Installing R packages

CRAN packages you will need installed on your machine:

dirmult
BiocManager
MASS
devtools
rstan (see the instructions below for installing rstan)

To install these, run:

list.of.packages <- c("dirmult", 
                      "BiocManager", 
                      "MASS",
                      "devtools")
new.packages <-
  list.of.packages[!(list.of.packages %in% installed.packages()[, "Package"])]
if (length(new.packages))
  install.packages(new.packages)

Many bioinformatic packages are not on CRAN but can be installed with other tools

DADA2 is only available through BiocManager. To install it run:

BiocManager::install("dada2")

Installing rstan

If you do not have rstan already installed, please see their detailed help page here to install it. Please follow their instructions carefully

RStan Getting Started

Installing Josh's package CNVRG for testing differences in proportions

It’s now on CRAN! Woot! Woot, Josh!

install.packages("CNVRG")