/
project.yaml
197 lines (188 loc) · 10 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_dataset:
run: >
databuilder:v0
generate-dataset analysis/databuilder_definition.py --output output/dataset_all.csv.gz
outputs:
highly_sensitive:
dataset_all: output/dataset_all.csv.gz
clean_the_data:
run: >
r:latest
analysis/010_import_data.R
needs: [generate_dataset]
outputs:
highly_sensitive:
cleandata: output/data_edited.gz.parquet
moderately_sensitive:
txt1: output/data_properties/clean_dataset_skim.txt
txt2: output/data_properties/clean_dataset_tabulate.txt
create_table1:
run: >
r:latest
analysis/020_create_table1.R
needs: [clean_the_data]
outputs:
moderately_sensitive:
table1: output/tables/shielding_table1.html
table1_r: output/tables/shielding_table1_redacted.html
table1_data: output/table1_data.csv
table2_shielding_v0: output/tables/shielding_table2.html
table2_shielding_v1: output/tables/shielding_v1_table2.html
table2_shielding_v2: output/tables/shielding_v2_table2.html
fit_HDdata:
#fit_HDdata_woIC:
run: >
r:latest
modelling/runmkd_main.R
needs: [clean_the_data]
outputs:
moderately_sensitive:
#HDdata.R - only run if iplatform>0
#csv011: output/HDsynthesis/J5bHbDhmdy3_Hdata_by_age.csv
csv012: output/HDsynthesis/J5bHbDhmdy3_Hdata_by_age_long.csv
#csv013: output/HDsynthesis/J5bHbDhmdy3_Hdata_by_age_merged_long.csv
#csv013: output/HDsynthesis/J5bHbDhmdy3_Hdata_by_shi.csv
#csv014: output/HDsynthesis/J5bHbDhmdy3_Hdata_s_by_age.csv
csv015: output/HDsynthesis/J5bHbDhmdy3_Hdata_s_by_age_long.csv
csv016: output/HDsynthesis/J5bHbDhmdy3_Hdata_all_long.csv
#csv021: output/HDsynthesis/J5bHbDhmdy3_DHdata_by_age.csv
csv022: output/HDsynthesis/J5bHbDhmdy3_DHdata_by_age_long.csv
#csv023: output/HDsynthesis/J5bHbDhmdy3_DHdata_by_age_merged_long.csv
#csv023: output/HDsynthesis/J5bHbDhmdy3_DHdata_by_shi.csv
#csv024: output/HDsynthesis/J5bHbDhmdy3_DHdata_s_by_age.csv
csv025: output/HDsynthesis/J5bHbDhmdy3_DHdata_s_by_age_long.csv
csv026: output/HDsynthesis/J5bHbDhmdy3_DHdata_all_long.csv
#csv031: output/HDsynthesis/J5bHbDhmdy3_DOdata_by_age.csv
csv032: output/HDsynthesis/J5bHbDhmdy3_DOdata_by_age_long.csv
#csv033: output/HDsynthesis/J5bHbDhmdy3_DOdata_by_age_merged_long.csv
#csv033: output/HDsynthesis/J5bHbDhmdy3_DOdata_by_shi.csv
#csv034: output/HDsynthesis/J5bHbDhmdy3_DOdata_s_by_age.csv
csv035: output/HDsynthesis/J5bHbDhmdy3_DOdata_s_by_age_long.csv
csv036: output/HDsynthesis/J5bHbDhmdy3_DOdata_all_long.csv
#REDACTION
csv701: output/HDsynthesis/J5bHbDhmdy3_Hdata_all_UNDERLIE.csv
csv702: output/HDsynthesis/J5bHbDhmdy3_Hdata_all_REDACTED.csv
csv703: output/HDsynthesis/J5bHbDhmdy3_Hdata_by_age_UNDERLIE.csv
csv704: output/HDsynthesis/J5bHbDhmdy3_Hdata_by_age_REDACTED.csv
csv705: output/HDsynthesis/J5bHbDhmdy3_Hdata_s_by_age_UNDERLIE.csv
csv706: output/HDsynthesis/J5bHbDhmdy3_Hdata_s_by_age_REDACTED.csv
csv711: output/HDsynthesis/J5bHbDhmdy3_DHdata_all_UNDERLIE.csv
csv712: output/HDsynthesis/J5bHbDhmdy3_DHdata_all_REDACTED.csv
