## The `ovensong' data are pooled from 75 replicate positions of a
## 4-microphone array. The array positions are coded as the first 4
## digits of each sound identifier. The sound data are initially in the
## object `signalCH'. We first impose a 52.5 dB signal threshold as in
## Dawson & Efford (2009, J. Appl. Ecol. 46:1201--1209). The vector nj
## includes 33 positions at which no ovenbird was heard. The first and
## second columns of `temp' hold the estimated effective sampling area
## and its standard error.
if (FALSE) {
signalCH.525 <- subset(signalCH, cutval = 52.5)
nonzero.counts <- table(substring(rownames(signalCH.525),1,4))
nj <- c(nonzero.counts, rep(0, 75 - length(nonzero.counts)))
temp <- derived(ovensong.model.1, se.esa = TRUE)
derivednj(nj, temp["esa",1:2])
## The result is very close to that reported by Dawson & Efford
## from a 2-D Poisson model fitted by maximizing the full likelihood.
## If nj vector has length 1, a theoretical variance is used...
msk <- ovensong.model.1$mask
A <- nrow(msk) * attr(msk, "area")
derivednj (sum(nj), temp["esa",1:2], method = "poisson")
derivednj (sum(nj), temp["esa",1:2], method = "binomial", area = A)
## Set up an array of small (4 x 4) grids,
## simulate a Poisson-distributed population,
## sample from it, plot, and fit a model.
## mash() condenses clusters to a single cluster
testregion <- data.frame(x = c(0,2000,2000,0),
y = c(0,0,2000,2000))
t4 <- make.grid(nx = 4, ny = 4, spacing = 40)
t4.16 <- make.systematic (n = 16, cluster = t4,
region = testregion)
popn1 <- sim.popn (D = 5, core = testregion,
buffer = 0)
capt1 <- sim.capthist(t4.16, popn = popn1)
fit1 <- secr.fit(mash(capt1), CL = TRUE, trace = FALSE)
## Visualize sampling
tempmask <- make.mask(t4.16, spacing = 10, type =
"clusterbuffer")
plot(tempmask)
plot(t4.16, add = TRUE)
plot(capt1, add = TRUE)
## Compare model-based and empirical variances.
## Here the answers are similar because the data
## were simulated from a Poisson distribution,
## as assumed by \code{derived}
derived(fit1)
derivedMash(fit1)
## Now simulate a patchy distribution; note the
## larger (and more credible) SE from derivedMash().
popn2 <- sim.popn (D = 5, core = testregion, buffer = 0,
model2D = "hills", details = list(hills = c(-2,3)))
capt2 <- sim.capthist(t4.16, popn = popn2)
fit2 <- secr.fit(mash(capt2), CL = TRUE, trace = FALSE)
derived(fit2)
derivedMash(fit2)
## The detection model we have fitted may be extrapolated to
## a more fine-grained systematic sample of points, with
## detectors operated on a single occasion at each...
## Total effort 400 x 1 = 400 detector-occasions, compared
## to 256 x 5 = 1280 detector-occasions for initial survey.
t1 <- make.grid(nx = 1, ny = 1)
t1.100 <- make.systematic (cluster = t1, spacing = 100,
region = testregion)
capt2a <- sim.capthist(t1.100, popn = popn2, noccasions = 1)
## one way to get number of animals per point
nj <- attr(mash(capt2a), "n.mash")
derivedExternal (fit2, nj = nj, cluster = t1, buffer = 100,
noccasions = 1)
## Review plots
library(MASS)
base.plot <- function() {
eqscplot( testregion, axes = FALSE, xlab = "",
ylab = "", type = "n")
polygon(testregion)
}
par(mfrow = c(1,3), xpd = TRUE, xaxs = "i", yaxs = "i")
base.plot()
plot(popn2, add = TRUE, col = "blue")
mtext(side=3, line=0.5, "Population", cex=0.8, col="black")
base.plot()
plot (capt2a, add = TRUE,title = "Extensive survey")
base.plot()
plot(capt2, add = TRUE, title = "Intensive survey")
par(mfrow = c(1,1), xpd = FALSE, xaxs = "r", yaxs = "r") ## defaults
## Weighted variance
derivedSession(ovenbird.model.1, method = "R2")
}
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