knitr::opts_chunk$set(warning = FALSE, eval = FALSE)
library(tbinenglanddataclean) ## rebuild existing data sets rebuild <- FALSE ## Analysis running in docker or locally? if local set ~ if in docker set .. run_envir <- ".."
if (!file.exists(paste0(run_envir, "/data/tb_data/tbinenglanddataclean/clean_ets_2016.rds")) || rebuild) { clean_munge_ets_2016(data_path = paste0(run_envir, "/data/tb_data/ETS/ETS_2016_extract/SAbbott_BCG dataset_version2_final140217.dta"), return = FALSE, save = TRUE, save_name = "clean_ets_2016", save_path = paste0(run_envir, "/data/tb_data/tbinenglanddataclean"), save_format = c("rds", "csv"), verbose = TRUE) }
if (!file.exists(paste0(run_envir,"/data/tb_data/tbinenglanddataclean/E_demo_2000_2015.rds")) || rebuild) { clean_demographics_uk(data_path = paste0(run_envir, "/data/tb_data/UK_demographics"), demo_2000 = "UK_2000_age.csv", demo_2001_2015 = "UK_2001_2015_age.csv", countries = c("E"), return = FALSE, save = TRUE, save_name = "E_demo_2000_2015", save_path = paste0(run_envir, "/data/tb_data/tbinenglanddataclean"), save_format = c("rds", "csv"), verbose = TRUE) }
if (!file.exists(paste0(run_envir, "/data/tb_data/tbinenglanddataclean/formatted_LFS_2000_2016.rds")) || rebuild) { clean_labour_force_survey(data_path = paste0(run_envir, "/data/tb_data/LFS"), years = 2000:2016, years_var = list( '2000' = c('age', 'sex', 'cry', 'govtof', 'pwt07'), '2001' = c('age', 'sex', 'cry01', 'country', 'pwt07'), '2002' = c('AGE', 'SEX', 'CRY01', 'COUNTRY', 'PWT14'), '2003' = c('AGE', 'SEX', 'CRY01', 'COUNTRY', 'PWT14'), '2004' = c('AGE', 'SEX', 'CRY01', 'COUNTRY', 'PWT14'), '2005' = c('AGE', 'SEX', 'CRY01', 'COUNTRY', 'PWT14'), '2006' = c('AGE', 'SEX', 'CRY01', 'COUNTRY', 'PWT14'), '2007' = c('AGE', 'SEX', 'CRY01', 'COUNTRY', 'PWT14'), '2008' = c('AGE', 'SEX', 'CRY01', 'COUNTRY', 'PWT14'), '2009' = c('AGE', 'SEX', 'CRY01', 'COUNTRY', 'PWT14'), '2010' = c('AGE', 'SEX', 'CRY01', 'COUNTRY', 'PWT14'), '2011' = c('AGE', 'SEX', 'CRY01', 'COUNTRY', 'PWT14'), '2012' = c('AGE', 'SEX', 'CRY12', 'COUNTRY', 'PWT14'), '2013' = c('AGE', 'SEX', 'CRY12', 'COUNTRY', 'PWT16'), '2014' = c('AGE', 'SEX', 'CRY12', 'COUNTRY', 'PWT16'), '2015' = c('AGE', 'SEX', 'CRY12', 'COUNTRY', 'PWT16'), '2016' = c('AGE', 'SEX', 'CRY12', 'COUNTRY', 'PWT16')), return = FALSE, save = TRUE, save_name = "formatted_LFS_2000_2016", save_path = paste0(run_envir, "/data/tb_data/tbinenglanddataclean"), save_format = c("rds", "csv"), verbose = TRUE) }
if (!file.exists(paste0(run_envir, "/data/tbinenglanddataclean/E_ons_lfs_2000_2016.rds")) || rebuild) { combine_ons_with_lfs(data_path = paste0(run_envir, "/data/tb_data/tbinenglanddataclean"), ons_name = "E_demo_2000_2015.rds", lfs_name = "formatted_LFS_2000_2016.rds", countries = "England", return = FALSE, save = TRUE, save_name = "E_ons_lfs_2000_2016", save_path = paste0(run_envir, "/data/tb_data/tbinenglanddataclean"), save_format = c("rds", "csv"), verbose = TRUE) }
if (!file.exists(paste0(run_envir, "/data/tb_data/tbinenglanddataclean/england_births.rds")) || rebuild) { clean_and_munge_england_births(birth_path = paste0(run_envir, "/data/tb_data/UK_demographics/annual_reference_table.xls"), projected_birth_path = paste0(run_envir, "/data/tb_data/UK_demographics/england_population_projections.xls"), return = FALSE, save = TRUE, save_name = "england_births", save_path = paste0(run_envir, "/data/tb_data/tbinenglanddataclean"), save_format = c("rds", "csv"), verbose = TRUE) }
if (!file.exists(paste0(run_envir, "/data/tb_data/tbinenglanddataclean/england_mortality_rate.rds")) || rebuild) { clean_and_munge_england_life_expectancy(life_tables_path = paste0(run_envir, "/data/tb_data/UK_demographics/england_life_tables.xls"), sheets = paste0(seq(2013,1998, -1), "-", seq(2015,2000, -1)), return = FALSE, save = TRUE, save_name = "england_mortality_rates", save_path = paste0(run_envir, "/data/tb_data/tbinenglanddataclean"), save_format = c("rds", "csv"), verbose = TRUE) }
if (!file.exists(paste0(run_envir, "/data/tb_data/tbinenglanddataclean/cases_demo_incidence.rds")) || rebuild) { calculate_incidence_ets_lfs_ons(data_path = paste0(run_envir, "/data/tb_data/tbinenglanddataclean"), ets_name = "clean_ets_2016.rds", demo_name = "E_ons_lfs_2000_2016.rds", return = FALSE, save = TRUE, incidence_name = "incidence", grouped_incidence_name = "age_grouped_incidence", condensed_grouped_incidence_name = "condensed_age_group_incidence", cases_demo_incidence_name = "cases_demo_incidence", save_path = paste0(run_envir, "/data/tb_data/tbinenglanddataclean"), save_format = c("rds", "csv"), verbose = TRUE) }
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