The American College of Rheumatology (ACR) and the European League Against Rheumatism (EULAR) individually and collaboratively have produced diagnositic classification, response and functional status criteria for a range of different rheumatic diseases. The acreular package aims to bring together methods for calculating these measures into a single R package, making it simpler to calculate these values for whole patient cohorts. Calculations can be performed either from within R or by using the accompanying web application, which also enables the graphical visualisation of data and the calculation of comparative statistics.

The package is currently focused on ACR/EULAR RA related disease measures. However, we plan to further develop the package by adding additional RA related criteria and by adding ACR/EULAR related measures for other rheumatic disorders.

You can install acreular from GitHub with the command:

 # install.packages("devtools")
 devtools::install_github("fragla/acreular")

Load the package

library(acreular)

ACR/EULAR 2010 calculation

#create an acreular object

#using duration in days and apr and serology classifications
obj1 <- acrEularRA(ljc=8, sjc=12, duration=43, apr="Normal", serology="High")

#using onset/assessment dates and CRP/ESR, CCP/RF measurements (cut offs can be configured)
obj2 <- acrEularRA(ljc=8, sjc=12,
              onset=as.Date("2010-01-01"), assessment=as.Date("2010-02-13"),
              crp=5, esr=12, ccp=32, rf=71)

#both ways create identical objects
all.equal(obj1, obj2)
#> [1] TRUE

acrEularRAClassification(obj1)
#> [1] "RA (ACR/EULAR 2010)"

EULAR response

#single calculation
eularResponse(5.31, 1.3)
#> [1] "Good"

#multiple calculations
baseline <- c(5.24, 3.6, 1.2)
followup <- c(1.30, 3.3, 1.8)

eularResponse(baseline, followup)
#> [1] "Good"        "No response" "No response"

ACR 20/50/70

#create an acr objects
acr1 <- acrRA(sjc=8, tjc=12, ptGA=50, ptPain=35, phGA=60, haq=0.850, apr=15)
acr2 <- acrRA(sjc=4, tjc=7, ptGA=20, ptPain=25, phGA=30, haq=0.350, apr=10)

acrResponse(acr1, acr2)
#> [1] "ACR20"

The calculation (and visualisation) of ACR/EULAR classifications and EULAR response can also be performed by upload of a CSV or Excel file using the packaged Shiny app. This requires the shiny, DT, FSA, ggplot2, ggiraph, ggiraphExtra, mime, PMCMRplus, readxl, shinycssloaders and shinyWidgets packages. The CSV/Excel headers should be the same as the names of the vector passed to the acrEularRA function i.e. ljc, sjc, duration (or onset/assessment dates), apr classification (or CRP/ESR measurement) and serology classification (or CCP/RF measurement). Example data files are included with the web application.

The app is launched using the shiny_acreular function.

shiny_acreular()

Alternatively, it can be accessed without installing R/Shiny/eq5d by visiting shinyapps.io.

This project is licensed under the MIT License - see the LICENSE.md file for details.