wa_agesex_snsro.r

wa_agesex_snsro <- function(username, password, 
                         site_no, user_id, 
                         start_date, end_date) {
  require(httr, quietly = T)
  require(glue, quietly = T)
  require(purrr, quietly = T)
  
  start_date = format(as.Date(start_date) , "%d%b%Y")
  end_date = format(as.Date(end_date) , "%d%b%Y")
  site_no = as.character(site_no)
  
  clean_var_names <- purrr::compose(
    # remove extreme "_"
    function(x) gsub("^_|_$", "", x, perl = T), 
    # remove repeat "_"
    function(x) gsub("(_)(?=_*\\1)", "", x, perl = T), 
    # not [A-Za-z0-9_] and replace with "_"
    function(x) gsub("\\W", "_", x), 
    # parenthesis/bracket and its contents
    function(x) gsub("\\(.+\\)", "", x),
    function(x) gsub("\\[.+\\]", "", x),
    tolower)
  
  url <- glue::glue("https://essence.syndromicsurveillance.org/nssp_essence/api/tableBuilder/csv?endDate={end_date}&ccddCategory=cdc%20suicidal%20ideation%20v1&ccddCategory=cdc%20suicide%20attempt%20v1&ccddCategory=sdc%20suicide%20related%20v1&percentParam=ccddCategory&geographySystem=hospital&datasource=va_hosp&detector=nodetectordetector&startDate={start_date}&timeResolution=monthly&hasBeenE=1&medicalGroupingSystem=essencesyndromes&userId={user_id}&site={site_no}&hospFacilityType=emergency%20care&aqtTarget=TableBuilder&rowFields=timeResolution&rowFields=site&rowFields=patientLoc&rowFields=sex&rowFields=ageTenYear&columnField=ccddCategory")
  
  api_response <- GET(url, authenticate(user = username, password = password))
  
  
  result_site_ageSex <- content(api_response, type = "text/csv") %>%
    set_names(clean_var_names) %>% 
    select(site,
           year_month = timeresolution,
           sex,
           age_ten_year = agetenyear,
           cdc_suicidal_ideation_v1_numerator=cdc_suicidal_ideation_v1_data_count,
           cdc_suicide_attempt_v1_numerator=cdc_suicide_attempt_v1_data_count,
           cdc_suicide_related_v1_numerator=sdc_suicide_related_v1_data_count,
           denominator=cdc_suicidal_ideation_v1_all_count)
  
  resultM_F <- result_site_ageSex %>%
    filter(sex %in% c("Male", "Female"))
  
  resultmissing <- result_site_ageSex %>%
    filter(sex %in% c("Not Reported", "Unknown")) %>%
    group_by(site, year_month, age_ten_year) %>%
    summarise_at(c("cdc_suicidal_ideation_v1_numerator",
                   "cdc_suicide_attempt_v1_numerator",
                   "cdc_suicide_related_v1_numerator",
                   "denominator"), sum) %>%
    mutate(sex = "Missing")
  
  result_site_ageSex <- bind_rows(resultM_F, resultmissing)
  
  result_site_ageSex %>%
    separate(year_month, c("Year", "Month")) %>%
    group_by(site,  Year,  Month, sex,   age_ten_year) %>%
    summarise_at(vars(cdc_suicidal_ideation_v1_numerator, cdc_suicide_attempt_v1_numerator, cdc_suicide_related_v1_numerator, denominator), sum) %>%
    ungroup
  
}