Analyzing Hospital Patient Outcomes using R

Data Analysis is increasingly becoming more and more important in healthcare. Hospitals are using Big Data to make decisions and improve patient care. At the same time, patients are using Big Data, or more likely the published results, to make decisions about where to receive healthcare. There is at least a third element as well, and that is that governments and agencies may use this data to actually impose fines against institutions not meeting certain minimums of care. One site which you can use to get large amounts of data on healthcare institutions is the Hospital Compare website http://hospitalcompare.hhs.gov. The website contains information about the quality and care at over 4,000 Medicare-certified hospitals in the U.S. In a recent school project I analyzed some of the Hospital Compare data. Specifically I used the following files, which represent only a small portion of the data available:

• outcome-of-care-measures.csv: Contains information about 30-day mortality and readmission rates for heart attacks, heart failure, and pneumonia for over 4,000 hospitals. • hospital-data.csv: Contains information about each hospital. • Hospital_Revised_Flatfiles.pdf: Descriptions of the variables in each file (i.e the code book). The data itself is in a raw format, giving all of the information necessary to mine all kinds of good information. I used this data, the R programming language, and its Lattice and Base graphics packages to make several analysis. I am presenting a few here along with the code that I used. Heart Attack 30-day Death Rate by State In this analysis, I composed a box-whiskers plot of the 30-day Death Rate by State for Heart Attack. I ranked the entire graphic by the median death rate for the state to give an appealing visualization. I removed states that contained less than 20 hospitals.

