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project.yaml
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version: '3.0'
expectations:
population_size: 20000
actions:
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml DIRECTLY
## This file is created by create_project_actions.R
## Edit and run create_project_actions.R to update the project.yaml
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
##
## Part 1. Generate Study Population
##
## Generate dummy data for all eligible population
generate_study_population_all:
run: cohortextractor:latest generate_cohort --study-definition study_definition_all
--output-format feather
outputs:
highly_sensitive:
cohort: output/input_all.feather
## Generate dummy data for study population - vaccinated
generate_study_population_vaccinated:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccinated
--output-format feather
outputs:
highly_sensitive:
cohort: output/input_vaccinated.feather
## Generate dummy data for study population - infected
generate_study_population_infected:
run: cohortextractor:latest generate_cohort --study-definition study_definition_infected
--output-format feather
outputs:
highly_sensitive:
cohort: output/input_infected.feather
## Part 2. Create Analysis Data Sets
## Data Cleaning
## Stage 0 Data Cleaning - all
stage0_data_cleaning_all:
run: r:latest analysis/stage0_data_cleaning.R all
needs:
- generate_study_population_all
outputs:
highly_sensitive:
cohort: output/input_stage0_all.rds
moderately_sensitive:
variable_check_table_CSV: output/not_for_review/descriptives/table_0_all.csv
variable_check_table_HTML: output/not_for_review/descriptives/table_0_all.html
histogram_numerical_variable: output/not_for_review/descriptives/histogram_*_all.svg
table_gp: output/not_for_review/descriptives/table_gp_*_all*
## Stage 0 Data Cleaning - vaccinated
stage0_data_cleaning_vaccinated:
run: r:latest analysis/stage0_data_cleaning.R vaccinated
needs:
- generate_study_population_vaccinated
outputs:
highly_sensitive:
cohort: output/input_stage0_vaccinated.rds
moderately_sensitive:
variable_check_table_CSV: output/not_for_review/descriptives/table_0_vaccinated.csv
variable_check_table_HTML: output/not_for_review/descriptives/table_0_vaccinated.html
histogram_numerical_variable: output/not_for_review/descriptives/histogram_*_vaccinated.svg
table_gp: output/not_for_review/descriptives/table_gp_*_vaccinated*
## Stage 0 Data Cleaning - infected
stage0_data_cleaning_infected:
run: r:latest analysis/stage0_data_cleaning.R infected
needs:
- generate_study_population_infected
outputs:
highly_sensitive:
cohort: output/input_stage0_infected.rds
moderately_sensitive:
variable_check_table_CSV: output/not_for_review/descriptives/table_0_infected.csv
variable_check_table_HTML: output/not_for_review/descriptives/table_0_infected.html
histogram_numerical_variable: output/not_for_review/descriptives/histogram_*_infected.svg
table_gp: output/not_for_review/descriptives/table_gp_*_infected*
## Define eligible population
## Stage 1 define eligible population - all
stage1_define_eligible_population_all:
run: r:latest analysis/stage1_define_eligible_population.R all
needs:
- stage0_data_cleaning_all
outputs:
highly_sensitive:
cohort: output/input_stage1_all.rds
moderately_sensitive:
flow_chart_csv: output/flow_chart_all.csv
flow_chart_html: output/flow_chart_all.html
## Stage 1 define eligible population - vaccinated
stage1_define_eligible_population_vaccinated:
run: r:latest analysis/stage1_define_eligible_population.R vaccinated
needs:
- stage0_data_cleaning_vaccinated
outputs:
highly_sensitive:
cohort: output/input_stage1_vaccinated.rds
moderately_sensitive:
flow_chart_csv: output/flow_chart_vaccinated.csv
flow_chart_html: output/flow_chart_vaccinated.html
## Stage 1 define eligible population - infected
stage1_define_eligible_population_infected:
run: r:latest analysis/stage1_define_eligible_population.R infected
needs:
- stage0_data_cleaning_infected
outputs:
highly_sensitive:
cohort: output/input_stage1_infected.rds
moderately_sensitive:
flow_chart_csv: output/flow_chart_infected.csv
flow_chart_html: output/flow_chart_infected.html
## Part 3. Figures and tables
## Table 1. Patient Characteristics - all
table_1_all:
run: r:latest analysis/table_1.R all
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
descriptive_table_CSV: output/review/descriptives/table_1_all.csv
descriptive_table_HTML: output/review/descriptives/table_1_all.html
## Table 1. Patient Characteristics - vaccinated
table_1_vaccinated:
run: r:latest analysis/table_1.R vaccinated
needs:
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
descriptive_table_CSV: output/review/descriptives/table_1_vaccinated.csv
