stephenrho

# https://www.countyhealthrankings.org/explore-health-rankings/our-methods/calculating-ranks

library(data.table)

chr = fread("https://www.countyhealthrankings.org/sites/default/files/media/document/analytic_data2022.csv", skip = 1)

# https://www.countyhealthrankings.org/sites/default/files/media/document/2022%20Ranked%20and%20Additional%20Measures%2C%20Data%20Sources%20and%20Years_0.pdf
measures = list(
  # note some are reverse coded (see -ve weights)
  health_behaviors = list(

stephenrho

# model from Sheyn et al. https://pubmed.ncbi.nlm.nih.gov/35830590/
# predictions recalibrated by Rhodea et al. [unpublished, will add link when published]
# set recalibrate = FALSE for original model
cms_model = function(Age, PVD=0, Diabetes_complicated=0, COPD=0, 
                     Mesh=0, Abdominal_sacrocolpopexy=0, Sling=0, 
                     Transfusion=0, Bowel_injury=0, Hemiplegia_or_paraplegia=0, 
                     return_lin_pred=FALSE, recalibrate = TRUE, intercept = -2.18, slope = 0.66){
  # Age = in years
  # PVD = Current peripheral vascular disease

stephenrho

# Note: I have only tested this on 2016-2020
# need `fs` and `readr` installed

#' Get NIS file specifications
#' 
#' @description
#' Uses stata load files from hcup-us.ahrq.gov to get specs for loading NIS files
#' 
#' @param year of interest
#' @param file "Core", "Hospital", or "Severity"

stephenrho

query_fda <- function(dname, route){
  dname <- gsub(" ", "%", dname)
  dname <- sprintf('"%s"', dname) # enclose in quotes
  
  if (!missing(route) & !is.null(route)){
    dname <- sprintf('%s+AND+route:"%s"', dname, route)
   }
  
  url <- sprintf('https://api.fda.gov/drug/ndc.json?search=generic_name:%s&limit=100', dname)
  res <- httr::GET(url)$content |>