chart_data_mothers_{season}"),
run = glue("r:latest analysis/cohort_processing_mothers.R {season_start_date} {season_end_date}"),
# arguments = c(season, season_start_date, season_end_date),
needs = list(glue("generate_flow_chart_data_mothers_{season}")),
highly_sensitive = lst(
dataset = glue("output/flow_chart/cohort_mothers_processed_{dates}.arrow"))
),
action(
name = glue("generate_flow_chart_data_{cohort}_{season}"),
run = glue("ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/{cohort}_{dates}_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_{cohort}_{dates}.arrow
-- {cohort} {season_start_date} {season_end_date}"),
# arguments = c(cohort, season, dates, season_start_date, season_end_date),
needs = list(glue("process_flow_chart_data_mothers_{season}")),
highly_sensitive = lst(
dataset = glue("output/flow_chart/{cohort}_{dates}_flow_chart.arrow"))
)
)
}
action_inclusion <- function(cohort, season, dates, season_start_date,
season_end_date) {
splice (
action(
name = glue("process_flow_chart_data_{cohort}_{season}"),
run = glue("r:latest analysis/cohort_criteria.R {cohort} {season_start_date} {season_end_date}"),
# arguments = c(cohort, season, dates, season_start_date, season_end_date),
needs = list(glue("generate_flow_chart_data_{cohort}_{season}")),
moderately_sensitive = lst(
csv = glue("output/flow_chart/flow_chart_processed_{cohort}_{dates}.csv"))
)
)
}
##household actions
action_household <- function(season, dates, season_start_date, season_end_date) {
splice (
action(
name = glue("extract_household_information_{season}"),
run = glue("ehrql:v1 generate-dataset analysis/dataset_definition_household.py
--output output/data/input_household_{dates}.arrow
--dummy-data-file analysis/dummydata/dummyextract_household_{dates}.arrow
-- {season_start_date} {season_end_date}"),
# arguments = c(season, dates, season_start_date, season_end_date),
needs = NULL,
highly_sensitive = lst(
dataset = glue("output/data/input_household_{dates}.arrow")
)
),
action(
name = glue("process_household_information_{season}"),
run = glue("r:latest analysis/data_processing_household.R {season_start_date} {season_end_date}"),
# arguments = c(season, dates, season_start_date, season_end_date),
needs = list(glue("extract_household_information_{season}")),
highly_sensitive = lst(
arrow = glue("output/data/input_household_processed_{dates}.arrow")
)
)
)
}
##actions for all cohorts/seasons
action_specified <- function(cohort, season, dates, codelist_type,
investigation_type, season_start_date,
season_end_date) {
splice(
action(
name = glue("generate_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("ehrql:v1 generate-dataset analysis/dataset_definition.py
--output output/data/input_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow
--dummy-data-file analysis/dummydata/dummyextract_{cohort}_{dates}.arrow
-- {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = NULL,
highly_sensitive = lst(
dataset = glue("output/data/input_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow")
)
),
action(
name = glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/data_processing.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = case_when(season == "s5" ~ list(list(
glue("generate_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
glue("process_household_information_{season}"))),
.default = list(list(glue("generate_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"))))[[1]],
highly_sensitive = lst(
dataset = glue("output/data/input_processed_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow")
)
),
action(
name = glue("describe_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/season_summary.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/rates/rates_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")
)
),
action(
name = glue("calculate_rates_rolling_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/rates_over_time.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
dataset = glue("output/results/rates/weekly/rates_over_time_*_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")
)
),
action(
name = glue("analyse_dataset_{cohort}_rsv_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_rsv/rsv_models_master.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/rsv_{investigation_type}/*_{cohort}_{dates}_{codelist_type}_*.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_flu_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_flu/flu_models_master.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/flu_{investigation_type}/*_{cohort}_{dates}_{codelist_type}_*.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_flu_further_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_flu/further_flu_models_master.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/flu_{investigation_type}/further_*_{cohort}_{dates}_{codelist_type}_*.csv"))
)
)
}
action_specified_sensitive <- function(cohort, season, dates, codelist_type,
investigation_type, season_start_date,
season_end_date) {
splice(
action(
name = glue("generate_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("ehrql:v1 generate-dataset analysis/dataset_definition.py
--output output/data/input_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow
--dummy-data-file analysis/dummydata/dummyextract_{cohort}_{dates}.arrow
-- {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = NULL,
highly_sensitive = lst(
dataset = glue("output/data/input_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow")
)
),
action(
name = glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/data_processing.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = case_when(season == "s5" ~ list(list(
glue("generate_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
glue("process_household_information_{season}"))),
.default = list(list(glue("generate_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"))))[[1]],
highly_sensitive = lst(
dataset = glue("output/data/input_processed_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow")
)
),
action(
name = glue("describe_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/season_summary.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/rates/rates_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")