descriptive_table_HTML: output/review/descriptives/table_1_vaccinated.html
## Table 1. Patient Characteristics - infected
table_1_infected:
run: r:latest analysis/table_1.R infected
needs:
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
descriptive_table_CSV: output/review/descriptives/table_1_infected.csv
descriptive_table_HTML: output/review/descriptives/table_1_infected.html
## Table_1_combined - all table 1 combined
table_1_combined:
run: r:latest analysis/table_1_combined.R
needs:
- table_1_all
- table_1_vaccinated
- table_1_infected
outputs:
moderately_sensitive:
table: output/review/descriptives/table_1_combined*
## Define eligible population
## Table 2. Event count and incidence rate - all
table_2_all:
run: r:latest analysis/table_2.R all
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
incidence_rate_table_CSV: output/review/descriptives/table_2_all.csv
incidence_rate_talbe_HTML: output/review/descriptives/table_2_all.html
## Table 2. Event count and incidence rate - all_vax_c
table_2_all_vax_c:
run: r:latest analysis/table_2.R all_vax_c
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
incidence_rate_table_CSV: output/review/descriptives/table_2_all_vax_c.csv
incidence_rate_talbe_HTML: output/review/descriptives/table_2_all_vax_c.html
## Table 2. Event count and incidence rate - vaccinated
table_2_vaccinated:
run: r:latest analysis/table_2.R vaccinated
needs:
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
incidence_rate_table_CSV: output/review/descriptives/table_2_vaccinated.csv
incidence_rate_talbe_HTML: output/review/descriptives/table_2_vaccinated.html
## Table 2. Event count and incidence rate - infected
table_2_infected:
run: r:latest analysis/table_2.R infected
needs:
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
incidence_rate_table_CSV: output/review/descriptives/table_2_infected.csv
incidence_rate_talbe_HTML: output/review/descriptives/table_2_infected.html
## Table_2_combined - all table 2 combined
table_2_combined:
run: r:latest analysis/table_2_combined.R
needs:
- table_2_all
- table_2_all_vax_c
- table_2_vaccinated
- table_2_infected
outputs:
moderately_sensitive:
table: output/review/descriptives/table_2_combined*
## table_3 - sequence count
table_3_all:
run: r:latest analysis/table_3.R
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
sequence_count_table_CSV: output/review/descriptives/table_3.csv
sequence_count_table_HTML: output/review/descriptives/table_3.html
## Figure_1 - long covid count
figure_1_all:
run: r:latest analysis/figure_1.R
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
figure_long_covid_count_all: output/figure_1_*.svg
table_csv_long_covid_count_all: output/review/descriptives/long_covid_count_*_all.csv
table_html_long_covid_count_all: output/review/descriptives/long_covid_count_*_all.html
## Figure_hist - Histogram of days from covid to long covid
figure_hist_all:
run: r:latest analysis/figure_hist.R
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
figure_days_c_to_lc: output/review/descriptives/figure_hist.svg
table_csv_summary: output/review/descriptives/summary_days_c_to_long.csv
table_bin_count: output/review/descriptives/hist_*
## Figure - cumulative probability plot
figure_cum_prob_km_all:
run: r:latest analysis/figure_cum_prob_km.R
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
cum_prob_plot: output/review/descriptives/figure_cum_*.svg
## Suppl_table_1 - frequencies of snomed code for long covid diagnosis
suppl_table_1_all:
run: r:latest analysis/suppl_table_1.R
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
pie_chart_long_covid_code: output/review/descriptives/suppl_figure_pie.svg
table_csv_long_covid_code: output/review/descriptives/suppl_table_1.csv
table_html_long_covid_code: output/review/descriptives/suppl_table_1.html
## Suppl_figure_1 - long covid count by region
suppl_figure_1_all:
run: r:latest analysis/suppl_figure_1.R
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
figure_long_covid_count_region: output/review/descriptives/suppl_figure_1_*.svg
table_csv_long_covid_count_region: output/review/descriptives/long_covid_count_*.csv
table_html_long_covid_region: output/review/descriptives/long_covid_count_*.html
## Summarise survival data
summarise_survival_data_all:
run: r:latest analysis/stage2_summarise_survival_data.R
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
summary_survival_data_CSV: output/review/descriptives/summarise_survival_data.csv
summary_survival_data_HTML: output/review/descriptives/summarise_survival_data.html
## Part 4. Modelling
## Development Cox model
## post-viral fatigue
development_cox_model_fatigue:
