cbrown5

#Written by Chris Brown at Griffith Uni

#Tips for setting up R packages on windows 10

I recommend installing packages to your local drive, not the shared network drive. Though R will default to the network drive (which is "\\\\staff\..."), so some knowledge is required to overcome this.
You could also ask IT to bind a letter to your network drive. I've read that works (see here: https://github.com/r-lib/devtools/issues/353)

Here's the steps I followed to install packages:
Create a shortcut to R on desktop.
Right click it

cbrown5

library(INLA)
nprec <- 100000
prec <- seq(0.05, 1000, length.out = nprec) #precisions
sd <- 1/sqrt(prec)
U <- 1
alpha <- 0.025
lambda <- -log(alpha)/U #rate for exponential on sd
pr_prec <- inla.pc.dprec(prec, U, alpha) #Density for the precision. 
pr_sd <- dexp(sd, rate = lambda) #Density for sd
#nb see inla.pc.dprec for how to get density for the precision. 

cbrown5

#Semivariance function for over water distance

 semivariance <- function(xdists, yresp, ncats = NA){
	#Function to calculate semivariance using a distance matrix
	#
	#Where:
	#xdists is the distance matrix
	#yresp is the response and rows of yresp correspond to sites in rows and columns of dists
	#ncats is the resolution. Defaults to sturges rule for histogram classes (as per Legendre book)
		

cbrown5

#Visualise priors for a variance component selected using the method of Fong et al. 2010 (see page 400 of that paper)
R <- log(10) #+-range. Use log for GLMs that have log-link functions(e.g. poisson) or no logs for a gaussian model with identity link
d <- 1 #Degrees of freedom for student t
quant <-0.95 #quantile you want random effect estimates to vary between

#Parameters of Gamma
a1 <- d/2 
qtemp <- 1-(1-quant)/2
a2 <- (d/2) * (R^2)/(qt(qtemp, df = 1)^2)

cbrown5

#
# Simulate data
#
a <- 2
x <- seq(0, 1, length.out = 100)
n <- length(x)
sigma <- 0.5
set.seed(42)
lny <- rnorm(n, mean = a*x, sd = sigma)
y <- exp(lny)