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

https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started

Installing Josh's package CNVRG for testing differences in proportions

It’s now on CRAN! Woot! Woot, Josh!

install.packages("CNVRG")