run: r:latest analysis/stage3_fatigue_survival_analysis.R
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
summary_survival_data: output/review/model/analysis_data_summary_fatigue*
cox_model_output: output/review/model/hazard_ratio_estimates_fatigue*
## Development Cox Model - all
development_cox_model_all:
run: r:latest analysis/stage3_model_development.R all
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
supporting_document_CSV: output/review/model/analysis_data_summary_all.csv
supporting_document_html: output/review/model/analysis_data_summary_all.html
hazard_ratios_CSV: output/review/model/hazard_ratio_estimates_*_all.csv
hazard_ratios_HTML: output/review/model/hazard_ratio_estimates_*_all.html
selected_variables: output/not_for_review/model/selected_variables_all.csv
model_selection: output/not_for_review/model/model_selection_all.csv
## Development Cox Model - all_vax_c
development_cox_model_all_vax_c:
run: r:latest analysis/stage3_model_development.R all_vax_c
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
supporting_document_CSV: output/review/model/analysis_data_summary_all_vax_c.csv
supporting_document_html: output/review/model/analysis_data_summary_all_vax_c.html
hazard_ratios_CSV: output/review/model/hazard_ratio_estimates_*_all_vax_c.csv
hazard_ratios_HTML: output/review/model/hazard_ratio_estimates_*_all_vax_c.html
selected_variables: output/not_for_review/model/selected_variables_all_vax_c.csv
model_selection: output/not_for_review/model/model_selection_all_vax_c.csv
## Development Cox Model - vaccinated
development_cox_model_vaccinated:
run: r:latest analysis/stage3_model_development.R vaccinated
needs:
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
supporting_document_CSV: output/review/model/analysis_data_summary_vaccinated.csv
supporting_document_html: output/review/model/analysis_data_summary_vaccinated.html
hazard_ratios_CSV: output/review/model/hazard_ratio_estimates_*_vaccinated.csv
hazard_ratios_HTML: output/review/model/hazard_ratio_estimates_*_vaccinated.html
selected_variables: output/not_for_review/model/selected_variables_vaccinated.csv
model_selection: output/not_for_review/model/model_selection_vaccinated.csv
## Development Cox Model - all_vax_td
development_cox_model_all_vax_td:
run: r:latest analysis/stage3_model_development.R all_vax_td
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
supporting_document_CSV: output/review/model/analysis_data_summary_all_vax_td.csv
supporting_document_html: output/review/model/analysis_data_summary_all_vax_td.html
hazard_ratios_CSV: output/review/model/hazard_ratio_estimates_*_all_vax_td.csv
hazard_ratios_HTML: output/review/model/hazard_ratio_estimates_*_all_vax_td.html
selected_variables: output/not_for_review/model/selected_variables_all_vax_td.csv
model_selection: output/not_for_review/model/model_selection_all_vax_td.csv
## Development Cox Model - infected
development_cox_model_infected:
run: r:latest analysis/stage3_model_development.R infected
needs:
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
supporting_document_CSV: output/review/model/analysis_data_summary_infected.csv
supporting_document_html: output/review/model/analysis_data_summary_infected.html
hazard_ratios_CSV: output/review/model/hazard_ratio_estimates_*_infected.csv
hazard_ratios_HTML: output/review/model/hazard_ratio_estimates_*_infected.html
selected_variables: output/not_for_review/model/selected_variables_infected.csv
model_selection: output/not_for_review/model/model_selection_infected.csv
## Development Cox Model - all
development_model_age_sex_all:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex.R all
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
fit_cox_model: output/not_for_review/model/fit_cox_model_age_sex_all.rds
hazard_ratios_CSV: output/review/model/hazard_ratio_estimates_age_sex_*_all.csv
hazard_ratios_HTML: output/review/model/hazard_ratio_estimates_age_sex_*_all.html
performance_measure_CSV: output/review/model/performance_measures_age_sex_*_all.csv
performance_measure_HTML: output/review/model/performance_measures_age_sex_*_all.html
survival_plot: output/review/model/survival_plot_*_age_sex_*_all.svg
## Development Cox Model - all_vax_c
development_model_age_sex_all_vax_c:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex.R all_vax_c
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
fit_cox_model: output/not_for_review/model/fit_cox_model_age_sex_all_vax_c.rds
hazard_ratios_CSV: output/review/model/hazard_ratio_estimates_age_sex_*_all_vax_c.csv
hazard_ratios_HTML: output/review/model/hazard_ratio_estimates_age_sex_*_all_vax_c.html
