mcradds's Introduction

mcradds

The mcradds R package is a complement to mcr package, contains common and solid functions for designing, analyzing and visualization in In Vitro Diagnostic trials. Most of the methods and algorithms refer to CLSI recommendations and NMPA guidelines.

The package provides a series of typical functionality, as shown below:

Estimation of sample size for trials, NMPA guideline.
Diagnostic accuracy with/without standard/golden reference, CLSI EP12-A2.
Regression analysis and plot in method comparison, CLSI EP09-A3.
Bland-Altman analysis and plot in method comparison, CLSI EP09-A3.
Outlier detection with 4E method from CLSI EP09-A2 and ESD from CLSI EP09-A3.
Evaluation of bias in medical decision level, CLSI EP09-A3.
Pearson and Spearman correlation adding hypothesis test and confidence interval.
Establishing of Reference Range/Interval, CLSI EP28-A3 and NMPA guideline.
Paired ROC/AUC test for superiority and non-inferiority trials, CLSI EP05-A3/EP15-A3.
Reproducibility analysis (reader precision) for immunohistochemical assays, CLSI I/LA28-A2 and NMPA guideline.
Evaluation of precision of quantitative measurements, CLSI EP05-A3.
Descriptive statistics summary.

Installation

mcradds is available on CRAN and you can install the latest released version with:

install.packages("mcradds")

or you can install the development version directly from GitHub with:

if (!require("devtools")) {
  install.packages("devtools")
}
devtools::install_github("kaigu1990/mcradds")

See package vignettes browseVignettes(package = "mcradds") for usage of this package.

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mcradds's Issues

Release mcradds 1.1.0

Prepare for release:

Submit to CRAN:

usethis::use_version('minor')
devtools::submit_cran()
Approve email

Wait for CRAN...

Release mcradds 1.0.1

First release:

usethis::use_cran_comments()
Update (aspirational) install instructions in README
Proofread Title: and Description:
Check that all exported functions have @return and @examples
Check that Authors@R: includes a copyright holder (role 'cph')
Check licensing of included files
Review https://github.com/DavisVaughan/extrachecks

Prepare for release:

git pull
Check if any deprecation processes should be advanced, as described in Gradual deprecation
usethis::use_github_links()
urlchecker::url_check()
devtools::build_readme()
devtools::check(remote = TRUE, manual = TRUE)
devtools::check_win_devel()
git push
Draft blog post

Submit to CRAN:

usethis::use_version('minor')
devtools::submit_cran()
Approve email

Wait for CRAN...

New features to V1.1.0 update

New features will be added:

Refresh mcr relevant functions that have been completed.
Add kappa with corresponding CI to diagnostic agreement performance.
Add descriptive statistical functions like descfreq() for categorical variables or descvar() for continuous variables.

`mcr` package is not available in CRAN

Given the mcr package is not available in CRAN, I have to remove regression related functions and keep them in a branch.

If the mcr package will be refreshed, merge the branch into main.
If the mcr package is removed from CRAN permanently, an option solution is to rebuild regression analysis functions in mcradds package.
If the mcr package can not be refreshed in the short period, a better solution is to keep preparing regression analysis.

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