Juan Sebastián Casallas casallas

Mimicing Matlab's `ezpolar` in R, with ggplot2

In MATLAB/octave plotting stuff in polar coordinates is really easy, e.g. the cardioid $r(\theta) = 1+cos(\theta)$, $0 < \theta < 2\pi$ is as simple as:

ezpolar('1+cos(t)',[0,2*pi])

In ggplot, more verbose is needed

Get authors:

Make an authors.txt file containing, e.g.,

author = Name LastName <[email protected]>
author2 = Name2 LastName2 <[email protected]>

lmm

Assumptions

Code based on: http://pages.stat.wisc.edu/~fyang/stat572/disc9.R

Homoscedasticity

# checking that e_i all have the same variance:
gsame_var &lt;- function(flmer){

Mavericks

gnutar

gnutar is no longer shipped with Mavericks, this may cause some issues, e.g. when running R devtools.Solution, based on this blogpost:

brew install gnu-tar
cd /usr/bin
sudo ln -s  `brew --prefix gnu-tar`/libexec/gnubin/tar /usr/bin/gnutar

To install

Install jags: in the terminal using homebrew brew install jags
Install rjags: in R

install.packages("rjags")
library(rjags)

Potential issues

This is introduced in Ch. ? from Gelman and Hill (2007). The following presentation offers some insight on that (and in general a tutorial for mixed-effects models) Slides: http://madere.biol.mcgill.ca/cchivers/rstats/linear_mixed_effects/Multilevel%20Models%20in%20R.pdf Code, data, ...: https://sites.google.com/site/mcgillbgsa/workshops/mixed-effects

Writing

Jones, Simon. How to write a great research paper: Seven simple suggestions. Great talk, mostly focused on CS, but applicable in other disciplines. https://www.youtube.com/watch?v=g3dkRsTqdDA

Goodson, Patricia. "Becoming an Academic Writer 50 Exercises for Paced, Productive, and Powerful Writing". General (e.g. get in the habit of writing) and concrete (i.e. per section) exercises to become a better writer. Additional book resources (writing log, article template). http://www.sagepub.com/goodson/study/resources.htm

Silvia, Paul. "How to write a lot"

Strunk, William. Elements of Style. Ithaca, N.Y.: Priv. print. [Geneva, N.Y.: Press of W.P. Humphrey], 1918; Bartleby.com, 1999. www.bartleby.com/141/. [Date of Printout].

	# Based on http://notstatschat.tumblr.com/post/63237480043/rock-paper-scissors-wilcoxon-test
	d1 <- c(4, 4, 4, 4, 0, 0)
	d2 <- c(3, 3, 3, 3, 3, 3)
	d3 <- c(6, 6, 2, 2, 2, 2)
	d4 <- c(5, 5, 5, 1, 1, 1)

	wilcox.test(d1, d2, alternative="greater")
	wilcox.test(d2, d3, alternative="greater")
	wilcox.test(d3, d4, alternative="greater")
	wilcox.test(d4, d1, alternative="greater")

	This chunk below is from the child document.

	<<set-parent, echo=FALSE, cache=FALSE>>=
	if(!exists("master_mode")) master_mode <- F
	if(!master_mode)
	knitr::set_parent('knitr-include.Rnw')
	@

	<<test-child, out.width='2in', fig.show='asis'>>=
	1+1

	res <- apply(installed.packages(), 1, function(ip){require(package=ip["Package"], lib.loc=ip["LibPath"], character.only=T)})
	res[res==F]