performance_measure_CSV: output/review/model/performance_measures_age_sex_*_all_vax_c.csv
performance_measure_HTML: output/review/model/performance_measures_age_sex_*_all_vax_c.html
survival_plot: output/review/model/survival_plot_*_age_sex_*_all_vax_c.svg
## Development Cox Model - vaccinated
development_model_age_sex_vaccinated:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex.R vaccinated
needs:
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
fit_cox_model: output/not_for_review/model/fit_cox_model_age_sex_vaccinated.rds
hazard_ratios_CSV: output/review/model/hazard_ratio_estimates_age_sex_*_vaccinated.csv
hazard_ratios_HTML: output/review/model/hazard_ratio_estimates_age_sex_*_vaccinated.html
performance_measure_CSV: output/review/model/performance_measures_age_sex_*_vaccinated.csv
performance_measure_HTML: output/review/model/performance_measures_age_sex_*_vaccinated.html
survival_plot: output/review/model/survival_plot_*_age_sex_*_vaccinated.svg
## Development Cox Model - all_vax_td
development_model_age_sex_all_vax_td:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex.R all_vax_td
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
fit_cox_model: output/not_for_review/model/fit_cox_model_age_sex_all_vax_td.rds
hazard_ratios_CSV: output/review/model/hazard_ratio_estimates_age_sex_*_all_vax_td.csv
hazard_ratios_HTML: output/review/model/hazard_ratio_estimates_age_sex_*_all_vax_td.html
performance_measure_CSV: output/review/model/performance_measures_age_sex_*_all_vax_td.csv
performance_measure_HTML: output/review/model/performance_measures_age_sex_*_all_vax_td.html
survival_plot: output/review/model/survival_plot_*_age_sex_*_all_vax_td.svg
## Development Cox Model - infected
development_model_age_sex_infected:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex.R infected
needs:
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
fit_cox_model: output/not_for_review/model/fit_cox_model_age_sex_infected.rds
hazard_ratios_CSV: output/review/model/hazard_ratio_estimates_age_sex_*_infected.csv
hazard_ratios_HTML: output/review/model/hazard_ratio_estimates_age_sex_*_infected.html
performance_measure_CSV: output/review/model/performance_measures_age_sex_*_infected.csv
performance_measure_HTML: output/review/model/performance_measures_age_sex_*_infected.html
survival_plot: output/review/model/survival_plot_*_age_sex_*_infected.svg
## Development Cox Model - all
development_model_age_sex_adjusted_all:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex_adjusted.R all
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
hazard_ratios_CSV: output/review/model/HR_estimates_age_sex_adjusted_all.csv
hazard_ratios_HTML: output/review/model/HR_estimates_age_sex_adjusted_all.html
performance_measure_CSV: output/review/model/performance_measures_age_sex_adjusted_all.csv
performance_measure_HTML: output/review/model/performance_measures_age_sex_adjusted_all.html
## Development Cox Model - all_vax_c
development_model_age_sex_adjusted_all_vax_c:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex_adjusted.R all_vax_c
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
hazard_ratios_CSV: output/review/model/HR_estimates_age_sex_adjusted_all_vax_c.csv
hazard_ratios_HTML: output/review/model/HR_estimates_age_sex_adjusted_all_vax_c.html
performance_measure_CSV: output/review/model/performance_measures_age_sex_adjusted_all_vax_c.csv
performance_measure_HTML: output/review/model/performance_measures_age_sex_adjusted_all_vax_c.html
## Development Cox Model - vaccinated
development_model_age_sex_adjusted_vaccinated:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex_adjusted.R vaccinated
needs:
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
hazard_ratios_CSV: output/review/model/HR_estimates_age_sex_adjusted_vaccinated.csv
hazard_ratios_HTML: output/review/model/HR_estimates_age_sex_adjusted_vaccinated.html
performance_measure_CSV: output/review/model/performance_measures_age_sex_adjusted_vaccinated.csv
performance_measure_HTML: output/review/model/performance_measures_age_sex_adjusted_vaccinated.html
## Development Cox Model - all_vax_td
development_model_age_sex_adjusted_all_vax_td:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex_adjusted.R all_vax_td
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
hazard_ratios_CSV: output/review/model/HR_estimates_age_sex_adjusted_all_vax_td.csv
hazard_ratios_HTML: output/review/model/HR_estimates_age_sex_adjusted_all_vax_td.html
performance_measure_CSV: output/review/model/performance_measures_age_sex_adjusted_all_vax_td.csv
performance_measure_HTML: output/review/model/performance_measures_age_sex_adjusted_all_vax_td.html