csv713: output/HDsynthesis/J5bHbDhmdy3_DHdata_by_age_UNDERLIE.csv
csv714: output/HDsynthesis/J5bHbDhmdy3_DHdata_by_age_REDACTED.csv
csv715: output/HDsynthesis/J5bHbDhmdy3_DHdata_s_by_age_UNDERLIE.csv
csv716: output/HDsynthesis/J5bHbDhmdy3_DHdata_s_by_age_REDACTED.csv
csv721: output/HDsynthesis/J5bHbDhmdy3_DOdata_all_REDACTED.csv
csv722: output/HDsynthesis/J5bHbDhmdy3_DOdata_all_UNDERLIE.csv
csv723: output/HDsynthesis/J5bHbDhmdy3_DOdata_by_age_REDACTED.csv
csv724: output/HDsynthesis/J5bHbDhmdy3_DOdata_by_age_UNDERLIE.csv
csv725: output/HDsynthesis/J5bHbDhmdy3_DOdata_s_by_age_UNDERLIE.csv
csv726: output/HDsynthesis/J5bHbDhmdy3_DOdata_s_by_age_REDACTED.csv
#contacts
txt010: output/modelling/J5bHbDhmdy3_Contact_matrix_year-start-27Jan20_stats.txt
#R0
csv040: output/modelling/J5bHbDhmdy3_Simul_R0_by_week.csv
svg010: output/modelling/J5bHbDhmdy3_Simul_R0_by_week.csv.svg
#simulation - only run if iplatform==0
#svg011: output/modelling/J5bHbDhmdy3_Simul_Infected_and_R0.pdf_1-3.svg
#svg012: output/modelling/J5bHbDhmdy3_Simul_Infected_and_R0.pdf_4-6.svg
#txt020: output/modelling/J5bHbDhmdy3_Simul_run.txt
#fit
#txt000: output/modelling/screen.txt
html01: output/modelling/J5bHbDhmdy3_Main_Fit_Report.html
txt021: output/modelling/J5bHbDhmdy3_Fit_summary_1.txt
txt022: output/modelling/J5bHbDhmdy3_Fit_summary_2.txt
svg031: output/modelling/J5bHbDhmdy3_Fit_MCMC_marginalPlot.svg
#svg032: output/modelling/J5bHbDhmdy3_Fit_MCMC_plotout_lastPage.svg
svg033: output/modelling/J5bHbDhmdy3_Fit_MCMC_correlationPlot.svg
svg034: output/modelling/J5bHbDhmdy3_Fit_MCMC_Overall.svg
svg035: output/modelling/J5bHbDhmdy3_Fit_MCMC_PosteriorSample.svg
svg037: output/modelling/J5bHbDhmdy3_Fit_MCMC_PosteriorSample_Prev_R0.svg
svg036: output/modelling/J5bHbDhmdy3_Fit_MCMC_AgeProfiles.svg
svg038: output/modelling/J5bHbDhmdy3_Fit_MCMC_plots_probs.svg
HD_data_questions:
run: >
r:latest
analysis/HDdata_questions.r
needs: [clean_the_data]
outputs:
moderately_sensitive:
txt01: output/HDsynthesis/JDat13_HDdata_questions_answered_Hospital_wCH.txt
txt02: output/HDsynthesis/JDat13_HDdata_questions_answered_Deaths_wCH.txt
txt03: output/HDsynthesis/JDat13_HDdata_questions_answered_Shielding_wCH.txt
txt04: output/HDsynthesis/JDat13_HDdata_questions_answered_Hospital.txt
txt05: output/HDsynthesis/JDat13_HDdata_questions_answered_Deaths.txt
txt06: output/HDsynthesis/JDat13_HDdata_questions_answered_Shielding.txt
HD_data:
run: >
r:latest
analysis/runmkd.R
needs: [clean_the_data]
outputs:
moderately_sensitive:
csv01b: output/HDsynthesis/JDat13_Carehomes_included_H.csv
svg01b: output/HDsynthesis/JDat13_Carehomes_included_H.svg
csv02b: output/HDsynthesis/JDat13_Carehomes_included_D.csv
svg02b: output/HDsynthesis/JDat13_Carehomes_included_D.svg
csv03b: output/HDsynthesis/JDat13_Carehomes_included_DH.csv
svg03b: output/HDsynthesis/JDat13_Carehomes_included_DH.svg
csv04b: output/HDsynthesis/JDat13_Carehomes_included_DO.csv
