Bland-Altman Method Comparison

Carries out Bland Altman analyses (also known as a Tukey mean-difference plot) as described by JM Bland and DG Altman in 1986 . This package was created in 2015 as existing Bland-Altman analysis functions did not calculate confidence intervals. This package was created to rectify this, and create reproducible plots. This package is also available as a module for the 'jamovi' statistical spreadsheet (see < https://www.jamovi.org> for more information).


blandr carries out Bland Altman analyses (also known as a Tukey mean-difference plot) as described by JM Bland and DG Altman in 1986.

This package was started in 2015 as existing Bland-Altman R functions did not calculate confidence intervals. The blandr was created to fulfil this need.

blandr has been improved iteratively over time, and hopefully this library will be useful to researchers as an open-source and reproducible package.

The benefits

  • Calculates confidence intervals
  • Outputs ggplot2 information to create extensible plots
  • Has a basic Jamovi module, to allow GUI analysis for those not comfortable with command line tools
  • Has a function to chart for proportional bias
  • If you get me through GitHub, I will do my best to maintain and improve this package

Citations

You can find the citation information through the usual R citation commands:

citation("blandr")
#> To cite blandr in publications, please use:
#> 
#>   Datta, D. (2017). blandr: a Bland-Altman Method Comparison
#>   package for R. Zenodo. DOI:10.5281/zenodo.824514
#>   https://github.com/deepankardatta/blandr
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {blandr: a Bland-Altman Method Comparison package for R},
#>     author = {Deepankar Datta},
#>     doi = {10.5281/zenodo.824514},
#>     year = {2017},
#>     url = {https://github.com/deepankardatta/blandr},
#>   }

The DOI will refer to all versions of blandr. If you need to cite specific releases DOIs, the full versioning information can be found at Zenodo (https://zenodo.org/record/824515), with the full source code at the blandr GitHub page (https://github.com/deepankardatta/blandr/).

Installation

blandr is available as a package from CRAN and can be installed with the following commands:

install.packages("blandr")
library(blandr)

You can install the blandr development version, hosted on github at https://github.com/deepankardatta/blandr/, with the following commands:

install.packages("devtools")
devtools::install_github("deepankardatta/blandr")

Example

This is a basic example which shows you how to solve a common problem:

library(blandr)
load(file="Data/bland.altman.PEFR.1986.rda")
blandr.display ( bland.altman.PEFR.1986$WrightFirst , bland.altman.PEFR.1986$MiniWrightFirst , sig.level=0.95 )
blandr.draw( bland.altman.PEFR.1986$WrightFirst , bland.altman.PEFR.1986$MiniWrightFirst )

The Jamovi module

One of the benefits of the current version is that it includes a basic module for the Jamovi GUI statistical spreadsheet (https://www.jamovi.org/). I'm a believer in making this tool more accesible and Jamovi is a way to do this. The Jamovi module is still under development, and will be submitted to the Jamovi module repository soon. However until this is done, it can be installed using the following commands:

install.packages('jmvtools', repos=c('https://repo.jamovi.org', 'https://cran.r-project.org'))
library(jmvtools)
jmvtools::install()

Why the name?

Thinking of a unique name was difficult - and it wasn't worth spending/wasting time on this initially. Curiously it was going to be called BlandAltmanEdinburgh (as I was in Edinburgh at the time I made this) until I considerd uploading this to GitHub and CRAN.

Hadley Wickham has an excellent set of documentation on creating packages. The one on naming (http://r-pkgs.had.co.nz/package.html) is worth a read. Reflecting on it a lot of the naming issues are to prevent collisions with similarly named packages, so using blandaltman in the name might have cause problems. Mirroring the pre-existing plyr and knitr I thought I'd just add a "r" to "bland": yes it doesn't involve Altman's name, but I couldn't think of anything better.

If you can think of a better name please let me know!

Further information

Further information can be found in the function help files in the package, as well as in the vignettes.

Future improvements

Whilst this package is good enough for use, there is the scope for iterative improvements.

Future works include:

  • There are a further few deprecated functions to delete (I just need to finish a few projects first!!).
  • The package needs to have to go through some validation and testing
  • For further testing I need to write some testhtat modules
  • The function descriptions needs to be improved
  • Some of the roxygen2 documentation can be improved by calling the import parameters function
  • I want to add a few more sample data packs: including some of my own if possible
  • Development of a report generator
  • Development of the Jamovi module

Help wanted!

Comments on the code, suggestions for improvement, verification tests, validation studies, and even code contributions would be gratefully accepted. Email me at [email protected] and I'll try and get back to you as soon as possible. Please do bear in mind this is a side-project, and I can be otherwise busy with a lot of other work.

News

NEWS

Deepankar Datta

NEWS for blandr

Version 0.4.4-devel: development version

  • 0.4.4-devel will not be tagged on GitHub
  • Development of rmarkdown auto-report function
  • Development of testthat cases

1st CRAN version - blandr 0.4.3 published on 2017-07-26

  • First version of blandr on CRAN published on 2017-07-27 as version 0.4.3.

Version 0.4.3: 2017-07-26

  • Minor changes to roxygen2 documentation from CRAN submission feedback
  • This involves examples into R source files
  • Some minor spelling and formatting corrections

Version 0.4.2: 2017-07-08

  • Minor changes to documentation from CRAN submission feedback
  • No changes to functions

Version 0.4.1: 2017-07-05

  • The preparation of the files for upload to GitHub and CRAN broke a few things
  • There's been a rebuilding of a few files to unbreak the package
  • The Bland-Altman PEFR data has been re-structured into a data-frame
  • Some of the functions have had their roxygen2 documentation changed to use inherit parameters to allow easier future maintainance of the manuals
  • There are no errors / warnings / notes - so hopefully can upload to CRAN now!

Version 0.4: 2017-06-30

  • Updated to fully use ggplot 2
  • Version changed to version 0.4
  • Start of changes to prepare to upload to GitHub and CRAN
  • Name changed from BlandAltmanEdinburgh to blandr

Version 0.3: 2016-02-04

  • updated to help with a few studies

Version 0.2: 2015-11-14

  • first proper R packaged version

Version 0.1: early 2015

  • first preliminary coding

Reference manual

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install.packages("blandr")

0.5.1 by Deepankar Datta, a year ago


https://github.com/deepankardatta/blandr/


Report a bug at https://github.com/deepankardatta/blandr/issues


Browse source code at https://github.com/cran/blandr


Authors: Deepankar Datta [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Imports ggplot2, knitr, stringr, jmvcore, R6, rmarkdown

Suggests testthat

System requirements: pandoc (>=1.12.3)


See at CRAN