In Public-Health-Scotland/hsmr: Reproducible Analytical Pipeline of Hospital Standardised Mortality Ratios Quarterly Publication

# Load environment file
source(here::here("setup_environment.R"))

# Read in SMR data, filtered on latest period/reported hospitals
smr_data          <- read_csv(paste0(data_folder, pub_day, "/output/", 
                 pub_day,  "_SMR-data.csv")) %>% 
  filter(period == 3 & location %in% c(hosp_filter, scot_filter)) %>%
  mutate(st_err = round_half_up(sqrt(1/round_half_up(pred, 8)), 8),
       z = if_else(location_type == "hospital",
                   round_half_up(((round_half_up(smr, 8) - 1)/round_half_up(st_err,8)), 8),
                   0)) %>%
  mutate(
    z_max = max(z),
    z_min = min(z),
    z_flag = case_when(z == z_max ~ 1,
                       z == z_min ~ -1,
                       TRUE ~ 0),
    z = if_else(z == z_max | z == z_min, 0, z),
    z_max = max(z),
    z_min = min(z),
    z = case_when(z_flag == 1 ~ z_max,
                  z_flag == -1 ~ z_min,
                  TRUE ~ z),
    z_flag = if_else(z != 0, 1, 0),
    w_score = round_half_up(sqrt(sum(round_half_up(z * z, 8))/sum(z_flag)),8)) %>%
  # Calculate funnel limits for funnel plot
  mutate(uwl = 1 + 1.96 * round_half_up(st_err * w_score,8),
         ucl = 1 + 3.09 * round_half_up(st_err * w_score,8),
         lwl = 1 - 1.96 * round_half_up(st_err * w_score,8),
         lcl = 1 - 3.09 * round_half_up(st_err * w_score,8)) %>%  

  # Create flag for where hospital sits on funnel plot
  mutate(flag = case_when(smr > ucl ~ "2",
                          smr > uwl & smr <= ucl ~ "1",
                          smr < lwl & smr >= lcl ~ "1",
                          TRUE ~ "0"))

#Create contact information
#contact1 <- "Isabella Tortora Brayda | Senior Information Analyst | <[e-mail]>" 
#contact2 <- "Paul Ogharanduku | Senior Information Analyst | <[e-mail]>"
contact1 <- "Charlotte Hill | Information Analyst | <[e-mail]>"
contact2 <- "Echo Lian | Senior Information Analyst | <[e-mail]>"

Hospital Standardised Mortality Ratios

`r yr(end_date)`

An Accredited official statistics release for Scotland

Publication date: `r format(pub_day, "%d %B %Y")`

RESTRICTED STATISTICS: embargoed to 09:30 `r format(pub_day, "%d/%m/%Y")`

About this release

This release by Public Health Scotland (PHS) provides information on Hospital Standardised Mortality Ratios (HSMRs) for the period `r format(start_date_trends, "%B %Y")` to `r format(end_date, "%B %Y")`. These statistics are updated on a quarterly basis and reflect the HSMR for the latest 12-month reporting period, whilst crude mortality data is presented by quarter and month to show trends.