SimplyAgree

SimplyAgree: An R package and jamovi Module for Simplifying Agreement and Reliability Analyses - Published in JOSS (2022)

https://github.com/arcaldwell49/simplyagree

Keywords from Contributors

Scientific Fields

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A simple R package for calculating absolute agreement and estimating required sample sizes for studies of absolute agreement

README.Rmd

---
title: "SimplyAgree R Package"
output: github_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(SimplyAgree)
#![Sticker](https://raw.githubusercontent.com/arcaldwell49/SimplyAgree/master/images/sticker.png)
```




*Artwork courtesy of Chelsea Parlett Pelleriti*


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Please see the package's [website](https://aaroncaldwell.us/SimplyAgree/) for updates, vignettes, and other details about the package.

# Background

`SimplyAgree` is an R package, and [jamovi](https://www.jamovi.org/) module, created to make agreement and reliability analyses easier for the average researcher. The two primary functions are `agreement_limit` and `tolerance_limit` for assessing "agreement" between two methods. Reliability can be assessed via the `reli_stats`, or `reli_aov`, function. In addition, `blandPowerCurve` could be utilized for power analysis purposes for studies of agreement.

## Installing SimplyAgree

You can install the most up-to-date version of `SimplyAgree` from
[GitHub](https://github.com/arcaldwell49/SimplyAgree) with:

``` r
devtools::install_github("arcaldwell49/SimplyAgree")
```

# Contributing

We are happy to receive bug reports, suggestions, questions, and (most
of all) contributions to fix problems and add features. Pull Requests
for contributions are encouraged.

Here are some simple ways in which you can contribute (in the increasing
order of commitment):

-   Read and correct any inconsistencies in the documentation
-   Raise issues about bugs or wanted features
-   Review code
-   Add new functionality


## Code of Conduct

Please note that the concurve project is released with a [Contributor
Code of
Conduct](https://aaroncaldwell.us/SimplyAgree/CODE_OF_CONDUCT.html). By
contributing to this project, you agree to abide by its terms.

# References

The functions in this package are largely based on the following works:

Francq, B. G., Berger, M., & Boachie, C. (2020). To tolerate or to agree: A tutorial on tolerance intervals in method comparison studies with BivRegBLS R Package. *Statistics in Medicine*, 39(28), 4334-4349. 

Francq, B. G., Lin, D., & Hoyer, W. (2019). Confidence, prediction, and tolerance in linear mixed models. *Statistics in Medicine*, 38(30), 5603-5622. 

Lin L (1989). A concordance correlation coefficient to evaluate reproducibility. *Biometrics* 45: 255 - 268. 

Shieh, G. (2019). Assessing agreement between two methods of quantitative measurements: Exact test procedure and sample size calculation. *Statistics in Biopharmaceutical Research*, 1-8. 

Parker, R. A., et al (2016). Application of mixed effects limits of agreement in the presence of multiple sources of variability: exemplar from the comparison of several devices to measure respiratory rate in COPD patients. Plos one, 11(12), e0168321. 

Zou, G. Y. (2013). Confidence interval estimation for the Bland–Altman limits of agreement with multiple observations per individual. *Statistical methods in medical research*, 22(6), 630-642. 

Weir, J. P. (2005). Quantifying test-retest reliability using the intraclass correlation coefficient and the SEM. *The Journal of Strength & Conditioning Research*, 19(1), 231-240.

Lu, Meng-Jie, et al (2016). "Sample Size for Assessing Agreement between Two Methods of Measurement by Bland−Altman Method" *The International Journal of Biostatistics*, 12(2),  

King, TS and Chinchilli, VM. (2001). A generalized concordance correlation coefficient for continuous and categorical data. *Statistics in Medicine*, 20, 2131:2147.

King, TS, Chinchilli, VM, and Carrasco, JL. (2007). A repeated measures concordance correlation coefficient. *Statistics in Medicine*, 26, 3095:3113.

Carrasco, JL, et al. (2013). Estimation of the concordance correlation coefficient for repeated measures using SAS and R. *Computer Methods and Programs in Biomedicine*, 109, 293-304.

Owner

JOSS Publication

SimplyAgree: An R package and jamovi Module for Simplifying Agreement and Reliability Analyses

Published

March 22, 2022

DOI

10.21105/joss.04148

Volume 7, Issue 71, Page 4148

Authors

Aaron R. Caldwell
United States Army Research Institute of Environmental Medicine, Natick, MA, the United States of America, Oak Ridge Institute of Science and Education, Oak Ridge, TN, the United States of America

Editor

Frederick Boehm

Tags

statistics reliability agreement Bland-Altman

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