Charlson Comorbidity Index Calculator

The Charlson index is a commonly used tool to assess medical commodities, and to adjust for risk in health-care services and research 1, 2. Electronic medical records(EMR) are widespread today, and diagnosis codes are usually easily extracted from the EMR. The program here processes ICD9 codes for a given number of patients, and produces a Charlson comorbidity table along with a calculated Charlson score.

How to use the program

The program is written in the R programming language 3. It requires R to be installed, along with the following packages: reshape2, plyr, and ggplot2. In order to use the program, you will have to add patient identifiers, along with corresponding ICD9 codes to the input folder. With this current built, some test patients are added so that the program can run. Here is what you need to do:

• Replace Patients1.csv. This file contains patients identifiers (MRN), date of birth (DOB), and date of hospitalization (DOH). Here is how the file look like:

##   MRN        DOB        DOH
## 1  26 1941-11-30 2014-02-19
## 2  27 1942-07-26 2012-04-14
## 3  28 1959-11-12 2014-03-16
## 4  29 1976-08-10 2014-06-19
## 5  30 1934-09-22 2013-09-17
## 6  31 1936-02-22 2014-01-10

• Replace Patients2.csv. This file contains the ICD9 codes along with the dates when the diagnoses were made. Here is how the file looks like:

##   MRN  ICD9 DiagnosisDate
## 1  26 27541    2013-12-18
## 2  26 27541    2013-12-21
## 3  26 27541    2013-12-24
## 4  26 27541    2013-12-28
## 5  26 27541    2013-12-31
## 6  26 27541    2014-01-01

• All the dates should be in the following format: YYYY-MM-DD

• ICD9 codes are formatted as series of digits with no spaces or other characters(such as .). For example, an ICD9 code of 275.41 or 275 41 or 275-41 should be entered as 27541.

• Note also that leading 0 in ICD9 codes are important. For example an ICD9 code of 0021 should not be entered as 21.

• The program defaults to only accepting ICD9 diagnoses that were made within 5 years of the hospitalization date. However, you can change this by changing the number in CharlsonRules4.csv file.

• After you change the files as outlined above, run CharlsonCalc.R file. Make sure that the working directory is set to where this file is. You can use setwd function to change the working directory.

Output

The information is processed, and two files are written to the output folder. Charlson.csv is a table with the patients, their comorbidities, and their Charlson score. Graph.png summarizes the comorbidities for all patients. A snapshot of the output is shown below. Your feedback is always appreciated. Thanks!

##                                  [,1]    [,2]    [,3]    [,4]    [,5]   
## MRN                              "26"    "27"    "28"    "29"    "30"   
## Myocardial Infarction            "FALSE" "FALSE" "FALSE" "FALSE" " TRUE"
## Congestive Heart Failure         "FALSE" " TRUE" "FALSE" "FALSE" " TRUE"
## Peripheral Vascular Disease      " TRUE" "FALSE" "FALSE" "FALSE" "FALSE"
## Cerebrovascular Disease          "FALSE" " TRUE" " TRUE" "FALSE" "FALSE"
## Dementia                         "FALSE" "FALSE" "FALSE" "FALSE" "FALSE"
## Chronic Pulmonary Disease        "FALSE" " TRUE" "FALSE" "FALSE" " TRUE"
## Connective Tissue Disease        "FALSE" " TRUE" "FALSE" "FALSE" "FALSE"
## Peptic Ulcer Disease             "FALSE" "FALSE" "FALSE" "FALSE" "FALSE"
## Mild Liver Disease               "FALSE" "FALSE" " TRUE" "FALSE" "FALSE"
## Diabetes without Complications   "FALSE" "FALSE" " TRUE" "FALSE" "FALSE"
## Diabetes with Complications      "FALSE" "FALSE" " TRUE" " TRUE" "FALSE"
## Hemiplegia or Paraplegia         "FALSE" "FALSE" "FALSE" "FALSE" "FALSE"
## Moderate or Severe Renal Disease "TRUE"  "TRUE"  "TRUE"  "TRUE"  "TRUE" 
## Malignancy without Metastases    "FALSE" "FALSE" "FALSE" "FALSE" "FALSE"
## Lymphoma or Leukemia             "FALSE" "FALSE" "FALSE" "FALSE" "FALSE"
## Moderate or Severe Liver Disease "FALSE" "FALSE" " TRUE" "FALSE" "FALSE"
## Metastatic Solid Tumor           "FALSE" "FALSE" "FALSE" "FALSE" "FALSE"
## AIDS                             "FALSE" "FALSE" "FALSE" "FALSE" "FALSE"
## Charlson Score                   "6"     "9"     "9"     "4"     "8"    
##                                  [,6]    [,7]    [,8]    [,9]    [,10]  
## MRN                              "31"    "32"    "33"    "34"    "35"   
## Myocardial Infarction            "FALSE" "FALSE" " TRUE" "FALSE" "FALSE"
## Congestive Heart Failure         " TRUE" "FALSE" " TRUE" " TRUE" "FALSE"
## Peripheral Vascular Disease      "FALSE" "FALSE" " TRUE" "FALSE" " TRUE"
## Cerebrovascular Disease          "FALSE" " TRUE" "FALSE" "FALSE" "FALSE"
## Dementia                         "FALSE" "FALSE" "FALSE" "FALSE" "FALSE"
## Chronic Pulmonary Disease        "FALSE" "FALSE" "FALSE" "FALSE" "FALSE"
## Connective Tissue Disease        "FALSE" "FALSE" "FALSE" " TRUE" "FALSE"
## Peptic Ulcer Disease             "FALSE" "FALSE" "FALSE" "FALSE" "FALSE"
## Mild Liver Disease               "FALSE" "FALSE" "FALSE" "FALSE" " TRUE"
## Diabetes without Complications   " TRUE" "FALSE" " TRUE" "FALSE" " TRUE"
## Diabetes with Complications      " TRUE" "FALSE" " TRUE" "FALSE" "FALSE"
## Hemiplegia or Paraplegia         "FALSE" "FALSE" "FALSE" "FALSE" "FALSE"
## Moderate or Severe Renal Disease "TRUE"  "TRUE"  "TRUE"  "TRUE"  "TRUE" 
## Malignancy without Metastases    "FALSE" "FALSE" "FALSE" "FALSE" "FALSE"
## Lymphoma or Leukemia             "FALSE" "FALSE" "FALSE" "FALSE" "FALSE"
## Moderate or Severe Liver Disease "FALSE" "FALSE" "FALSE" "FALSE" " TRUE"
## Metastatic Solid Tumor           "FALSE" "FALSE" "FALSE" "FALSE" "FALSE"
## AIDS                             "FALSE" "FALSE" "FALSE" "FALSE" "FALSE"
## Charlson Score                   "8"     "5"     "9"     "5"     "9"