HealthCare Data

Health policy researchers and the media download the Hospital Compare database as an easy way to obtain a large set of data regarding outcome of care for a number of different conditions including heart attack, pneumonia, and heart failure. The data in the Downloadable Database come from the data that are displayed on Hospital Compare, but also include additional information about the hospital ownership that is not displayed on the website. You can find Hospital Compare data on data.medicare.gov. This website allows you to view the data files embedded on a webpage without downloading them, but as of July 2013, the downloadable data is not available here.

The collection period for the process of care quality measures is generally 12 months. As new measures are added, the collection period varies.

What was the goal of the project?

In this project, I was interested in querying quality of care for different conditions including heart attack, pneumonia, and heart failure across different states. I wrote a script which allows the user to find hospitals with a given rank of quality of care measures for any of the conditions listed in "outcome-of-care-measures.csv".

First, we read in outcome data and isolate for the columns that we are interested in. In this case, we care about the hospital name, state, and the three health conditions, “heart attack”, “heart failure”, and “pneumonia.”

tableAll <- read.csv("outcome-of-care-measures.csv", colClasses = "character")

tableAll <- tableAll[, c(2, 7, 11, 17, 23)]

names(tableAll) <- c("Hospital.Name", "State", "heart.attack", "heart.failure", "pneumonia")

Next, let’s pretend that we are interested in the outcome “heart failure”. To deal with the way that R names columns, we need to do a tiny bit of processing on the name and check that it is in our dataframe. If it isn’t, we throw an error.

outcome <- "heart failure"

outcome <- gsub(" ", ".", outcome)

## Check that state and outcome are valid

if(!(outcome %in% names(tableAll)))
{
    stop("invalid outcome")
}

Next, we’d like to find hospitals of a given rank in all states. Let’s say we are looking for the “best” hospital in each state for quality of care for heart failure.

num <- 1

tableAll <- data.frame(tableAll[1:2], lapply(tableAll[3:5], as.numeric))
## Warning in lapply(tableAll[3:5], as.numeric): NAs introduced by coercion

## Warning in lapply(tableAll[3:5], as.numeric): NAs introduced by coercion

## Warning in lapply(tableAll[3:5], as.numeric): NAs introduced by coercion
good <- complete.cases(tableAll) #make sure the hospitals have data for the condition we are looking for

tableAll <- tableAll[good,]

s <- split(tableAll, tableAll$State)

s <- lapply(s, function(x) x[order(x[[outcome]], x$Hospital.Name), ])

if(num == "best")
{
    num = 1
}

s <- lapply(s, function(x) if(num <=  nrow(x)) x[num, ] else NA)

s <- do.call(rbind.data.frame, s)

s <- s[order(s$State), ][, c(1,2)]

s
##                                                        Hospital.Name State
## AK                                    MAT-SU REGIONAL MEDICAL CENTER    AK
## AL                                GEORGE H. LANIER MEMORIAL HOSPITAL    AL
## AR                      VA CENTRAL AR. VETERANS HEALTHCARE SYSTEM LR    AR
## AZ                              BANNER GOOD SAMARITAN MEDICAL CENTER    AZ
## CA                                 CENTINELA HOSPITAL MEDICAL CENTER    CA
## CO                                         PARKER ADVENTIST HOSPITAL    CO
## CT                                           YALE-NEW HAVEN HOSPITAL    CT
## DC                                               PROVIDENCE HOSPITAL    DC
## DE                                 BAYHEALTH - KENT GENERAL HOSPITAL    DE
## FL                         FLORIDA HOSPITAL HEARTLAND MEDICAL CENTER    FL
## GA                                            HOUSTON MEDICAL CENTER    GA
## GU                                  GUAM MEMORIAL HOSPITAL AUTHORITY    GU
## HI                                            KUAKINI MEDICAL CENTER    HI
## IA                               MERCY MEDICAL CENTER - CEDAR RAPIDS    IA
## ID                            SAINT ALPHONSUS MEDICAL CENTER - NAMPA    ID
## IL                                    RUSH UNIVERSITY MEDICAL CENTER    IL
## IN                                         ST CATHERINE HOSPITAL INC    IN
## KS                                               HAYS MEDICAL CENTER    KS
## KY                                   OWENSBORO MEDICAL HEALTH SYSTEM    KY
## LA                                    WILLIS KNIGHTON MEDICAL CENTER    LA
## MA                                     ST ELIZABETH'S MEDICAL CENTER    MA
## MD                                   MEDSTAR GOOD SAMARITAN HOSPITAL    MD
## ME                MILES MEMORIAL HOSPITAL (LINCOLN COUNTY HEALTHCARE    ME
## MI                                        HARPER UNIVERSITY HOSPITAL    MI
## MN                        ESSENTIA HEALTH ST JOSEPH'S MEDICAL CENTER    MN
## MO                                        NORTH KANSAS CITY HOSPITAL    MO
## MS                                         SOUTH CENTRAL REG MED CTR    MS
## MT                                      COMMUNITY MEDICAL CENTER INC    MT
## NC                               FIRSTHEALTH MOORE REGIONAL HOSPITAL    NC
## ND                                             ESSENTIA HEALTH-FARGO    ND
## NE                                       FREMONT AREA MEDICAL CENTER    NE
## NH                                          VALLEY REGIONAL HOSPITAL    NH
## NJ                                      EAST ORANGE GENERAL HOSPITAL    NJ
## NM                                     MINERS' COLFAX MEDICAL CENTER    NM
## NV                                             MOUNTAINVIEW HOSPITAL    NV
## NY                                  KINGSBROOK JEWISH MEDICAL CENTER    NY
## OH                                                 FAIRVIEW HOSPITAL    OH
## OK                                     DUNCAN REGIONAL HOSPITAL, INC    OK
## OR                                        PORTLAND VA MEDICAL CENTER    OR
## PA                                    PHILADELPHIA VA MEDICAL CENTER    PA
## PR                                  SAN LUKE'S MEMORIAL HOSPITAL INC    PR
## RI                                                 WESTERLY HOSPITAL    RI
## SC                                           PALMETTO HEALTH BAPTIST    SC
## SD                          AVERA HEART HOSPITAL OF SOUTH DAKOTA LLC    SD
## TN                                         CENTENNIAL MEDICAL CENTER    TN
## TX                                        FORT DUNCAN MEDICAL CENTER    TX
## UT VA SALT LAKE CITY HEALTHCARE - GEORGE E. WAHLEN VA MEDICAL CENTER    UT
## VA                                          SENTARA POTOMAC HOSPITAL    VA
## VI                            GOV JUAN F LUIS HOSPITAL & MEDICAL CTR    VI
## VT                                              SPRINGFIELD HOSPITAL    VT
## WA                                         HARBORVIEW MEDICAL CENTER    WA
## WI                                    AURORA ST LUKES MEDICAL CENTER    WI
## WV                                         FAIRMONT GENERAL HOSPITAL    WV
## WY                                  CHEYENNE REGIONAL MEDICAL CENTER    WY

We can check for the best hospital for heart failure in California with

s["CA",]
##                        Hospital.Name State
## CA CENTINELA HOSPITAL MEDICAL CENTER    CA