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")