Nothing
library(unmarked)
library(rbenchmark)
set.seed(34537)
nSites <- 100
T <- 10
covariates <- data.frame(veght=rnorm(nSites),
habitat=factor(c(rep('A', 50), rep('B', 50))))
lampars <- c(-1, 0, 0)
gampars <- c(-1, 0, 0)
ompars <- c(2, -1, 0)
ppars <- c(1, 0, 0)
X <- model.matrix(~veght+habitat, covariates) # design matrix
lam <- exp(X %*% lampars)
gam <- exp(X %*% gampars)
om <- plogis(X %*% ompars)
p <- plogis(X %*% ppars)
y <- N <- matrix(NA, nSites, T)
N[,1] <- rnbinom(nSites, size=1, mu=lam) # true abund
for(t in 2:T) {
S <- rbinom(nSites, N[,t-1], om)
G <- rpois(nSites, gam)
N[,t] <- S+G
}
y[] <- rbinom(nSites*T, N, p)
#y[1,5] <- NA
#covariates[2,] <- NA
umf <- unmarkedFramePCO(y = y, siteCovs = covariates, numPrimary=T)
head(umf)
summary(umf)
system.time(fm <- pcountOpen(~veght+habitat, ~1, ~veght, ~veght, umf,
K=20, control=list(trace=TRUE, REPORT=1),
se=FALSE)) # 105 (was 722)!!
benchmark(pcountOpen(~1, ~1, ~veght, ~1, umf, K=15, se=FALSE,
starts=c(-1,-1,2,-1,1),
control=list(trace=TRUE, REPORT=1)),
columns=c("test", "elapsed", "relative"),
replications=5) # 94.25 was 275.43
st2 <- system.time(fm2C <- pcountOpen(~1, ~1, ~veght, ~1, umf, K=15,
control=list(trace=TRUE, REPORT=1),
se=TRUE)) # 51.46 was 155.5
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