Count Regression for Correlated Observations with the Beta-binomial
To download the corncob package, use the code below.
# install.packages("devtools") devtools::install_github("bryandmartin/corncob") library(corncob)
Instead of installing corncob to your local system, you can use corncob via the pre-compiled Docker image:
The vignette demonstrates example usage of all main functions. Please file an issue if you have a request for a tutorial that is not currently included. You can see the vignette by using the following code (note that this requires a TeX installation to view properly):
# install.packages("devtools") devtools::install_github("bryandmartin/corncob", build_vignette = TRUE, build_opts = c()) library(corncob) # Use this to view the vignette in the corncob HTML help help(package = "corncob", help_type = "html") # Use this to view the vignette as an isolated HTML file utils::browseVignettes(package = "corncob")
Note that R does not allow variable names to start with numbers. Sometimes, when going directly from QIIME2 to phyloseq objects, taxa names will be a large string starting with numbers. To clean these taxa names for use with corncob, use
?clean_taxa_names for details.
The preprint describing the corncob methodology is available here. The manuscript has been accepted to appear in Annals of Applied Statistics.
Bug Reports / Change Requests
If you encounter a bug or would like make a change request, please file it as an issue here.