COPD Rehab

The National Heart Lung and Blood Institute gives the following explanation of COPD: COPD, or chronic obstructive pulmonary (PULL-mun-ary) disease, is a progressive disease that makes it hard to breathe. “Progressive” means the disease gets worse over time. COPD can cause coughing that produces large amounts of mucus (a slimy substance), wheezing, shortness of breath, chest tightness, and other symptoms. Cigarette smoking is the leading cause of COPD. Most people who have COPD smoke or used to smoke. Long-term exposure to other lung irritants, such as air pollution, chemical fumes, or dust, also may contribute to COPD. A study was conducted in the United Kingdom to determine if there is a difference in the effectiveness of community-based rehabilitation program compared to hospital-based rehabilitation. Because hospital-based rehabilitation tends to be more expensive, the researchers wanted to assess if there is a significant difference in the patients’ improvement under the two programs. If not, then it makes sense to refer patients to the less expensive treatment option. Patients suffering from COPD were randomly assigned to either the community or hospital group. Twice a week for six weeks, they participated in two-hour educational and exercise sessions. Patients were also encouraged to exercise between sessions. The effectiveness of the program was measured based on the total distance patients could walk at one time at a particular pace. This is called the endurance shuttle walking test (ESWT). This was measured at the beginning of the study and again at the end of the six-week rehabilitation period. Negative values indicate that the distance decreased.
MATH221
health
Author

MATH 221

Published

May 2, 2024

Data details

There are 85 rows and 2 columns. The data source1 is used to create our data that is stored in our pins table. You can access this pin from a connection to posit.byui.edu using hathawayj/copd_rehab.

This data is available to all.

Variable description

  • Community: Difference in ESWT score over course of study for participants in community-based rehab.
  • Hospital: Difference in ESWT score over course of study for participants in hospital-based rehab. Note: Higher scores indicate improvement, and negative scores indicate deterioration.

Variable summary

Variable type: numeric

skim_variable n_missing complete_rate mean sd p0 p25 p50 p75 p100 hist
Community 9 0.89 216.12 339.90 -402 -40.5 169.5 444.25 1000 ▃▇▅▃▂
Hospital 0 1.00 283.38 359.94 -540 -1.0 292.0 525.00 1031 ▁▇▇▇▃ 
NULL
Explore generating code using R 
library(tidyverse)
library(pins)
library(connectapi)

copd_rehab <- read_csv('https://github.com/byuistats/data/raw/master/COPD-Rehab/COPD-Rehab.csv')


# Publish the data to the server with Bro. Hathaway as the owner.
board <- board_connect()
pin_write(board, copd_rehab, type = "parquet", access_type = "all")

pin_name <- "copd_rehab"
meta <- pin_meta(board, paste0("hathawayj/", pin_name))
client <- connect()
my_app <- content_item(client, meta$local$content_id)
set_vanity_url(my_app, paste0("data/", pin_name))

Access data

This data is available to all.

Direct Download: copd_rehab.parquet

R and Python Download:

URL Connections:

For public data, any user can connect and read the data using pins::board_connect_url() in R.

library(pins)
url_data <- "https://posit.byui.edu/data/copd_rehab/"
board_url <- board_connect_url(c("dat" = url_data))
dat <- pin_read(board_url, "dat")

Use this custom function in Python to have the data in a Pandas DataFrame.

import pandas as pd
import requests
from io import BytesIO

def read_url_pin(name):
  url = "https://posit.byui.edu/data/" + name + "/" + name + ".parquet"
  response = requests.get(url)
  if response.status_code == 200:
    parquet_content = BytesIO(response.content)
    pandas_dataframe = pd.read_parquet(parquet_content)
    return pandas_dataframe
  else:
    print(f"Failed to retrieve data. Status code: {response.status_code}")
    return None

# Example usage:
pandas_df = read_url_pin("copd_rehab")

Authenticated Connection:

Our connect server is https://posit.byui.edu which you assign to your CONNECT_SERVER environment variable. You must create an API key and store it in your environment under CONNECT_API_KEY.

Read more about environment variables and the pins package to understand how these environment variables are stored and accessed in R and Python with pins.

library(pins)
board <- board_connect(auth = "auto")
dat <- pin_read(board, "hathawayj/copd_rehab")
import os
from pins import board_rsconnect
from dotenv import load_dotenv
load_dotenv()
API_KEY = os.getenv('CONNECT_API_KEY')
SERVER = os.getenv('CONNECT_SERVER')

board = board_rsconnect(server_url=SERVER, api_key=API_KEY)
dat = board.pin_read("hathawayj/copd_rehab")