Rafael Maia rmaia

rmaia / regplots.R

Created October 28, 2012 23:40

example regression plots with pretty CI shades

	require(RColorBrewer)

	# RColorBrewer provides the palettes developped by Cynthia Brewer, you can check them
	# out at http://colorbrewer2.org/ .

	# make some mock data with interaction

	x1 <- factor(rep(c('a','b','c'),each=33))
	x2 <- rnorm(99,10,2)

rmaia / ggplot_chulls.R

Last active November 29, 2023 07:54

Plot convex hulls according to a factor

rmaia / label_specs.R

Created April 8, 2013 12:28

Adding the sample name to the end of the plotted spectra

	data(sicalis)

	# plot the desired spectra, leaving room horizontally to add labels

	plot(sicalis, select=2:4, xlim=c(300,800))

	# find the y position to add the labels right where they finish (wavelength=700)
	# using nrow to select the last row (for the last wavelength value)

	# subset the last wavelength value (column 1)

rmaia / radial_phylo_bars.R

Last active December 15, 2015 23:49

plot a radial ("fan") tree with a phenotypic trait as a bar plot

	require(ape)
	require(geiger)

	# use Geospiza data for example
	data(geospiza)

	phylo <- drop.tip(geospiza$geospiza.tree, 'olivacea')

	bardata <- setNames(geospiza$geospiza.data$beakD, rownames(geospiza$geospiza.data))

rmaia / lmer_pbmc.R

Last active December 16, 2015 11:48

Hypothesis testing in mixed-effects linear models based on parametric bootstrap and monte carlo simulations

	# PARAMETRIC BOOTSTRAP NULL HYPOTHESIS TESTING OF FIXED-EFFECT IN A MIXED MODEL
	# Same rationale can be used to test random effects
	# adapted from Faraway 2006

	require(lme4)

	# build the models to be tested
	# note that to test fixed effects, one should use ML and not REML estimation

	fm1 <- lmer(Reaction ~ Days + (Days\|Subject), sleepstudy, REML=F)

rmaia / tcs_s3d.R

Last active December 16, 2015 13:09

Use scatterplot3d to plot a tetrahedral color space

	# (very convoluted) function to plot tetrahedral colorspace

	require(pavo)
	require(scatterplot3d)
	require(RColorBrewer)

	# get the data
	data(sicalis)
	tcsdat <- tcs(vismodel(sicalis))

rmaia / phylostan_1tree.R

Created July 5, 2013 18:55

Bayesian phylogenetic regression

	require(rstan)
	require(geiger)
	require(MCMCglmm)

	# load data
	data(geospiza)

	# get the inverse of the phylogenetic variance-covariance matrix
	tr <- drop.tip(geospiza$geospiza.tree, 'olivacea')
	invA <- solve(vcv.phylo(tr))

rmaia / phylostan_Ktrees.R

Last active May 23, 2017 12:55

Bayesian phylogenetic regression incorporating phylogenetic uncertainty by sampling from multiple trees (work in progress)

	require(rstan)
	require(geiger)
	require(MCMCglmm)

	# load data
	data(geospiza)
	dat <- geospiza$geospiza.data

	# create fake sample of trees
	tr <- drop.tip(geospiza$geospiza.tree, 'olivacea')

rmaia / mcmcglmm_lambda.R

Last active January 1, 2016 03:28

Does MCMCglmm heritability correspond to lambda estimates?

rmaia / plot_phylowbars.R

Created May 4, 2016 15:51

Plot a phylogeny with bars, as separate plots, combined

	require(ape)
	require(geiger)

	# use Geospiza data for example
	data(geospiza)

	phylo <- drop.tip(geospiza$geospiza.tree, 'olivacea')

	bardata <- setNames(geospiza$geospiza.data[,'beakD'], rownames(geospiza$geospiza.data))