In huangrh/rstarating: CMS Hospital Compare Star Rating Replicate

require(rstarating);require(relvm);require(rclus);require(cmsdata);require(reshape2)

# "C:/rhuang/cmsdata/2018/20180126/Hospital_Revised_Flatfiles",
# "Complications and Deaths - Hospital.csv"  
# "HOSPITAL_QUARTERLY_AHRQ_PSI_90_6decimals.csv"
file <- file.path("T:/Clinical Excellence/Analytics/Data Sources/cmsData/2017/20171221/Hospital_Revised_Flatfiles20171221", 
          "Complications and Deaths - Hospital.csv")

# 
psi_ <- read_csv(file) %>%
  subset(select=c("ccnid","measure_id","score","denominator")) %>%
  subset(.$measure_id %in% grep("psi",.$measure_id,value=T)) %>%
  subset(!(.$measure_id %in% c("psi_4_surg_comp","psi_90_safety")))

psi_score=  psi_%>% 
      dcast(ccnid~measure_id,value.var="score") 
psi_den = psi_ %>% 
      dcast(ccnid~measure_id,value.var="denominator") 

psi <- merge(x=psi_score,y=psi_den,by="ccnid",all=T,suffixes = c("","_den"))

# 
input <- cms_star_rating_input_2017dec %>%
  colnames_wiper("provider_id","ccnid") %>%
  cols_str_wiper(index="ccnid",pattern="^b'0|^b'|'$",with="") %>% 
  subset(select=!(grepl("psi_90_safety",names(.)))) %>%
  merge(y= psi, by="ccnid",all=T)


mtbl <- create_measure_tbl(input) 
mtbl[mtbl$group=="outcome_safty",]

sort_by_group <- function(y) {
  merge(x=create_measure_tbl(mstbl(input)$mstbl_std)[c("name","group")],
        y=y,by="name",all.y=T) %>%
    cols_sort(by=c("group","name"))  %>%
    subset(group == "outcome_safty") %>% 
    rownames_wiper()
}

# Test 1: replace psi90 with 10 of psi 90 componet measures. 
fit1 <- relvm(mstbl(input))

par1 <- sort_by_group(fit1$groups$pars)

# Test 2 : put all the den to 100. 
input2 <- input

for (idx in grep("_den",colnames(input2),value=T)) {
  input2[,idx] <- ifelse(is.na(input2[,idx]),NA, 100)
}
fit2 <- relvm(mstbl(input2))

par2 <- sort_by_group(fit2$groups$pars)

# TEst 3 remove hai_ and comp_hip_knee measure. psi_components only 
input3 <- input2
for (idx in c(grep("comp_hip_knee|hai_",names(input2),value=T))) {
  input3[idx] <- NULL

}

fit3 <- relvm(mstbl(input3))
par3 <- sort_by_group(fit3$groups$pars)

# TEst 4 remove psi_components and comp_hip_knee.  
input4 <- input2
for (idx in c(grep("comp_hip_knee|psi_",names(input4),value=T))) {
  input4[idx] <- NULL

}

fit4 <- relvm(mstbl(input4))
par4 <- sort_by_group(fit4$groups$pars)

# test 5 original denominator, but remove comp_hip_knee and hai_ measures. So 
input5 <- input
for (idx in c(grep("comp_hip_knee|hai_",names(input5),value=T))) {
  input5[idx] <- NULL
}

fit5 <- relvm(mstbl(input5))
par5 <- sort_by_group(fit5$groups$pars)

require(rio)
file <- file.path("T:/Clinical Excellence/Analytics/Personal Development Folders/RenHuai/star/TEP",
                  'cms_star_dec2017_den_100_v3.xlsx')
export(par1,file,which="repalce psi 90",overwrite=T)
export(par2,file,which="then replace den 100",overwrite=T)
export(par3,file,which="psi component only",overwrite=T)
export(par4,file,which="hai only",overwrite=T)
export(par5,file,which="psi_components_den_original",overwrite=T)