Exposure to secondhand smoke.R

# ScotPHO indicator:Exposure to secondhand smoke

#   Part 1 - Prepare basefiles
#   Part 2 - Run analysis functions

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## Packages/Filepaths/Functions ----
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source("1.indicator_analysis.R") #Normal indicator functions

###############################################.
## Part 1 - Prepare basefile ----
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#data from child health team
exposure_smoking <- read_csv(paste0(data_folder, "Received Data/Exposure to secondhand smoke/IR2023-00861_secondhandsmoke_valid.csv")) %>%
  setNames(tolower(names(.))) %>% #set names to lower case
  mutate(year=case_when(nchar(fin_year)==3 ~ paste0("200",substr(fin_year,1,1)), 
                        TRUE ~ paste0("20",substr(fin_year,1,2)))) # fin year

#removes all other geographies apart from datazone(needed if received data contains Scotland and hb data)
exposure_smoking <- exposure_smoking %>%
  filter(!(is.na(datazone2011))) %>%
  select(-ca2019) %>%
  rename(numerator = passive_smoke_yes, denominator = totvalid_6to8wk)

ca_lookup <- readRDS('/conf/linkage/output/lookups/Unicode/Geography/Scottish Postcode Directory/Scottish_Postcode_Directory_2023_2.rds') %>% 
  setNames(tolower(names(.))) %>%   #variables to lower case
  select(datazone2011, ca2019) %>% distinct()

exposure_geography <- left_join(exposure_smoking, ca_lookup, by = "datazone2011") %>% 
  rename(ca = ca2019 ) %>% group_by(ca, year) %>% 
  summarise(numerator = sum(numerator), denominator = sum(denominator)) %>% 
  ungroup() %>% 
  # Selecting out a few cases from early years in Highland CA before the system was 
  # properly in place that would cause confusion.
  filter(!(ca == "S12000017" & year<2007))

saveRDS(exposure_geography, file=paste0(data_folder, 'Prepared Data/exposure_smoking_raw.rds'))

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## Part 2 - Run analysis functions ----
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analyze_first(filename = "exposure_smoking", geography = "council", hscp = T,
              measure = "percent", yearstart = 2002, yearend = 2022, time_agg = 3)

analyze_second(filename = "exposure_smoking", measure = "percent", time_agg = 3,  
               ind_id = 13037, year_type = "financial")

##END