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@dill /example.R
Last active Aug 27, 2016

What would you like to do?
Visualising concurvity between terms in a GAM
# example from ?mgcv::concurvity
library(mgcv)
## simulate data with concurvity...
set.seed(8);n<- 200
f2 <- function(x) 0.2 * x^11 * (10 * (1 - x))^6 + 10 *
(10 * x)^3 * (1 - x)^10
t <- sort(runif(n)) ## first covariate
## make covariate x a smooth function of t + noise...
x <- f2(t) + rnorm(n)*3
## simulate response dependent on t and x...
y <- sin(4*pi*t) + exp(x/20) + rnorm(n)*.3
## fit model...
b <- gam(y ~ s(t,k=15) + s(x,k=15),method="REML")
vis.concurvity(b)
# visualise the between term concurvity
# David L Miller 2015, MIT license
# arguments:
# b -- a fitted gam
# type -- concurvity measure to plot, see ?concurvity
vis.concurvity <- function(b, type="estimate"){
cc <- concurvity(b, full=FALSE)[[type]]
diag(cc) <- NA
cc[lower.tri(cc)]<-NA
layout(matrix(1:2, ncol=2), widths=c(5,1))
opar <- par(mar=c(5, 6, 5, 0) + 0.1)
# main plot
image(z=cc, x=1:ncol(cc), y=1:nrow(cc), ylab="", xlab="",
axes=FALSE, asp=1, zlim=c(0,1))
axis(1, at=1:ncol(cc), labels = colnames(cc), las=2)
axis(2, at=1:nrow(cc), labels = rownames(cc), las=2)
# legend
opar <- par(mar=c(5, 0, 4, 3) + 0.1)
image(t(matrix(rep(seq(0, 1, len=100), 2), ncol=2)),
x=1:3, y=1:101, zlim=c(0,1), axes=FALSE, xlab="", ylab="")
axis(4, at=seq(1,101,len=5), labels = round(seq(0,1,len=5),1), las=2)
par(opar)
}
Owner

dill commented Oct 9, 2015

Example of what this looks like with a more complex model...

screen shot 2015-10-09 at 10 23 20

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