hSDM.siteocc.RdThe hSDM.siteocc function can be used to model
species distribution including different processes in a hierarchical
Bayesian framework: a \(\mathcal{B}ernoulli\) suitability
process (refering to environmental suitability) and a
\(\mathcal{B}ernoulli\) observability process (refering
to various ecological and methodological issues explaining the species
detection). The hSDM.siteocc function calls a Gibbs sampler
written in C code which uses a Metropolis algorithm to estimate the
conditional posterior distribution of hierarchical model's
parameters.
hSDM.siteocc(# Observations
presence, observability, site, data.observability,
# Habitat
suitability, data.suitability,
# Predictions
suitability.pred = NULL,
# Chains
burnin = 1000, mcmc = 1000, thin = 1,
# Starting values
beta.start,
gamma.start,
# Priors
mubeta = 0, Vbeta = 1.0E6,
mugamma = 0, Vgamma = 1.0E6,
# Various
seed = 1234, verbose = 1,
save.p = 0)A vector indicating the presence/absence for each observation.
A one-sided formula of the form \(\sim w_1+...+w_q\) with \(q\) terms specifying the explicative variables for the observability process.
A vector indicating the site identifier (from one to the total number of sites) for each observation. Several observations can occur at one site. A site can be a raster cell for example.
A data frame containing the model's variables for the observability process.
A one-sided formula of the form \(\sim x_1+...+x_p\) with \(p\) terms specifying the explicative variables for the suitability process.
A data frame containing the model's variables for the suitability process.
An optional data frame in which to look for variables with which to predict. If NULL, the observations are used.
The number of burnin iterations for the sampler.
The number of Gibbs iterations for the sampler. Total
number of Gibbs iterations is equal to
burnin+mcmc. burnin+mcmc must be divisible by 10 and
superior or equal to 100 so that the progress bar can be displayed.
The thinning interval used in the simulation. The number of mcmc iterations must be divisible by this value.
Starting values for \(\beta\) parameters of the suitability process. This can either be a scalar or a \(p\)-length vector.
Starting values for \(\beta\) parameters of the observability process. This can either be a scalar or a \(q\)-length vector.
Means of the priors for the \(\beta\) parameters
of the suitability process. mubeta must be either a scalar or a
p-length vector. If mubeta takes a scalar value, then that value will
serve as the prior mean for all of the betas. The default value is set
to 0 for an uninformative prior.
Variances of the Normal priors for the \(\beta\)
parameters of the suitability process. Vbeta must be either a
scalar or a p-length vector. If Vbeta takes a scalar value,
then that value will serve as the prior variance for all of the
betas. The default variance is large and set to 1.0E6 for an
uninformative flat prior.
Means of the Normal priors for the \(\gamma\)
parameters of the observability process. mugamma must be either
a scalar or a p-length vector. If mugamma takes a scalar value,
then that value will serve as the prior mean for all of the
gammas. The default value is set to 0 for an uninformative prior.
Variances of the Normal priors for the
\(\gamma\) parameters of the observability
process. Vgamma must be either a scalar or a p-length
vector. If Vgamma takes a scalar value, then that value will
serve as the prior variance for all of the gammas. The default
variance is large and set to 1.0E6 for an uninformative flat prior.
The seed for the random number generator. Default set to 1234.
A switch (0,1) which determines whether or not the progress of the sampler is printed to the screen. Default is 1: a progress bar is printed, indicating the step (in %) reached by the Gibbs sampler.
A switch (0,1) which determines whether or not the
sampled values for predictions are saved. Default is 0: the
posterior mean is computed and returned in the lambda.pred
vector. Be careful, setting save.p to 1 might require a large
amount of memory.
An mcmc object that contains the posterior sample. This object can be summarized by functions provided by the coda package. The posterior sample of the deviance \(D\), with \(D=-2\log(\prod_{it} P(y_{it},N_i|...))\), is also provided.
If save.p is set to 0 (default),
theta.pred is the predictive posterior mean of the
probability associated to the suitability process for each
prediction. If save.p is set to 1, theta.pred is an
mcmc object with sampled values of the probability associated
to the suitability process for each prediction.
