Calculate Model-Based Metrics of Proportionality on Count-Based Compositional Data

Calculates metrics of proportionality using the logit-normal multinomial model. It can also provide empirical and plugin estimates of these metrics.

countprop: Calculate Model-Based Metrics of Proportionality on Count-Based Compositional Data

This package allows estimation of several types of proportionality metrics for count-based compositional data such as 16S, metagenomic, and single-cell sequencing data. The package includes functions that allow standard empirical estimates of these proportionality metrics, as well as estimates based on the multinomial logit-normal model.

countprop is available on CRAN. To install, run the following R code:

install.packages("countprop")

Alternatively, to install this package from github, run the following code:

if (!require(devtools)) {
  install.packages("devtools")
  library(devtools)
}
install_github("kevinmcgregor/countprop", dependencies=TRUE, build_vignettes=TRUE)

Once the package is loaded into R, you can view the vignette:

library(countprop)
vignette("countprop")