Tim Lucas timcdlucas

U. of Leicester lecturer studying zoonotic and vector-borne disease, air pollution, human movement and geostatistics.

timcdlucas / gist:4c44c0b4fe59592d385a

Created February 15, 2016 17:48

Compare slopes bewteen two datasets.


	# Make up some data
	data1 <- data.frame(length = rnorm(20, 8), weight = 1:20)

	data2 <- data.frame(length = rnorm(30, 8), weight = 1:30)


	# add a dummy variable and combine the data

	data1$dummy <- 'data1'

timcdlucas / Mathematica2R.R

Created February 4, 2016 14:58

Convert Mathematica array text to R array



	#' Turn a string copied from Mathematica into an R array
	#'
	#'@param text Text representation of a mathematica array.
	#'@param drop Logical. If TRUE, 1 and 2 dimensional arrays will be returned as vectors and matrices.
	#' If FALSE, 1 and 2 dimensional arrays will be returned.
	#'
	#'@return An array
	#'@export

timcdlucas / r2math.R

Last active January 26, 2016 15:23

R to Mathematica

	# Print an R matrix in a form that can be copied straight into mathematica

	MathematicaPaste.matrix <- function(m){

	charmat <- apply(m, 2, as.numeric)
	charmat[, -NCOL(charmat)] <- paste0(charmat[, -NCOL(charmat)], ',')

	charmat <- rbind('{', t(charmat), '},')
	charmat[dim(charmat)[1], dim(charmat)[2]] <- '}'

timcdlucas / cloglog.R

Created January 20, 2016 11:37

equations for predicting cloglog models


	d <- data.frame(x = rnorm(100) + c(1, 2), y = c(0, 1))

	m <- glm(y ~ x, data = d, family = binomial(link = cloglog))


	newx <- seq(-5, 5, length.out = 100)
	predict.line <- predict(m, newdata = data.frame(x = newx), type = 'response')

	plot(y ~ x, d)

timcdlucas / scrapeCitations.R

Last active October 27, 2015 21:04

Scrape pubmed or scholar

timcdlucas / gist:536bae09750236dc356b

Created August 25, 2015 09:13

Greys


	library(ggplot2)

	x <- data.frame(y = rnorm(100), g = rep(letters[1:4], 25))


	ggplot(x, aes(y = y, x = g, fill = g)) +
	geom_boxplot() +
	ylim(c(-15, 15)) +
	scale_fill_manual(values = grey(c(0, 0.5, 0.9, 1))) +

timcdlucas / gist:b54c199f16cd3cfa01e4

Created August 2, 2015 00:14

	data(shorebird)
	shorebird <- comparative.data(shorebird.tree, shorebird.data, Species, vcv=TRUE, vcv.dim=3)
	mod1 <- pgls(log(Egg.Mass) ~ log(M.Mass) * log(F.Mass), shorebird)
	print(mod1)

	mod1.sum <- summary(mod1)
	print(mod1.sum)
	mod1.aov <- anova(mod1)
	print(mod1.aov)

timcdlucas / pubmedCites.R

Created July 25, 2015 10:40

Scrape the number of citations on pubmed


	scrapePub <- function(sp){

	Sys.sleep(2)
	spString <- tolower(gsub(' ', '+', sp))

	url <- paste0('http://www.ncbi.nlm.nih.gov/pubmed/?term=%22', spString, '%22')


	page <- html(url)

timcdlucas / scholarCites.R

Created July 23, 2015 21:56

Scrape the number of references found on google scholar.


	library(rvest)
	library(magrittr)

	# Our search string
	sp <- "Myotis myotis"

	spString <- tolower(gsub(' ', '+', sp))

	url <- paste0('https://scholar.google.co.uk/scholar?hl=en&q=%22',

timcdlucas / test.html

Created April 22, 2015 21:07

test.html

	<!DOCTYPE html>
	<html>
	<head>
	<meta charset="utf-8"/>
	<script src="lib/htmlwidgets-0.3.2/htmlwidgets.js"></script>
	<script src="lib/jquery-1.11.1/jquery.min.js"></script>
	<link href="lib/leaflet-0.7.3/leaflet.css" rel="stylesheet" />
	<script src="lib/leaflet-0.7.3/leaflet.js"></script>
	<link href="lib/leafletfix-1.0.0/leafletfix.css" rel="stylesheet" />
	<script src="lib/leaflet-binding-0.0.11/leaflet.js"></script>