programming assignment 3 hospital quality

Programming Assignment 3: Hospital Quality

My code repository for coursera data science specialization by john hopkins university, assignment instructions.

The data for this assignment come from the Hospital Compare web site (http://hospitalcompare.hhs.gov) run by the U.S. Department of Health and Human Services. The purpose of the web site is to provide data and information about the quality of care at over 4,000 Medicare-certified hospitals in the U.S. This dataset es- sentially covers all major U.S. hospitals. This dataset is used for a variety of purposes, including determining whether hospitals should be fined for not providing high quality care to patients (see http://goo.gl/jAXFX for some background on this particular topic).

The Hospital Compare web site contains a lot of data and we will only look at a small subset for this assignment. The zip file for this assignment contains three files

• 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).

A description of the variables in each of the files is in the included PDF file named Hospital_Revised_Flatfiles.pdf. This document contains information about many other files that are not included with this programming assignment. You will want to focus on the variables for Number 19 (“Outcome of Care Measures.csv”) and Number 11 (“Hospital Data.csv”). You may find it useful to print out this document (at least the pages for Tables 19 and 11) to have next to you while you work on this assignment. In particular, the numbers of the variables for each table indicate column indices in each table (i.e. “Hospital Name” is column 2 in the outcome-of-care-measures.csv file)

More information about the assignment here

Data zip file - link

1 Plot the 30-day mortality rates for heart attack - outcome.R

2 Finding the best hospital in a state - best.R

Write a function called best that take two arguments: the 2-character abbreviated name of a state and an outcome name. The function reads the outcome-of-care-measures.csv file and returns a character vector with the name of the hospital that has the best (i.e. lowest) 30-day mortality for the specified outcome in that state. The hospital name is the name provided in the Hospital.Name variable. The outcomes can be one of “heart attack”, “heart failure”, or “pneumonia”. Hospitals that do not have data on a particular outcome should be excluded from the set of hospitals when deciding the rankings.

3 Ranking hospitals by outcome in a state - rankhospital.R

Write a function called rankhospital that takes three arguments: the 2-character abbreviated name of a state (state), an outcome (outcome), and the ranking of a hospital in that state for that outcome (num). The function reads the outcome-of-care-measures.csv file and returns a character vector with the name of the hospital that has the ranking specified by the num argument. For example, the call rankhospital(“MD”, “heart failure”, 5) would return a character vector containing the name of the hospital with the 5th lowest 30-day death rate for heart failure. The num argument can take values “best”, “worst”, or an integer indicating the ranking (smaller numbers are better). If the number given by num is larger than the number of hospitals in that state, then the function should return NA. Hospitals that do not have data on a particular outcome should be excluded from the set of hospitals when deciding the rankings.

4 Ranking hospitals in all states - rankall.R

Write a function called rankall that takes two arguments: an outcome name (outcome) and a hospital ranking (num). The function reads the outcome-of-care-measures.csv file and returns a 2-column data frame containing the hospital in each state that has the ranking specified in num. For example the function call rankall(“heart attack”, “best”) would return a data frame containing the names of the hospitals that are the best in their respective states for 30-day heart attack death rates. The function should return a value for every state (some may be NA). The first column in the data frame is named hospital, which contains the hospital name, and the second column is named state, which contains the 2-character abbreviation for the state name. Hospitals that do not have data on a particular outcome should be excluded from the set of hospitals when deciding the rankings.

R Programming Assignment 3: Hospital Quality

Introduction.

Download the file ProgAssignment3-data.zip file containing the data for Programming Assignment 3 from the Coursera web site. Unzip the file in a directory that will serve as your working directory. When you start up R make sure to change your working directory to the directory where you unzipped the data.

The data for this assignment come from the Hospital Compare web site ( http://hospitalcompare.hhs.gov ) run by the U.S. Department of Health and Human Services. The purpose of the web site is to provide data and information about the quality of care at over 4,000 Medicare-certified hospitals in the U.S. This dataset essentially covers all major U.S. hospitals. This dataset is used for a variety of purposes, including determining whether hospitals should be fined for not providing high quality care to patients (see http://goo.gl/jAXFX for some background on this particular topic).

The Hospital Compare web site contains a lot of data and we will only look at a small subset for this assignment. The zip file for this assignment contains three files:

• 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).

A description of the variables in each of the files is in the included PDF file named Hospital_Revised_Flatfiles.pdf . This document contains information about many other files that are not included with this programming assignment. You will want to focus on the variables for Number 19 (“Outcome of Care Measures.csv”) and Number 11 (“Hospital Data.csv”). You may find it useful to print out this document (at least the pages for Tables 19 and 11) to have next to you while you work on this assignment. In particular, the numbers of the variables for each table indicate column indices in each table (i.e. “Hospital Name” is column 2 in the outcome-of-care-measures.csv file).