)
),
action(
name = glue("calculate_rates_rolling_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/rates_over_time.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
dataset = glue("output/results/rates/weekly/rates_over_time_*_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")
)
),
action(
name = glue("analyse_dataset_{cohort}_rsv_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_rsv/rsv_models_master.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/rsv_{investigation_type}/*_{cohort}_{dates}_{codelist_type}_*.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_flu_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_flu/flu_models_master.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/flu_{investigation_type}/*_{cohort}_{dates}_{codelist_type}_*.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_flu_further_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_flu/further_flu_models_master.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/flu_{investigation_type}/further_*_{cohort}_{dates}_{codelist_type}_*.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_overall_and_all_cause_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models_master.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/overall_and_all_cause_{investigation_type}/*_{cohort}_{dates}_{codelist_type}_*.csv"))
)
)
}
action_specified_infants <- function(cohort, season, dates, codelist_type,
investigation_type, season_start_date,
season_end_date) {
splice(
action(
name = glue("generate_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("ehrql:v1 generate-dataset analysis/dataset_definition.py
--output output/data/input_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow
--dummy-data-file analysis/dummydata/dummyextract_{cohort}_{dates}.arrow
-- {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = NULL,
highly_sensitive = lst(
dataset = glue("output/data/input_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow")
)
),
action(
name = glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/data_processing.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# 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}")),
highly_sensitive = lst(
dataset = glue("output/data/input_processed_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow")
)
),
action(
name = glue("describe_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/season_summary.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/rates/rates_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")
)
),
action(
name = glue("calculate_rates_rolling_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/rates_over_time.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
dataset = glue("output/results/rates/weekly/rates_over_time_*_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")
)
),
action(
name = glue("analyse_dataset_{cohort}_rsv_ethnicity_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_rsv/rsv_ethnicity_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/rsv_{investigation_type}/rsv_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_flu_ethnicity_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_flu/flu_ethnicity_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/flu_{investigation_type}/flu_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_rsv_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_rsv/rsv_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/rsv_{investigation_type}/rsv_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_flu_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_flu/flu_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/flu_{investigation_type}/flu_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_rsv/rsv_ethnicity_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/rsv_{investigation_type}/rsv_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_flu_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_flu/flu_ethnicity_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/flu_{investigation_type}/flu_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv"))
)
)
}
action_specified_infants_sensitive <- function(cohort, season, dates,
codelist_type, investigation_type,
season_start_date,
season_end_date) {
splice(
action(
name = glue("generate_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("ehrql:v1 generate-dataset analysis/dataset_definition.py
--output output/data/input_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow
--dummy-data-file analysis/dummydata/dummyextract_{cohort}_{dates}.arrow
-- {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = NULL,
highly_sensitive = lst(
dataset = glue("output/data/input_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow")
)
),
action(
name = glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/data_processing.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# 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}")),
highly_sensitive = lst(
dataset = glue("output/data/input_processed_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow")
)
),
action(
name = glue("describe_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/season_summary.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/rates/rates_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")
)
),
action(
name = glue("calculate_rates_rolling_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/rates_over_time.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
dataset = glue("output/results/rates/weekly/rates_over_time_*_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")
)
),
action(
