# ADAPT ## Installation There are two ways of installing the package. One is through the GitHub repository and the other is through the Bioconductor repository. ```{r, eval=FALSE} # install Bioconductor first if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # the first way is to install from GitHub if (!require("ADAPT")) BiocManager::install("mkbwang/ADAPT", build_vignettes = TRUE) # the second way is install from Bioconductor repository if (!require("ADAPT")) BiocManager::install("ADAPT", version="devel", build_vignettes = TRUE) ``` The installation may take around five minutes. _The authors are preparing to submit this package to bioconductor._ ## Introduction `ADAPT` stands for "Analysis of microbiome differential abundance by pooling Tobit models". There are two main innovations: * `ADAPT` treats zero counts as left censored observations and use Tobit models to model the log count ratios. * `ADAPT` has an innovative way of selecting non-differentially abundant taxa as reference taxa. It then uses the reference taxa to find the differentially abundant ones. To learn more about the usage of `ADAPT`, type in R console ```{r, eval=FALSE} library(ADAPT) browseVignettes(package="ADAPT") ``` The codes of simulation studies and real data analyses in the manuscript are in this [GitHub repository](https://github.com/mkbwang/ADAPT_example).