Quit attempts - total.R

# ScotPHO indicators: Quit attempts total number

#   Part 1 - Create basefile
#   Part 2 - Run analysis function
#   Part 3 - Format the file for Shiny tool

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

###############################################.
## Part 1 - Create basefile ----
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#Reading data extracted from table from Smoking cessation annual publication
quit_total <- read_csv(paste0(data_folder, "Received Data/Smoking quit attempts/quit_attempts_total_2022.csv")) %>% 
  setNames(tolower(names(.))) %>%    #variables to lower case
  gather("year", "numerator", -council) %>% #from wide to long format
  mutate(year = substr(year,1,4)) #fin year

# converting council names into codes. First bring lookup.
ca_lookup <- readRDS("/PHI_conf/ScotPHO/Profiles/Data/Lookups/Geography/CAdictionary.rds") %>% 
  setNames(tolower(names(.))) %>% #set variables to lower case
  rename(ca=code)

quit_total <- left_join(quit_total, ca_lookup, 
                        by = c("council" = "areaname")) %>% 
  select(-council) %>% 
  mutate(denominator = NA_integer_) # needed for the function

saveRDS(quit_total, file=paste0(data_folder, 'Prepared Data/quitattempts_total_raw.rds'))

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## Part 2 - Run first analysis functions ----
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# to generate geographical aggregations
analyze_first(filename = "quitattempts_total", geography = "council", 
              measure = "percent", yearstart = 2009, yearend = 2021, time_agg = 1)

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## Part 3 - Format the file for Shiny tool ----
###############################################.
quit_total <- readRDS(file=paste0(data_folder, "Temporary/quitattempts_total_formatted.rds")) %>% 
  #creating labels and indicator id
  mutate(trend_axis = paste0(year, "/", substr(year+1, 3, 4)),
         def_period = paste0(trend_axis, " financial year"),
         ind_id = 1505, 
         lowci = NA_real_, 
         upci = NA_real_, 
         rate = numerator) %>%  # use numerator as rate to ensure plots correctly in profiles tool
  # mutate_at(c("lowci", "upci", "rate"),  ~NA_real_) %>% #empty for tool
  select(-denominator) %>% 
  filter(!is.na(code)) #taking out empty rows

#Preparing data for Shiny tool. Including both rds and csv file for now
saveRDS(quit_total, paste0(data_folder, "Data to be checked/quitattempts_total_shiny.rds"))
write_csv(quit_total, paste0(data_folder, "Data to be checked/quitattempts_total_shiny.csv"))

##END