Predictive posterior mean of the probability associated to the suitability process for each site.
Predictive posterior mean of the probability associated to the observability process for each observation.
The model integrates two processes, an ecological process associated to the presence or absence of the species due to habitat suitability and an observation process that takes into account the fact that the probability of detection of the species is inferior to one.
Ecological process: $$z_i \sim \mathcal{B}ernoulli(\theta_i)$$ $$logit(\theta_i) = X_i \beta$$
Observation process: $$y_{it} \sim \mathcal{B}ernoulli(z_i * \delta_{it})$$ $$logit(\delta_{it}) = W_{it} \gamma$$
MacKenzie, D. I.; Nichols, J. D.; Lachman, G. B.; Droege, S.; Andrew Royle, J. and Langtimm, C. A. (2002) Estimating site occupancy rates when detection probabilities are less than one. Ecology, 83, 2248-2255.
if (FALSE) {
#==============================================
# hSDM.siteocc()
# Example with simulated data
#==============================================
#=================
#== Load libraries
library(hSDM)
#==================
#== Data simulation
#= Number of observation sites
nsite <- 200
#= Set seed for repeatability
seed <- 4321
#= Ecological process (suitability)
set.seed(seed)
x1 <- rnorm(nsite,0,1)
set.seed(2*seed)
x2 <- rnorm(nsite,0,1)
X <- cbind(rep(1,nsite),x1,x2)
beta.target <- c(-1,1,-1) # Target parameters
logit.theta <- X %*% beta.target
theta <- inv.logit(logit.theta)
set.seed(seed)
Z <- rbinom(nsite,1,theta)
#= Number of visits associated to each observation point
set.seed(seed)
visits <- rpois(nsite,3)
visits[visits==0] <- 1
# Vector of observation points
sites <- vector()
for (i in 1:nsite) {
sites <- c(sites,rep(i,visits[i]))
}
#= Observation process (detectability)
nobs <- sum(visits)
set.seed(seed)
w1 <- rnorm(nobs,0,1)
set.seed(2*seed)
w2 <- rnorm(nobs,0,1)
W <- cbind(rep(1,nobs),w1,w2)
gamma.target <- c(-1,1,-1) # Target parameters
logit.delta <- W %*% gamma.target
delta <- inv.logit(logit.delta)
set.seed(seed)
Y <- rbinom(nobs,1,delta*Z[sites])
#= Data-sets
data.obs <- data.frame(Y,w1,w2,site=sites)
data.suit <- data.frame(x1,x2)
#================================
#== Parameter inference with hSDM
#==================================
Start <- Sys.time() # Start the clock
mod.hSDM.siteocc <- hSDM.siteocc(# Observations
presence=data.obs$Y,
observability=~w1+w2,
site=data.obs$site,
data.observability=data.obs,
# Habitat
suitability=~x1+x2,
data.suitability=data.suit,
# Predictions
suitability.pred=NULL,
# Chains
burnin=2000, mcmc=2000, thin=2,
# Starting values
beta.start=0,
gamma.start=0,
# Priors
mubeta=0, Vbeta=1.0E6,
mugamma=0, Vgamma=1.0E6,
# Various
seed=1234, verbose=1, save.p=0)
Time.hSDM <- difftime(Sys.time(),Start,units="sec") # Time difference
#= Computation time
Time.hSDM
#==========
#== Outputs
#= Parameter estimates
summary(mod.hSDM.siteocc$mcmc)
pdf(file="Posteriors_hSDM.siteocc.pdf")
plot(mod.hSDM.siteocc$mcmc)
dev.off()
#= Predictions
summary(mod.hSDM.siteocc$theta.latent)
summary(mod.hSDM.siteocc$delta.latent)
summary(mod.hSDM.siteocc$theta.pred)
pdf(file="Pred-Init.pdf")
plot(theta,mod.hSDM.siteocc$theta.pred)
abline(a=0,b=1,col="red")
dev.off()
}