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# package coenoflex is missing from CRAN since Summer 2014
# switched to package coenocliner
coenoflex <- function (i = 30, j = 20, gradients = 2, seed = NULL, ...) {
if (!is.null(seed)) set.seed(seed)
# taken from coenocliner vignette page 9
N <- i # number of plots
M <- j # number of species
# first gradient
min1 <- 0
max1 <- 1
loc1 <- seq(min1, max1, length = N)[sample(1:N, N)] # shuffle
opt1 <- runif(M, min = min1, max = max1)
tol1 <- rep(0.25, M)
h <- ceiling(rlnorm(M, meanlog = 3)) # mimic percentages
h <- ceiling(h / max(h) * 100)
par1 <- cbind(opt = opt1, tol = tol1, h = h)
# second gradient
min2 <- 0
max2 <- 1
loc2 <- seq(min2, max2, length = N)[sample(1:N, N)]
opt2 <- runif(M, min = min2, max = max2)
tol2 <- ceiling(runif(M, min = 0.15, max = 0.85))
par2 <- cbind(opt = opt2, tol = tol2)
if (gradients == 1) {
locs <- loc1
pars <- par1
}
if (gradients == 2) {
pars <- list(px = par1, py = par2)
locs <- cbind(x = loc1, y = loc2)
}
r <- coenocline(locs, responseModel = "gaussian",
params = pars,
expectation = FALSE)
r <- as(r, "Vegsoup")
return(r)
}
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