name = glue("analyse_dataset_{cohort}_rsv_ethnicity_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_rsv/rsv_ethnicity_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/rsv_{investigation_type}/rsv_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_flu_ethnicity_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_flu/flu_ethnicity_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/flu_{investigation_type}/flu_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/overall_and_all_cause_{investigation_type}/overall_and_all_cause_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_rsv_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_rsv/rsv_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/rsv_{investigation_type}/rsv_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_flu_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_flu/flu_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/flu_{investigation_type}/flu_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/overall_and_all_cause_{investigation_type}/overall_and_all_cause_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_rsv/rsv_ethnicity_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/rsv_{investigation_type}/rsv_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_flu_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_flu/flu_ethnicity_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/flu_{investigation_type}/flu_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/overall_and_all_cause_{investigation_type}/overall_and_all_cause_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv"))
)
)
}
action_specified_infants_sub <- function(season, dates, codelist_type,
investigation_type, season_start_date,
season_end_date) {
splice(
action(
name = glue("generate_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}"),
run = glue("ehrql:v1 generate-dataset analysis/dataset_definition.py
--output output/data/input_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_{dates}.arrow
-- infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = NULL,
highly_sensitive = lst(
dataset = glue("output/data/input_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.arrow")
)
),
action(
name = glue("process_mothers_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/data_processing_mothers.R {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("generate_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
highly_sensitive = lst(
dataset = glue("output/data/input_mothers_processed_{dates}_{codelist_type}_{investigation_type}.arrow"))
),
action(
name = glue("generate_maternal_characteristics_{season}_{codelist_type}_{investigation_type}"),
run = glue("ehrql:v1 generate-dataset analysis/dataset_definition_mothers.py
--output output/data/input_maternal_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.arrow
--dummy-data-file analysis/dummydata/dummyextract_maternal_{dates}.arrow
-- infants_subroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("generate_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}"),
glue("process_mothers_{season}_{codelist_type}_{investigation_type}")),
highly_sensitive = lst(
dataset = glue("output/data/input_maternal_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.arrow"))
),
action(
name = glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/data_processing.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("generate_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}"),
glue("process_mothers_{season}_{codelist_type}_{investigation_type}"),
glue("generate_maternal_characteristics_{season}_{codelist_type}_{investigation_type}")),
highly_sensitive = lst(
dataset = glue("output/data/input_processed_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.arrow")
)
),
action(
name = glue("describe_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/season_summary.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/rates/rates_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv")
)
),
action(
name = glue("calculate_rates_rolling_infants_subgroup_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/rates_over_time.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
dataset = glue("output/results/rates/weekly/rates_over_time_*_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv")
)
),
action(
name = glue("analyse_dataset_infants_subgroup_rsv_ethnicity_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/rsv_{investigation_type}/rsv_ethnicity_model_outputs_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_infants_subgroup_flu_ethnicity_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_flu/flu_ethnicity_models.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/flu_{investigation_type}/flu_ethnicity_model_outputs_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_infants_subgroup_rsv_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_rsv/rsv_ses_models.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/rsv_{investigation_type}/rsv_ses_model_outputs_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_infants_subgroup_flu_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_flu/flu_ses_models.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/flu_{investigation_type}/flu_ses_model_outputs_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_infants_subgroup_rsv_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_rsv/rsv_ethnicity_ses_models.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/rsv_{investigation_type}/rsv_ethnicity_ses_model_outputs_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_infants_subgroup_flu_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_flu/flu_ethnicity_ses_models.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/flu_{investigation_type}/flu_ethnicity_ses_model_outputs_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv"))
)
)
}
action_specified_infants_sub_sensitive <- function(season, dates, codelist_type,
investigation_type,
season_start_date,
season_end_date) {
splice(
action(
name = glue("generate_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}"),
run = glue("ehrql:v1 generate-dataset analysis/dataset_definition.py
--output output/data/input_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_{dates}.arrow
-- infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = NULL,
highly_sensitive = lst(
dataset = glue("output/data/input_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.arrow")
)
),
action(
name = glue("process_mothers_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/data_processing_mothers.R {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("generate_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
highly_sensitive = lst(
dataset = glue("output/data/input_mothers_processed_{dates}_{codelist_type}_{investigation_type}.arrow"))
),
