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library(RcppAlgos)

#' Calculate number of choices made by Shannon's bot
#' @description
#' Shannon's bot selects randomly answers to a multiple choice question the same
#' number of times as there is options to choose from.
#' It moves to the next question if at least 1 choice remains chosen after all
#' choices are made.
#' If not, i.e. nothing remains selected, the question is retried again, until 
#' at least one choice remains.

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# Test if R/Rstudio can run Stan with multiple cores or just hangs

t1dat = list(N=100, y = rnorm(100))

default_Stan_normal = "
// The input data is a vector 'y' of length 'N'.
data {
  int<lower=0> N;
  vector[N] y;
}

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git fetch origin pull/NN/head:prNN   ## check the PR number - this is what goes between pull and head. After the : is the name of the branch - makes sense to call it like this prID where ID is PR number
git checkout prNN ## After checking out you can compile, edit, do whatever to the PR branch
git checkout main ## If you're happy switch back to main branch before merging
git merge  --no-ff prNN
git status
git log
git push origin main ## push to Github

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# Prior to the tutorial make sure that the script below runs without error on your R installation.
# What you need is a working installation of Stan: http://mc-stan.org/ .
# For installation instructions, see here: 
# https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started

# After installation you should be able to run this script which should output
# some summary statistics and some pretty plots, :)

# Generating some fake data
set.seed(123)

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# From comments on https://stackoverflow.com/a/19610840/3275826 
# and https://stackoverflow.com/a/1395280/3275826
#
# Using mget can avoid the problems of having an object with the same name
# as the function argument confusing the results, here `x` in the line
#   `sizes = sapply(list_obj, function(x) object.size(get(x)), simplify = FALSE)`
# If you were to use this instead and assigned x to a large enough object, 
# then the output of this function would be different to a straight object.size(x) call
#
# object.size can be replaced by pryr::object_size

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#!/usr/bin/awk -f
# http://stackoverflow.com/a/1729980/3275826
# Make sure this directory/file is in your $PATH
# then call as transpose.awk fileName
{ 
    for (i=1; i<=NF; i++)  {
        a[NR,i] = $i
    }
}
NF>p { p = NF }

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/* Adapted from a .css file that is Copyright (c) 2009-2013 Jeremy Ashkenas
 * https://github.com/jashkenas/docco
 * NP modified 02/03/14
 * MIT licence */
/*--------------------- Typography ----------------------------*/

@font-face {
    font-family: 'fleurons';
    src: url('http://jashkenas.github.io/docco/resources/linear/public/fonts/fleurons.eot');
    src: url('http://jashkenas.github.io/docco/resources/linear/public/fonts/fleurons.eot?#iefix') format('embedded-opentype'),

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{
 "metadata": {
  "name": "plos_one_analysis"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {