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@richarddmorey
richarddmorey / funnel_no_pub_bias.R
Created Jan 9, 2016
A demonstration of how we can get asymmetric funnel plots with no publication bias
View funnel_no_pub_bias.R
Nmin = 20
Nmax = 100
Mmax = 100
Mtotal = 2*Nmin*Mmax
Num_sim_per_N = 10
N = rep(seq(Nmin,Nmax,10), each = Num_sim_per_N)
M = round( Mtotal / ( 2 * N ) )
@richarddmorey
richarddmorey / forNick.R
Created Feb 16, 2016
Compute correlations from a table of summary statistics
View forNick.R
x = scan()
35.84 8.71 38.14 8.55 -3.89 36 .000
38.22 7.66 39.73 7.80 -5.19 36 .000
67.16 8.05 68.65 8.78 -4.08 36 .000
22.08 3.28 22.68 3.58 -2.12 36 .041
22.30 2.46 23.03 2.65 -3.96 36 .000
22.78 2.97 22.95 2.91 -0.92 36 .362
60.73 2.75 63.76 2.80 -5.85 36 .000
18.19 1.68 19.84 1.52 -4.84 36 .000
@richarddmorey
richarddmorey / logRepresentedReal.R
Last active May 3, 2016
Representing real numbers using logarithms in R
View logRepresentedReal.R
###########
# S4 class to represent real numbers as logarithms
# Includes standard arithmetic operations +,-,*,/, and ^
# Richard D. Morey (richarddmorey@gmail.com)
# November 2014
###########
# Compute log(exp(a) + exp(b))
logExpAplusExpB <- function(a, b)
{
@richarddmorey
richarddmorey / varPost-gist-1.R
Created May 3, 2016
variance stability post, code part 1
View varPost-gist-1.R
# Install the BayesFactor and devtools packages, if you don't already have them
# Load my S4 class for representing real numbers with logarithms
# and performing arithmetic on them
# See the code at https://gist.github.com/richarddmorey/3c77d0065983e31241bff3807482443e
devtools::source_gist('3c77d0065983e31241bff3807482443e')
# set random seed so results are reproducible
set.seed(2)
@richarddmorey
richarddmorey / test_gist.Rnw
Created May 26, 2016
A test of importing gists inside a latex (really, Sweave) document compiled with knitr in Rstudio.
View test_gist.Rnw
\documentclass{article}
\usepackage{fancyvrb, listings, xcolor}
\usepackage{hyperref}
\definecolor{dkgreen}{rgb}{0,0.6,0}
\definecolor{mauve}{rgb}{0.88, 0.69, 1.0}
\lstset{ %
language=R, % the language of the code
basicstyle=\footnotesize, % the size of the fonts that are used for the code
@richarddmorey
richarddmorey / binomial-beta.Rnw
Created Jun 4, 2016
A demonstration of Bayes' theorem as "selecting subsets" using R markdown and interactive 3D plots
View binomial-beta.Rnw
---
title: "Joint and conditional, binomial/beta example"
author: "Richard D. Morey"
date: "4 June 2016"
output: html_document
---
```{r,echo=FALSE,warning=FALSE}
library(rgl)
library(knitr)
@richarddmorey
richarddmorey / do_plots.R
Last active Aug 8, 2016
Comparison between normal and logistic priors for proportion Bayes factors
View do_plots.R
devtools::source_gist("e49c345fcd6cfe8f32535eda4bd8c29b", filename='utility_functions.R')
# Prior Setup
p0 = .5
rscale = .5
interval = c(.5,1)
# Do not change shift unless you want different prior shift
# will cause deviation from BayesFactor package
# (not that there's anything wrong with that, but changes demo)
shift = qlogis(p0)
@richarddmorey
richarddmorey / beta.binomial.R
Created Aug 10, 2016
example, Essex, beta/binomial
View beta.binomial.R
y = 13
N = 35
a = 1
b = 1
theta = seq(0, 1, len = 100)
likelihood = theta ^ y * (1-theta)^(N-y) #dbinom(y, N, theta)
prior = theta ^ (a-1) * (1-theta)^(b-1) #dbeta(theta, a, b)
posterior1 = prior * likelihood
@richarddmorey
richarddmorey / runAll.R
Last active Aug 11, 2016
Run the Essex Data Analysis Summer School JAGS demo in R
View runAll.R
devtools::source_gist("2bd1b7a409fad3d71fc2d60884c85e50", filename = "runJAGSDemo.R")
@richarddmorey
richarddmorey / normal.xml
Created Oct 28, 2016
example XML for distribution
View normal.xml
<?xml version="1.0" encoding="utf-8"?>
<distribution>
<names>
<shortname>Normal</shortname>
<longname>Normal</longname>
<alternate>Gaussian</alternate>
<id>normal</id>
</names>
<type>continuous</type>
<support>
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