svg04b: output/HDsynthesis/JDat13_Carehomes_included_DO.svg
csv051: output/HDsynthesis/JDat13_Hdata_all.csv
svg051: output/HDsynthesis/JDat13_Hdata_all.svg
csv052: output/HDsynthesis/JDat13_Hdata_by_age.csv
csv055: output/HDsynthesis/JDat13_Hdata_by_age_long.csv
svg052: output/HDsynthesis/JDat13_Hdata_by_age.svg
csv05m: output/HDsynthesis/JDat13_Hdata_by_age_merged.csv
csv05l: output/HDsynthesis/JDat13_Hdata_by_age_merged_long.csv
svg05m: output/HDsynthesis/JDat13_Hdata_by_age_merged.svg
csv053: output/HDsynthesis/JDat13_Hdata_by_shi.csv
svg053: output/HDsynthesis/JDat13_Hdata_by_shi.svg
csv054: output/HDsynthesis/JDat13_Hdata_s_by_age.csv
svg054: output/HDsynthesis/JDat13_Hdata_s0_by_age.svg
svg055: output/HDsynthesis/JDat13_Hdata_s1_by_age.svg
csv061: output/HDsynthesis/JDat13_HRdata_all.csv
svg061: output/HDsynthesis/JDat13_HRdata_all.svg
csv062: output/HDsynthesis/JDat13_HRdata_by_age.csv
svg062: output/HDsynthesis/JDat13_HRdata_by_age.svg
csv063: output/HDsynthesis/JDat13_HRdata_by_shi.csv
svg063: output/HDsynthesis/JDat13_HRdata_by_shi.svg
csv064: output/HDsynthesis/JDat13_HRdata_s_by_age.csv
svg064: output/HDsynthesis/JDat13_HRdata_s0_by_age.svg
svg065: output/HDsynthesis/JDat13_HRdata_s1_by_age.svg
csv071: output/HDsynthesis/JDat13_DHdata_all.csv
svg071: output/HDsynthesis/JDat13_DHdata_all.svg
csv072: output/HDsynthesis/JDat13_DHdata_by_age.csv
csv075: output/HDsynthesis/JDat13_DHdata_by_age_long.csv
svg072: output/HDsynthesis/JDat13_DHdata_by_age.svg
csv07m: output/HDsynthesis/JDat13_DHdata_by_age_merged.csv
csv07l: output/HDsynthesis/JDat13_DHdata_by_age_merged_long.csv
svg07m: output/HDsynthesis/JDat13_DHdata_by_age_merged.svg
csv073: output/HDsynthesis/JDat13_DHdata_by_shi.csv
svg073: output/HDsynthesis/JDat13_DHdata_by_shi.svg
csv074: output/HDsynthesis/JDat13_DHdata_s_by_age.csv
svg074: output/HDsynthesis/JDat13_DHdata_s0_by_age.svg
svg075: output/HDsynthesis/JDat13_DHdata_s1_by_age.svg
csv081: output/HDsynthesis/JDat13_DOdata_all.csv
svg081: output/HDsynthesis/JDat13_DOdata_all.svg
csv082: output/HDsynthesis/JDat13_DOdata_by_age.csv
csv085: output/HDsynthesis/JDat13_DOdata_by_age_long.csv
svg082: output/HDsynthesis/JDat13_DOdata_by_age.svg
csv08m: output/HDsynthesis/JDat13_DOdata_by_age_merged.csv
csv08l: output/HDsynthesis/JDat13_DOdata_by_age_merged_long.csv
svg08m: output/HDsynthesis/JDat13_DOdata_by_age_merged.svg
csv083: output/HDsynthesis/JDat13_DOdata_by_shi.csv
svg083: output/HDsynthesis/JDat13_DOdata_by_shi.svg
csv084: output/HDsynthesis/JDat13_DOdata_s_by_age.csv
svg084: output/HDsynthesis/JDat13_DOdata_s0_by_age.svg
svg085: output/HDsynthesis/JDat13_DOdata_s1_by_age.svg
csv091: output/HDsynthesis/JDat13_H,HR,DH,DOdata_H.csv
csv092: output/HDsynthesis/JDat13_H,HR,DH,DOdata_HR.csv
csv093: output/HDsynthesis/JDat13_H,HR,DH,DOdata_DH.csv
csv094: output/HDsynthesis/JDat13_H,HR,DH,DOdata_DO.csv
svg09b: output/HDsynthesis/JDat13_H,HR,DH,DOdata.svg
html01: output/HDsynthesis/JDat13_Report_HDdata.html