BayesAndBagelsCode.md

#Bayes and Bagels Code

A place to stash potentially helpful code for Bayes and Bagels workshop

ReThinkInstall.md

Installing rethinking package

MPC

• Dependencies
• Thinking cap
• Headache?

The book is pretty self-explanatory about this, but just in case. We can walk through the steps.

Dependencies

First we need some dependencies. Packages the rethinking depends on. We use install.packages to get these.

install.packages(c("coda","mvtnorm","devtools"),repos="http://cran.mtu.edu/")

## Installing packages into '/Users/michaelcolaresi/Library/R/3.2/library'
## (as 'lib' is unspecified)

## 
## The downloaded binary packages are in
##  /var/folders/f9/2cy3ssy1309cgxyk57db2wnr0000gn/T//RtmpmjpQm7/downloaded_packages

library(devtools)

## Warning: package 'devtools' was built under R version 3.2.5

devtools::install_github("rmcelreath/rethinking")

## Skipping install for github remote, the SHA1 (e71dbc12) has not changed since last install.
##   Use `force = TRUE` to force installation

Thinking cap

If that worked, then you will be able to type:

library(rethinking)

## Loading required package: rstan

## Warning: package 'rstan' was built under R version 3.2.3

## Loading required package: ggplot2

## Warning: package 'ggplot2' was built under R version 3.2.4

## rstan (Version 2.9.0-3, packaged: 2016-02-11 15:54:41 UTC, GitRev: 05c3d0058b6a)

## For execution on a local, multicore CPU with excess RAM we recommend calling
## rstan_options(auto_write = TRUE)
## options(mc.cores = parallel::detectCores())

## Loading required package: parallel

## Loading required package: methods

## rethinking (Version 1.58)

and not get an error.

Headache?

If this does not work (you get a package not found error) then you may need to revert to an older version of the knitr package. Like so:

packageurl <- "http://cran.r-project.org/src/contrib/Archive/knitr/knitr_1.12.tar.gz"
install.packages(packageurl, repos=NULL, type="source")