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vax_eligibility_inputs.R
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vax_eligibility_inputs.R
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# # # # # # # # # # # # # # # # # # # # #
# This script:
# creates metadata for aspects of the study design
# # # # # # # # # # # # # # # # # # # # #
# Import libraries ----
library('tidyverse')
library('here')
# create study_dates ----
study_dates <-
list(
ref_age_1 = "2021-03-31", # reference date for calculating age for phase 1 groups
ref_age_2 = "2021-07-01", # reference date for calculating age for phase 2 groups
ref_cev = "2021-01-18", # reference date for calculating eligibility for phase 1 group 4 (CEV)
ref_ar = "2021-02-15", # reference date for calculating eligibility for phase 1 group 5 (at-risk)
pandemic_start = "2020-01-01", # rough start date for pandemic in UK
start_date = "2020-12-08", # start of phase 1 vaccinations
start_date_pfizer = "2020-12-08",
start_date_az = "2021-01-04",
start_date_moderna = "2021-03-04",
end_date = "2021-09-15" # last date of available vaccination data. NEED TO ALSO CHECK END DATES FOR OTHER DATA SOURCES
)
jsonlite::write_json(study_dates, path = "output/vax_study_dates.json", auto_unbox = TRUE, pretty=TRUE)
# create jcvi_groups ----
jcvi_groups <-
tribble(
~group, ~definition,
"01", "longres_group AND vax_jcvi_age_1 > 65",
"02", "vax_jcvi_age_1 >=80",
"03", "vax_jcvi_age_1 >=75",
"04", "vax_jcvi_age_1 >=70 OR (cev_group AND vax_jcvi_age_1 >=16 AND NOT preg_group)",
"05", "vax_jcvi_age_1 >=65",
"06", "atrisk_group AND vax_jcvi_age_1 >=16",
"07", "vax_jcvi_age_1 >=60",
"08", "vax_jcvi_age_1 >=55",
"09", "vax_jcvi_age_1 >=50",
"10", "vax_jcvi_age_2 >=40",
"11", "vax_jcvi_age_2 >=30",
"12", "vax_jcvi_age_2 >=18",
"99", "DEFAULT",
)
readr::write_csv(jcvi_groups, "output/vax_jcvi_groups.csv")
# create elig_dates ----
elig_dates <-
tribble(
~date, ~description, ~jcvi_groups,
"2020-12-08", "vax_cat_jcvi_group='01' OR vax_cat_jcvi_group='02' OR vax_cat_jcvi_group='03'", "01, 02, 03",
"2021-01-18", "vax_cat_jcvi_group='04'", "04",
###
"2021-02-15", "vax_cat_jcvi_group='05' OR vax_cat_jcvi_group='06'", "05, 06",
###
"2021-02-22", "vax_jcvi_age_1 >= 64 AND vax_jcvi_age_1 < 65", "07",
"2021-03-01", "vax_jcvi_age_1 >= 60 AND vax_jcvi_age_1 < 64", "07",
###
"2021-03-08", "vax_jcvi_age_1 >= 56 AND vax_jcvi_age_1 < 60", "08",
"2021-03-09", "vax_jcvi_age_1 >= 55 AND vax_jcvi_age_1 < 56", "08",
###
"2021-03-19", "vax_jcvi_age_1 >= 50 AND vax_jcvi_age_1 < 55", "09",
###
"2021-04-13", "vax_jcvi_age_2 >= 45 AND vax_jcvi_age_1 < 50", "10",
"2021-04-26", "vax_jcvi_age_2 >= 44 AND vax_jcvi_age_1 < 45", "10",
"2021-04-27", "vax_jcvi_age_2 >= 42 AND vax_jcvi_age_1 < 44", "10",
"2021-04-30", "vax_jcvi_age_2 >= 40 AND vax_jcvi_age_1 < 42", "10",
###
"2021-05-13", "vax_jcvi_age_2 >= 38 AND vax_jcvi_age_2 < 40", "11",
"2021-05-19", "vax_jcvi_age_2 >= 36 AND vax_jcvi_age_2 < 38", "11",
"2021-05-21", "vax_jcvi_age_2 >= 34 AND vax_jcvi_age_2 < 36", "11",
"2021-05-25", "vax_jcvi_age_2 >= 32 AND vax_jcvi_age_2 < 34", "11",
"2021-05-26", "vax_jcvi_age_2 >= 30 AND vax_jcvi_age_2 < 32", "11",
###
"2021-06-08", "vax_jcvi_age_2 >= 25 AND vax_jcvi_age_2 < 30", "12",
"2021-06-15", "vax_jcvi_age_2 >= 23 AND vax_jcvi_age_2 < 25", "12",
"2021-06-16", "vax_jcvi_age_2 >= 21 AND vax_jcvi_age_2 < 23", "12",
"2021-06-18", "vax_jcvi_age_2 >= 18 AND vax_jcvi_age_2 < 21", "12",
"2100-12-31", "DEFAULT", "NA",
)
readr::write_csv(elig_dates, "output/vax_eligible_dates.csv")