In SwissTPH/timci: Data management and visualisation for the TIMCI project

\clearpage

write(formats2h2("Generate the faciliy assessment subsection"), stderr())

r h1_spa_fa

n <- nrow(spa_fa_data)
cond <- n > 0

r n submissions

timci::generate_calendar_heatmap2(spa_fa_data,
                                  date,
                                  legendtitle = "Number of submissions")

Basic services

all <- spa_fa_data %>% 
  rename(facility_name = "fname",
         upgraded_from_designation = "b2_2",
         inpatient_beds = "b2_7")

summary <- list(
  "Summary" = list(
    "Upgraded" = ~qwraps2::n_perc(upgraded_from_designation == 1, prec),
    "Number of inpatient beds" = ~qwraps2::mean_sd(inpatient_beds, denote_sd = "paren", na_rm = TRUE)
    )
)
out <- format_summary_table(all, summary, facility_name)
out %>% 
  kableExtra::kbl(booktabs = TRUE,
                  linesep = "",
                  align = c("c", "c", "c", "c"),
                  caption = "Statistical summary of basic services") %>% 
  kableExtra::kable_styling(latex_options = c("HOLD_position", "repeat_header"), font_size = table_fs) %>%
  kableExtra::row_spec(0, bold = TRUE) %>%
  kableExtra::row_spec(1, color = total_row_ft2, background = total_row_bg2, bold = TRUE) %>%
  kableExtra::row_spec(1:(nrow(out)/2) * 2, background = striped_row_bg)