richarddmorey

# This file is to demonstrate the output. 
# It is not needed.

testRmd = "https://gist.githubusercontent.com/richarddmorey/c4dd7d1fba2aa055a6f71286baedac25/raw/c256dd9f1ca0b22dfbce12443e1cb98ed5bb9d86/demo.Rmd"

tf = tempfile(fileext = ".Rmd")
tf_out = tempfile(fileext = ".html")
cat(RCurl::getURL(testRmd), file = tf)

richarddmorey

## First install the devtools package if necessary
devtools::install_github("richarddmorey/EssexSummerSchoolBayes", subdir = "shiny_demo/flexjags/flexjags")

flexjags::run_flexjags()

richarddmorey

M = 1000
N = round(sort(rpois(M, 10)^1.5, decreasing = TRUE)) + 20
pows = c(.5,.8,.95)

setup = expand.grid(N=N, pow = pows)

es = mapply(FUN = function(n, power, alpha) power.t.test(n = n, sig.level = alpha, power = power)$delta,
       n = setup$N, power = setup$pow, MoreArgs = list(alpha = .05))

dim(es) = c(setup$es,length(N), length(pows))

richarddmorey

---
output: 
  html_document:
    dev: svg
    fig_width: 5
    fig_height: 4
---

<!-- The output of this file can be found at
http://rpubs.com/richarddmorey/fonts

richarddmorey

## Paper is here: http://www.ejwagenmakers.com/2011/WetzelsEtAl2011_855.pdf
## Load the three data files

one_sample = read.delim("https://gist.githubusercontent.com/richarddmorey/e44df8750d69b5c0cd8db9513e75fba4/raw/a476c41e23d944bcf1ac6d84860218900bec0fe1/data_onesample.txt")
two_sample = read.delim("https://gist.githubusercontent.com/richarddmorey/e44df8750d69b5c0cd8db9513e75fba4/raw/a476c41e23d944bcf1ac6d84860218900bec0fe1/data_twosample.txt")
paired_sample = read.delim("https://gist.githubusercontent.com/richarddmorey/e44df8750d69b5c0cd8db9513e75fba4/raw/a476c41e23d944bcf1ac6d84860218900bec0fe1/data_pairedsample.txt")

# Define N1 and N2 for one sample tests
# for convenience
colnames(one_sample)[1] = "N1"

richarddmorey

data(attitude)
o = lm(rating ~ complaints, data = attitude)
par(mfrow=c(1,2), bg="white")
plot(rating ~ complaints, data = attitude)
abline(o, col = "red")
plot(o, ask = FALSE)

richarddmorey

x = rnorm(1000)
y = rnorm(1000)
plot(x,y,pch=19,col=rgb(0,0,1,.2))

richarddmorey

---
runtime: shiny
---

```{r echo=FALSE, message=FALSE, warning=FALSE}
require(shinyjs)
useShinyjs(rmd=TRUE)

observe({
  updateTextInput(session, 'ID', value = "Updated.")

richarddmorey

## Richard D. Morey
## 3 Nov 2017

# Redirect plots to temp directory
# We just want the variables
wd = getwd()
setwd(tempdir())
source('https://osf.io/x73zq/download?version=1')
setwd(wd)

richarddmorey

## Given a (scaled Cauchy) Bayes factor for the null against the 
## alternative (Rouder et al 2009), yields the t statistic
## that would yield it. The ... arguments are passed to 
## the ttest.tstat function.
bf.inv = Vectorize(function(b10, ...){
  fn = Vectorize(function(t,...){
    BayesFactor::ttest.tstat(t,...)[["bf"]]
  }, "t")
  t0 = optimize(function(t0, ...){