## Development Cox Model - infected
development_model_age_sex_adjusted_infected:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex_adjusted.R infected
needs:
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
hazard_ratios_CSV: output/review/model/HR_estimates_age_sex_adjusted_infected.csv
hazard_ratios_HTML: output/review/model/HR_estimates_age_sex_adjusted_infected.html
performance_measure_CSV: output/review/model/performance_measures_age_sex_adjusted_infected.csv
performance_measure_HTML: output/review/model/performance_measures_age_sex_adjusted_infected.html
## Evaluation Cox model
evaluation_cox_model_all:
run: r:latest analysis/stage4_model_evaluation.R all
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
performance_measure_CSV: output/review/model/performance_measures_*_all.csv
performance_measure_HTML: output/review/model/performance_measures_*_all.html
survival_plot: output/review/model/survival_plot_*_all.svg
evaluation_cox_model_all_vax_c:
run: r:latest analysis/stage4_model_evaluation.R all_vax_c
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
performance_measure_CSV: output/review/model/performance_measures_*_all_vax_c.csv
performance_measure_HTML: output/review/model/performance_measures_*_all_vax_c.html
survival_plot: output/review/model/survival_plot_*_all_vax_c.svg
evaluation_cox_model_vaccinated:
run: r:latest analysis/stage4_model_evaluation.R vaccinated
needs:
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
performance_measure_CSV: output/review/model/performance_measures_*_vaccinated.csv
performance_measure_HTML: output/review/model/performance_measures_*_vaccinated.html
survival_plot: output/review/model/survival_plot_*_vaccinated.svg
evaluation_cox_model_all_vax_td:
run: r:latest analysis/stage4_model_evaluation.R all_vax_td
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
performance_measure_CSV: output/review/model/performance_measures_*_all_vax_td.csv
performance_measure_HTML: output/review/model/performance_measures_*_all_vax_td.html
survival_plot: output/review/model/survival_plot_*_all_vax_td.svg
evaluation_cox_model_infected:
run: r:latest analysis/stage4_model_evaluation.R infected
needs:
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
performance_measure_CSV: output/review/model/performance_measures_*_infected.csv
performance_measure_HTML: output/review/model/performance_measures_*_infected.html
survival_plot: output/review/model/survival_plot_*_infected.svg
## Validation Cox model
## Validation Cox Model - all
validation_cox_model_all:
run: r:latest analysis/stage5_model_validation_iecv_revised2.R all
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
val_performance_measure_CSV: output/review/model/iecv_performance_measures_all.csv
val_performance_measure_html: output/review/model/iecv_performance_measures_all.html
val_cal_plot: output/review/model/iecv_calibration_plot_*_all.svg
## Validation Cox Model - all_vax_c
validation_cox_model_all_vax_c:
run: r:latest analysis/stage5_model_validation_iecv_revised2.R all_vax_c
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
val_performance_measure_CSV: output/review/model/iecv_performance_measures_all_vax_c.csv
val_performance_measure_html: output/review/model/iecv_performance_measures_all_vax_c.html
val_cal_plot: output/review/model/iecv_calibration_plot_*_all_vax_c.svg
## Validation Cox Model - vaccinated
validation_cox_model_vaccinated:
run: r:latest analysis/stage5_model_validation_iecv_revised2.R vaccinated
needs:
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
val_performance_measure_CSV: output/review/model/iecv_performance_measures_vaccinated.csv
val_performance_measure_html: output/review/model/iecv_performance_measures_vaccinated.html
val_cal_plot: output/review/model/iecv_calibration_plot_*_vaccinated.svg
## Validation Cox Model - all_vax_td
validation_cox_model_all_vax_td:
run: r:latest analysis/stage5_model_validation_iecv_revised2.R all_vax_td
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
val_performance_measure_CSV: output/review/model/iecv_performance_measures_all_vax_td.csv
val_performance_measure_html: output/review/model/iecv_performance_measures_all_vax_td.html
val_cal_plot: output/review/model/iecv_calibration_plot_*_all_vax_td.svg
## Validation Cox Model - infected
validation_cox_model_infected:
run: r:latest analysis/stage5_model_validation_iecv_revised2.R infected
needs:
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
val_performance_measure_CSV: output/review/model/iecv_performance_measures_infected.csv
val_performance_measure_html: output/review/model/iecv_performance_measures_infected.html
val_cal_plot: output/review/model/iecv_calibration_plot_*_infected.svg