Part 1: Plot the 30-day mortality rates for heart attack

Read the outcome data into R via the read.csv function and look at the first few rows.

There are many columns in this dataset. You can see how many by typing ncol(outcome) (you can see the number of rows with the nrow function). In addition, you can see the names of each column by typing names(outcome) (the names are also in the PDF document).

To make a simple histogram of the 30-day death rates from heart attack (column 11 in the outcome dataset), run

Because we originally read the data in as character (by specifying colClasses = “character” we need to coerce the column to be numeric. You may get a warning about NAs being introduced but that is okay.

There is nothing to submit for this part.

Part 2: Finding the best hospital in a state

Write a function called best that take two arguments: the 2-character abbreviated name of a state and an outcome name. The function reads the outcome-of-care-measures.csv file and returns a character vector with the name of the hospital that has the best (i.e. lowest) 30-day mortality for the specified outcome in that state. The hospital name is the name provided in the Hospital.Name variable. The outcomes can be one of “heart attack”, “heart failure”, or “pneumonia”. Hospitals that do not have data on a particular outcome should be excluded from the set of hospitals when deciding the rankings.

Handling ties. If there is a tie for the best hospital for a given outcome, then the hospital names should be sorted in alphabetical order and the first hospital in that set should be chosen (i.e. if hospitals “b”, “c”, and “f” are tied for best, then hospital “b” should be returned).

The function should use the following template.

The function should check the validity of its arguments. If an invalid state value is passed to best , the function should throw an error via the stop function with the exact message “invalid state”. If an invalid outcome value is passed to best , the function should throw an error via the stop function with the exact message “invalid outcome”.

Here is some sample output from the function.

Save your code for this function to a file named best.R .

Part 3: Ranking hospitals by outcome in a state

Write a function called rankhospital that takes three arguments: the 2-character abbreviated name of a state ( state ), an outcome ( outcome ), and the ranking of a hospital in that state for that outcome ( num ). The function reads the outcome-of-care-measures.csv file and returns a character vector with the name of the hospital that has the ranking specified by the num argument. For example, the call

would return a character vector containing the name of the hospital with the 5th lowest 30-day death rate for heart failure. The num argument can take values “best”, “worst”, or an integer indicating the ranking (smaller numbers are better). If the number given by num is larger than the number of hospitals in that state, then the function should return NA . Hospitals that do not have data on a particular outcome should be excluded from the set of hospitals when deciding the rankings.

Handling ties . It may occur that multiple hospitals have the same 30-day mortality rate for a given cause of death. In those cases ties should be broken by using the hospital name. For example, in Texas (“TX”), the hospitals with lowest 30-day mortality rate for heart failure are shown here.

Note that Cypress Fairbanks Medical Center and Detar Hospital Navarro both have the same 30-day rate (8.7). However, because Cypress comes before Detar alphabetically, Cypress is ranked number 3 in this scheme and Detar is ranked number 4. One can use the order function to sort multiple vectors in this manner (i.e. where one vector is used to break ties in another vector).

The function should check the validity of its arguments. If an invalid state value is passed to rankhospital , the function should throw an error via the stop function with the exact message “invalid state”. If an invalid outcome value is passed to rankhospital , the function should throw an error via the stop function with the exact message “invalid outcome”.

Save your code for this function to a file named rankhospital.R .

Part 4: Ranking hospitals in all states

Write a function called rankall that takes two arguments: an outcome name ( outcome ) and a hospital ranking ( num ). The function reads the outcome-of-care-measures.csv file and returns a 2-column data frame containing the hospital in each state that has the ranking specified in num . For example the function call rankall(“heart attack”, “best”) would return a data frame containing the names of the hospitals that are the best in their respective states for 30-day heart attack death rates. The function should return a value for every state (some may be NA ). The first column in the data frame is named hospital , which contains the hospital name, and the second column is named state , which contains the 2-character abbreviation for the state name. Hospitals that do not have data on a particular outcome should be excluded from the set of hospitals when deciding the rankings.

Handling ties . The rankall function should handle ties in the 30-day mortality rates in the same way that the rankhospital function handles ties.

NOTE : For the purpose of this part of the assignment (and for efficiency), your function should NOT call the rankhospital function from the previous section.

The function should check the validity of its arguments. If an invalid outcome value is passed to rankall , the function should throw an error via the stop function with the exact message “invalid outcome”. The num variable can take values “best”, “worst”, or an integer indicating the ranking (smaller numbers are better). If the number given by num is larger than the number of hospitals in that state, then the function should return NA .

