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Fig. 2.11: Examples of (simulated) species distribution maps produced using common statistical models.![]() library(geoR) library(spatstat) set.seed(312) cp <- expand.grid(seq(0, 1, l=10), seq(0, 1, l=10)) # unconditional gaussian simulations (psill=1, mean=0): s <- grf(100, grid="reg", cov.pars=c(1, 0.2), cov.model="mat", kappa=1.5) hist(s$data) # define your own model, e.g. poisson: lambda <- 0.2*exp(0.5 +s$data) y <- rpois(length(s$data), lambda=lambda) image(s, col=gray(seq(1, 0.5, l=21))) text(s$coords, label=y, pos=3, offset=-0.2, cex=1.5) hist(y) dev.off() # simulate a point pattern: sm <- list(x=seq(0, 1, l=10), y=seq(0, 1, l=10), z=matrix(y, nrow=10)) y.p <- rpoint(n=sum(y), f=as.im(sm)) image(s, col=gray(seq(1, 0.5, l=21))) points(y.p, pch="+", cex=1.5) # yes/no events: y.b <- ifelse(y>0, 1, 0) sb <- s sb$data <- y image(sb, col=gray(c(0.95,rep(0.5, 10)))) text(s$coords, label=y.b, pos=3, offset=-0.2, cex=1.5) # binomial model: p <- exp(0.1+s$data)/(1+exp(0.1+s$data)) y <- rbinom(length(s$data), size=100, prob=p)/100 image(s, col=gray(seq(1, 0.5, l=21))) text(s$coords, label=y, pos=3, offset=-0.2, cex=1.2) hist(y) dev.off() # bernoulli model: p <- 0.2*exp(s$data)/(1+exp(s$data)) ind <- seq(1, 401, by=8) y <- rbinom(length(s$data), size=1, prob=p) y <- rbinom(p[ind], size=1, prob=p) image(s, col=grey(0.8)) text(s$coords, label=y, pos=3, offset=-0.2, cex=1.5) hist(y) # uniform distribution: y.cdf <- ecdf(s$data) y <- y.cdf(s$data) image(s, col=gray(seq(1, 0.5, l=21))) text(s$coords, label=y, pos=3, offset=-0.2, cex=1.2) dev.off() hist(y) |
Testimonials"Hi Tom. I have uploaded some comments on your book. You should check if you are able to run the code on upgraded versions of R. Otherwise fine, nice set of full-scale examples." Poll |
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