# **********************************
# LTBI screening
# N Green
#
# data summary table
source("scripts/create_LTBI_input_workspace.R")
# load(file = "ext-data/LTBI_input_workspace.RData")
IMPUTED_sample_year_cohort <- dplyr::filter(IMPUTED_sample,
issdt_year == year_cohort)
out <-
cbind(
"Description" = c("Observed non-TB cases in EWNI",
"Observed TB cases in EWNI",
"Imputed non-TB cases in EWNI",
"Imputed TB cases in EWNI",
"Imputed non-TB cases after exit",
"Imputed TB cases after exit",
"Imputed non-case-fatalities all TB",
"Imputed case-fatalities all TB"),
rbind(
cbind("Total" = table(IMPUTED_sample_year_cohort$uk_tb_orig),
table(IMPUTED_sample_year_cohort$uk_tb_orig, IMPUTED_sample_year_cohort$who_inc_Pareek2011)),
cbind(table(IMPUTED_sample_year_cohort$uk_tb),
table(IMPUTED_sample_year_cohort$uk_tb, IMPUTED_sample_year_cohort$who_inc_Pareek2011)),
cbind(table(IMPUTED_sample_year_cohort$exituk_tb),
table(IMPUTED_sample_year_cohort$exituk_tb, IMPUTED_sample_year_cohort$who_inc_Pareek2011)),
cbind(table(IMPUTED_sample_year_cohort$tb_fatality),
table(IMPUTED_sample_year_cohort$tb_fatality, IMPUTED_sample_year_cohort$who_inc_Pareek2011)))#,
# rbind(
#
# table(IMPUTED_sample_year_cohort$uk_tb_orig, IMPUTED_sample_year_cohort$visatype2),
#
# table(IMPUTED_sample_year_cohort$uk_tb, IMPUTED_sample_year_cohort$visatype2),
#
# table(IMPUTED_sample_year_cohort$exituk_tb, IMPUTED_sample_year_cohort$visatype2),
#
# table(IMPUTED_sample_year_cohort$tb_fatality, IMPUTED_sample_year_cohort$visatype2))
)
rownames(out) <- NULL
out
write.csv(out, "output/data-summary-table.csv")
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