nearinj / corncob

Count Regression for Correlated Observations with the Beta-binomial

corncob

Count Regression for Correlated Observations with the Beta-binomial

Installation

To download the corncob package, use the code below.

# install.packages("devtools")
devtools::install_github("bryandmartin/corncob")
library(corncob)

Docker

Instead of installing corncob to your local system, you can use corncob via the pre-compiled Docker image: quay.io/fhcrc-microbiome/corncob.

Use

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(my_phyloseq_object), see ?clean_taxa_names for details.

Status

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.