hospital state

1 CRESTWOOD MEDICAL CENTER AL

2 PROVIDENCE ALASKA MEDICAL CENTER AK

3 MAYO CLINIC HOSPITAL AZ

4 ARKANSAS HEART HOSPITAL AR

5 GLENDALE ADVENTIST MEDICAL CENTER CA

6 ST MARYS HOSPITAL AND MEDICAL CENTER CO

7 WATERBURY HOSPITAL CT

8 BAYHEALTH - KENT GENERAL HOSPITAL DE

9 PROVIDENCE HOSPITAL DC

10 MOUNT SINAI MEDICAL CENTER FL

11 STEPHENS COUNTY HOSPITAL GA

12 HILO MEDICAL CENTER HI

13 PORTNEUF MEDICAL CENTER ID

14 SAINT JOSEPH HOSPITAL IL

15 ST VINCENT HEART CENTER OF INDIANA LLC IN

16 MARY GREELEY MEDICAL CENTER IA

17 KANSAS HEART HOSPITAL KS

18 ST ELIZABETH MEDICAL CENTER NORTH KY

19 ST FRANCIS MEDICAL CENTER LA

20 YORK HOSPITAL ME

21 JOHNS HOPKINS HOSPITAL, THE MD

22 BETH ISRAEL DEACONESS MEDICAL CENTER MA

23 MUNSON MEDICAL CENTER MI

24 ST MARYS HOSPITAL MN

25 WESLEY MEDICAL CENTER MS

26 BOONE HOSPITAL CENTER MO

27 BENEFIS HOSPITALS INC MT

28 FAITH REGIONAL HEALTH SERVICES NE

29 SUNRISE HOSPITAL AND MEDICAL CENTER NV

30 CATHOLIC MEDICAL CENTER NH

31 EAST ORANGE GENERAL HOSPITAL NJ

32 ST VINCENT HOSPITAL NM

33 NYU HOSPITALS CENTER NY

34 CAROLINAS MEDICAL CENTER-NORTHEAST NC

35 SANFORD MEDICAL CENTER FARGO ND

36 JEWISH HOSPITAL, LLC OH

37 OKLAHOMA HEART HOSPITAL SOUTH OK

38 PORTLAND VA MEDICAL CENTER OR

39 DOYLESTOWN HOSPITAL PA

40 HOSPITAL DR CAYETANO COLL Y TOSTE PR

41 MIRIAM HOSPITAL RI

42 MUSC MEDICAL CENTER SC

43 AVERA HEART HOSPITAL OF SOUTH DAKOTA LLC SD

44 METHODIST MEDICAL CENTER OF OAK RIDGE TN

45 CYPRESS FAIRBANKS MEDICAL CENTER TX

46 DIXIE REGIONAL MEDICAL CENTER UT

47 FLETCHER ALLEN HOSPITAL OF VERMONT VT

48 ROY LESTER SCHNEIDER HOSPITAL,THE VI

49 CHESAPEAKE REGIONAL MEDICAL CENTER VA

50 PROVIDENCE SACRED HEART MEDICAL CENTER WA

51 MONONGALIA COUNTY GENERAL HOSPITAL WV

52 BELLIN MEMORIAL HSPTL WI

53 WYOMING MEDICAL CENTER WY

54 GUAM MEMORIAL HOSPITAL AUTHORITY GU

The Worst

1 HELEN KELLER MEMORIAL HOSPITAL AL

2 MAT-SU REGIONAL MEDICAL CENTER AK

3 VERDE VALLEY MEDICAL CENTER AZ

4 MEDICAL CENTER SOUTH ARKANSAS AR

5 METHODIST HOSPITAL OF SACRAMENTO CA

6 NORTH SUBURBAN MEDICAL CENTER CO

7 JOHNSON MEMORIAL HOSPITAL CT

8 ST FRANCIS HEALTHCARE DE

9 HOWARD UNIVERSITY HOSPITAL DC

10 PALMETTO GENERAL HOSPITAL FL

11 WEST GEORGIA MEDICAL CENTER GA

12 PALI MOMI MEDICAL CENTER HI

13 EASTERN IDAHO REGIONAL MEDICAL CENTER ID

14 SAINT ANTHONY MEDICAL CENTER IL

15 MARION GENERAL HOSPITAL IN

16 BOONE COUNTY HOSPITAL IA

17 OLATHE MEDICAL CENTER KS

18 MURRAY-CALLOWAY COUNTY HOSPITAL KY

19 RIVER PARISHES HOSPITAL LA

20 PENOBSCOT VALLEY HOSPITAL ME

21 HARFORD MEMORIAL HOSPITAL MD

22 NOBLE HOSPITAL MA

23 HURLEY MEDICAL CENTER MI

24 HEALTHEAST ST JOHN'S HOSPITAL MN

25 SOUTHWEST MS REGIONAL MEDICAL CENTER MS

26 POPLAR BLUFF REGIONAL MEDICAL CENTER MO

27 BOZEMAN DEACONESS HOSPITAL MT

28 OMAHA VA MEDICAL CENTER (VA NEBRASKA WESTERN IOWA HEALTHCARE SYSTEM) NE

29 DESERT SPRINGS HOSPITAL NV

30 FRANKLIN REGIONAL HOSPITAL NH

31 ROBERT WOOD JOHNSON UNIVERSITY HOSPITAL AT RAHWAY NJ

32 MOUNTAIN VIEW REGIONAL MEDICAL CENTER NM

33 F F THOMPSON HOSPITAL NY

34 WAYNE MEMORIAL HOSPITAL NC

35 ALTRU HOSPITAL ND

36 MERCY FRANCISCAN HOSPITAL WESTERN HILLS OH

37 MERCY MEMORIAL HEALTH CENTER OK

38 THREE RIVERS COMMUNITY HOSPITAL OR

39 EPHRATA COMMUNITY HOSPITAL PA

40 DOCTORS' CENTER HOSPITAL, INC PR

41 WESTERLY HOSPITAL RI

42 WACCAMAW COMMUNITY HOSPITAL SC

43 PRAIRIE LAKES HOSPITAL SD

44 DYERSBURG REGIONAL MEDICAL CENTER TN

45 LAREDO MEDICAL CENTER TX

46 ST MARKS HOSPITAL UT

47 NORTHEASTERN VERMONT REGIONAL HOSPITAL VT

48 GOV JUAN F LUIS HOSPITAL & MEDICAL CTR VI

49 RIVERSIDE TAPPAHANNOCK HOSPITAL VA

50 KADLEC REGIONAL MEDICAL CENTER WA

51 THOMAS MEMORIAL HOSPITAL WV

52 HOLY FAMILY MEMORIAL INC WI

53 SHERIDAN MEMORIAL HOSPITAL WY

54 GUAM MEMORIAL HOSPITAL AUTHORITY GU

The code:

rankall <- function(outcome, num = "best") { ## Read outcome data outcomeData <- read.csv("outcome-of-care-measures.csv", colClasses = "character") if (outcome != "heart attack" && outcome != "heart failure" && outcome != "pneumonia") { stop("Invalid Outcome") } hospital <- character() statevector <- character() ## Return hospital name in that state with lowest 30-day death rate for(state in unique(outcomeData$State)) { stateIndex = which(outcomeData$State == state) outcomeDataState <- outcomeData if(outcome == "heart attack") { outcomeData.sorted <- outcomeDataState[order(as.numeric(outcomeDataState<,11>), outcomeDataState<,2>, na.last = NA),] } else if(outcome == "heart failure") { outcomeData.sorted <- outcomeDataState[order(as.numeric(outcomeDataState<,17>), outcomeDataState<,2>, na.last = NA),] } else if(outcome == "pneumonia") { outcomeData.sorted <- outcomeDataState[order(as.numeric(outcomeDataState<,23>), outcomeDataState<,2>, na.last = NA),] } if(num == "best") { rownum = 1 } else if(num == "worst") { rownum = nrow(outcomeData.sorted) } else { rownum = num } hospital <- c(hospital,outcomeData.sorted) statevector <- c(statevector,state) } df <- data.frame(hospital = hospital,state = statevector) return(df) }