Save your code for this function to a file named rankall.R .

My Solution

A good tutorial.

Link: https://github.com/DanieleP/PA3-tutorial

• 1. Introduction
• 2. Part 1: Plot the 30-day mortality rates for heart attack
• 3. Part 2: Finding the best hospital in a state
• 4. Part 3: Ranking hospitals by outcome in a state
• 5. Part 4: Ranking hospitals in all states
• 6. My Solution
• 8. A Good Tutorial

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In this course you will learn how to program in R and how to use R for effective data analysis. You will learn how to install and configure software necessary for a statistical programming environment and describe generic programming language concepts as they are implemented in a high-level statistical language. The course covers practical issues in statistical computing which includes programming in R, reading data into R, accessing R packages, writing R functions, debugging, profiling R code, and organizing and commenting R code. Topics in statistical data analysis will provide working examples.

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28 videos 9 readings 1 quiz 7 programming assignments

28 videos • Total 129 minutes

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• Subsetting - Basics • 4 minutes
• Subsetting - Lists • 4 minutes
• Subsetting - Matrices • 2 minutes
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1 quiz • Total 30 minutes

• Week 1 Quiz • 30 minutes

7 programming assignments • Total 1,260 minutes

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13 videos 3 readings 2 quizzes 3 programming assignments

13 videos • Total 90 minutes

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• Scoping Rules - Symbol Binding • 10 minutes
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3 readings • Total 30 minutes

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2 quizzes • Total 60 minutes

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• Programming Assignment 1: Quiz • 30 minutes

3 programming assignments • Total 540 minutes

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8 videos 2 readings 1 quiz 2 programming assignments 1 peer review

8 videos • Total 61 minutes

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2 readings • Total 20 minutes

• Week 3: Loop Functions and Debugging • 10 minutes
• Practical R Exercises in swirl Part 3 • 10 minutes
• Week 3 Quiz • 30 minutes

2 programming assignments • Total 360 minutes

• swirl Lesson 1: lapply and sapply • 180 minutes
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1 peer review • Total 60 minutes

• Programming Assignment 2: Lexical Scoping • 60 minutes

Week 4: Simulation & Profiling

This week covers how to simulate data in R, which serves as the basis for doing simulation studies. We also cover the profiler in R which lets you collect detailed information on how your R functions are running and to identify bottlenecks that can be addressed. The profiler is a key tool in helping you optimize your programs. Finally, we cover the str function, which I personally believe is the most useful function in R.

6 videos 4 readings 2 quizzes 3 programming assignments

6 videos • Total 42 minutes

• The str Function • 6 minutes • Preview module
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4 readings • Total 40 minutes

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R Programming Assignment Three

Fraser stark, coursera r programming - hospital care outcomes, introduction.

The data for this assignment come from the Hospital Compare web site ( http://hospitalcompare.hhs.gov ) run by the U.S. Department of Health and Human Services. The purpose of the web site is to provide data and information about the quality of care at over 4,000 Medicare-certified hospitals in the U.S. This dataset essentially covers all major U.S. hospitals. This dataset is used for a variety of purposes, including determining whether hospitals should be fined for not providing high quality care to patients (see http://goo.gl/jAXFX for some background on this particular topic).

Read the data

1. plot the 30-day mortality rates for heart attack, 2. finding the best hospital in a state.

Write a function called best that take two arguments: the 2-character abbreviated name of a state and an outcome name. The function reads the outcome-of-care-measures.csv file and returns a character vector with the name of the hospital that has the best (i.e. lowest) 30-day mortality for the specified outcome in that state. The hospital name is the name provided in the Hospital.Name variable. The outcomes can be one of “heart attack”, “heart failure”, or “pneumonia”. Hospitals that do not have data on a particular outcome should be excluded from the set of hospitals when deciding the rankings.

Some sample outputs

3. Ranking hospitals by outcome in a state

Write a function called rankhospital that takes three arguments: the 2-character abbreviated name of a state (state), an outcome (outcome), and the ranking of a hospital in that state for that outcome (num). The function reads the outcome-of-care-measures.csv file and returns a character vector with the name of the hospital that has the ranking specified by the num argument. For example, the call rankhospital(“MD”, “heart failure”, 5) would return a character vector containing the name of the hospital with the 5th lowest 30-day death rate for heart failure. The num argument can take values “best”, “worst”, or an integer indicating the ranking (smaller numbers are better). If the number given by num is larger than the number of hospitals in that state, then the function should return NA. Hospitals that do not have data on a particular outcome should be excluded from the set of hospitals when deciding the rankings.

