README.md

In fragla/acreular: Methods for Calculating 'ACR' and 'EULAR' based Scores and Classifications

acreular

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.

Installation

You can install acreular from GitHub with the command:

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

Quick Start

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"

Shiny web interface

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.

License

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

fragla/acreular documentation built on June 8, 2020, 2:46 p.m.