action(
name = glue("generate_maternal_characteristics_{season}_{codelist_type}_{investigation_type}"),
run = glue("ehrql:v1 generate-dataset analysis/dataset_definition_mothers.py
--output output/data/input_maternal_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.arrow
--dummy-data-file analysis/dummydata/dummyextract_maternal_{dates}.arrow
-- infants_subroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("generate_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}"),
glue("process_mothers_{season}_{codelist_type}_{investigation_type}")),
highly_sensitive = lst(
dataset = glue("output/data/input_maternal_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.arrow"))
),
action(
name = glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/data_processing.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("generate_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}"),
glue("process_mothers_{season}_{codelist_type}_{investigation_type}"),
glue("generate_maternal_characteristics_{season}_{codelist_type}_{investigation_type}")),
highly_sensitive = lst(
dataset = glue("output/data/input_processed_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.arrow")
)
),
action(
name = glue("describe_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/season_summary.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/rates/rates_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv")
)
),
action(
name = glue("calculate_rates_rolling_infants_subgroup_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/rates_over_time.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
dataset = glue("output/results/rates/weekly/rates_over_time_*_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv")
)
),
action(
name = glue("analyse_dataset_infants_subgroup_rsv_ethnicity_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/rsv_{investigation_type}/rsv_ethnicity_model_outputs_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_infants_subgroup_flu_ethnicity_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_flu/flu_ethnicity_models.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/flu_{investigation_type}/flu_ethnicity_model_outputs_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_infants_subgroup_overall_and_all_cause_ethnicity_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/overall_and_all_cause_{investigation_type}/overall_and_all_cause_ethnicity_model_outputs_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_infants_subgroup_rsv_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_rsv/rsv_ses_models.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/rsv_{investigation_type}/rsv_ses_model_outputs_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_infants_subgroup_flu_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_flu/flu_ses_models.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/flu_{investigation_type}/flu_ses_model_outputs_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_infants_subgroup_overall_and_all_cause_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_models.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/overall_and_all_cause_{investigation_type}/overall_and_all_cause_ses_model_outputs_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_infants_subgroup_rsv_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_rsv/rsv_ethnicity_ses_models.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/rsv_{investigation_type}/rsv_ethnicity_ses_model_outputs_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_infants_subgroup_flu_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_flu/flu_ethnicity_ses_models.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/flu_{investigation_type}/flu_ethnicity_ses_model_outputs_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv"))
),
action(
name = glue("analyse_dataset_infants_subgroup_overall_and_all_cause_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_ses_models.R infants_subgroup {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_infants_subgroup_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/models/overall_and_all_cause_{investigation_type}/overall_and_all_cause_ethnicity_ses_model_outputs_infants_subgroup_{dates}_{codelist_type}_{investigation_type}.csv"))
)
)
}
action_specified_infants_2020 <- function(cohort, season, dates, codelist_type,
investigation_type, season_start_date,
season_end_date) {
splice(
action(
name = glue("generate_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("ehrql:v1 generate-dataset analysis/dataset_definition.py
--output output/data/input_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow
--dummy-data-file analysis/dummydata/dummyextract_{cohort}_{dates}.arrow
-- {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = NULL,
highly_sensitive = lst(
dataset = glue("output/data/input_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow")
)
),
action(
name = glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/data_processing.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# 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_s5")),
highly_sensitive = lst(
dataset = glue("output/data/input_processed_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow")
)
),
action(
name = glue("describe_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/season_summary.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
csv = glue("output/results/rates/rates_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")
)
),
action(
name = glue("calculate_rates_rolling_{cohort}_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/rates_over_time.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,
# season_start_date, season_end_date),
needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")),
moderately_sensitive = lst(
dataset = glue("output/results/rates/weekly/rates_over_time_*_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")
)
),
action(
name = glue("analyse_dataset_{cohort}_rsv_ethnicity_{season}_{codelist_type}_{investigation_type}"),
run = glue("r:latest analysis/outcome_rsv/rsv_ethnicity_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"),
# arguments = c(cohort, season, dates, codelist_type, investigation_type,