Sample outputs

4. Ranking hospitals in all states

Write a function called rankall that takes two arguments: an outcome name (outcome) and a hospital ranking (num). The function reads the outcome-of-care-measures.csv file and returns a 2-column data frame containing the hospital in each state that has the ranking specified in num. For example the function call rankall(“heart attack”, “best”) would return a data frame containing the names of the hospitals that are the best in their respective states for 30-day heart attack death rates. The function should return a value for every state (some may be NA). The first column in the data frame is named hospital, which contains the hospital name, and the second column is named state, which contains the 2-character abbreviation for the state name. Hospitals that do not have data on a particular outcome should be excluded from the set of hospitals when deciding the rankings.

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R Programming Project 3

github repo for rest of specialization: Data Science Coursera

The zip file containing the data can be downloaded here: Assignment 3 Data

Part 1 Plot the 30-day mortality rates for heart attack ( outcome.R )

Part 2 Finding the best hospital in a state ( best.R )

Part 3 ranking hospitals by outcome in a state ( rankhospital.r ), part 4 ranking hospitals in all states ( rankall.r ).

Programming Assignment 3: Quiz >> R Programming

1. What result is returned by the following code?

• CAROLINAS HOSPITAL SYSTEM
• MCLEOD MEDICAL CENTER – DARLINGTON
• MUSC MEDICAL CENTER
• MARY BLACK MEMORIAL HOSPITAL
• LAKE CITY COMMUNITY HOSPITAL
• GRAND STRAND REG MED CENTER

2. What result is returned by the following code?

• MAIMONIDES MEDICAL CENTER
• NORTHERN DUTCHESS HOSPITAL
• HOSPITAL FOR SPECIAL SURGERY
• KINGSBROOK JEWISH MEDICAL CENTER
• BROOKS MEMORIAL HOSPITAL
• CROUSE HOSPITAL

3. What result is returned by the following code?

• PROVIDENCE ALASKA MEDICAL CENTER
• ALASKA NATIVE MEDICAL CENTER
• YUKON KUSKOKWIM DELTA REG HOSPITAL
• CENTRAL PENINSULA GENERAL HOSPITAL
• CORDOVA COMMUNITY MEDICAL CENTER
• MT EDGECUMBE HOSPITAL

4. What result is returned by the following code?

• CATAWBA VALLEY MEDICAL CENTER
• WAYNE MEMORIAL HOSPITAL
• WAKEMED, CARY HOSPITAL
• SPRUCE PINE COMMUNITY HOSPITAL
• CAROLINAS MEDICAL CENTER-NORTHEAST
• THOMASVILLE MEDICAL CENTER

5. What result is returned by the following code?

• YAKIMA VALLEY MEMORIAL HOSPITAL
• KENNEWICK GENERAL HOSPITAL
• ST ANTHONY HOSPITAL
• KADLEC REGIONAL MEDICAL CENTER
• JEFFERSON HEALTHCARE HOSPITAL
• TACOMA GENERAL ALLENMORE HOSPITAL

6. What result is returned by the following code?

• WEST HOUSTON MEDICAL CENTER
• SETON SMITHVILLE REGIONAL HOSPITAL
• MEMORIAL HERMANN NORTHEAST
• PROVIDENCE MEMORIAL HOSPITAL
• UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT TYLER
• SCENIC MOUNTAIN MEDICAL CENTER

7. What result is returned by the following code?

• FOREST HILLS HOSPITAL
• NASSAU UNIVERSITY MEDICAL CENTER
• BELLEVUE HOSPITAL CENTER
• UNIVERSITY HOSPITAL S U N Y HEALTH SCIENCE CENTER
• FLUSHING HOSPITAL MEDICAL CENTER
• ADIRONDACK MEDICAL CENTER

8. What result is returned by the following code?

• NORTH COUNTRY HOSPITAL AND HEALTH CENTER
• CASTLE MEDICAL CENTER
• SANFORD USD MEDICAL CENTER
• ST FRANCIS MEDICAL CENTER
• PARKLAND HEALTH AND HOSPITAL SYSTEM
• CLARK REGIONAL MEDICAL CENTER

9. What result is returned by the following code?

• POTTSTOWN MEMORIAL MEDICAL CENTER
• BERGEN REGIONAL MEDICAL CENTER
• LAURENS COUNTY HEALTHCARE SYSTEM
• TERREBONNE GENERAL MEDICAL CENTER
• BAY AREA HOSPITAL
• LAKES REGION GENERAL HOSPITAL

10. What result is returned by the following code?

• HAWAII MEDICAL CENTER EAST
• RENOWN SOUTH MEADOWS MEDICAL CENTER
• CARY MEDICAL CENTER
• CARONDELET ST JOSEPHS HOSPITAL
• YORK GENERAL HOSPITAL

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