occuTTD: Fit Single-Season and Dynamic Time-to-detection Occupancy...

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/occuTTD.R

Description

Fit time-to-detection occupancy models of Garrard et al. (2008, 2013), either single-season or dynamic. Time-to-detection can be modeled with either an exponential or Weibull distribution.

Usage

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occuTTD(psiformula= ~1, gammaformula =  ~ 1, epsilonformula = ~ 1,
    detformula = ~ 1, data, ttdDist = c("exp", "weibull"), 
    linkPsi = c("logit", "cloglog"), starts, method="BFGS", se=TRUE, 
    engine = c("C", "R"), ...)

Arguments

psiformula

Right-hand sided formula for the initial probability of occupancy at each site.

gammaformula

Right-hand sided formula for colonization probability.

epsilonformula

Right-hand sided formula for extinction probability.

detformula

Right-hand sided formula for mean time-to-detection.

data

unmarkedFrameOccuTTD object that supplies the data (see unmarkedFrameOccuTTD).

ttdDist

Distribution to use for time-to-detection; either "exp" for the exponential, or "weibull" for the Weibull, which adds an additional shape parameter k.

linkPsi

Link function for the occupancy model. Options are "logit" for the standard occupancy model or "cloglog" for the complimentary log-log link, which relates occupancy to site-level abundance.

starts

optionally, initial values for parameters in the optimization.

method

Optimization method used by optim.

se

logical specifying whether or not to compute standard errors.

engine

Either "C" or "R" to use fast C++ code or native R code during the optimization.

...

Additional arguments to optim, such as lower and upper bounds

Details

Estimates site occupancy and detection probability from time-to-detection (TTD) data, e.g. time to first detection of a particular bird species during a point count or time-to-detection of a plant species while searching a quadrat (Garrard et al. 2008). Time-to-detection can be modeled as an exponential (ttdDist="exp") or Weibull (ttdDist="weibull") random variable with rate parameter λ and, for the Weibull, an additional shape parameter k. Note that occuTTD puts covariates on λ and not 1/λ, i.e., the expected time between events.

In the case where there are no detections before the maximum sample time at a site (surveyLength) is reached, we are not sure if the site is unoccupied or if we just didn't wait long enough for a detection. We therefore must censor the exponential or Weibull distribution at the maximum survey length, Tmax. Thus, assuming true site occupancy at site i is z_i, an exponential distribution for the TTD y_i, and that d_i = 1 indicates y_i is censored (Kery and Royle 2016):

d_i = z_i * I(y_i > Tmax_i) + (1 - z_i)

and

y_i|z_i \sim Exponential(λ_i), d_i = 0

y_i|z_i = Missing, d_i = 1

Because in unmarked values of NA are typically used to indicate missing values that were a result of the sampling structure (e.g., lost data), we indicate a censored y_i in occuTTD instead by setting y_i = Tmax_i in the y matrix provided to unmarkedFrameOccuTTD. You can provide either a single value of Tmax to the surveyLength argument of unmarkedFrameOccuTTD, or provide a matrix, potentially with a unique value of Tmax for each value of y. Note that in the latter case the value of y that will be interpreted by occuTTD as a censored observation (i.e., Tmax) will differ between observations!

Occupancy and detection can be estimated with only a single survey per site, unlike a traditional occupancy model that requires at least two replicated surveys at at least some sites. However, occuTTD also supports multiple surveys per site using the model described in Garrard et al. (2013). Furthermore, multi-season dynamic models are supported, using the same basic structure as for standard occupancy models (see colext).

When linkPsi = "cloglog", the complimentary log-log link function is used for psi instead of the logit link. The cloglog link relates occupancy probability to the intensity parameter of an underlying Poisson process (Kery and Royle 2016). Thus, if abundance at a site is can be modeled as N_i ~ Poisson(λ_i), where log(λ_i) = α + β*x, then presence/absence data at the site can be modeled as Z_i ~ Binomial(ψ_i) where cloglog(ψ_i) = α + β*x.

Value

unmarkedFitOccuTTD object describing model fit.

Author(s)

Ken Kellner contact@kenkellner.com

References

Garrard, G.E., Bekessy, S.A., McCarthy, M.A. and Wintle, B.A. 2008. When have we looked hard enough? A novel method for setting minimum survey effort protocols for flora surveys. Austral Ecology 33: 986-998.

Garrard, G.E., McCarthy, M.A., Williams, N.S., Bekessy, S.A. and Wintle, B.A. 2013. A general model of detectability using species traits. Methods in Ecology and Evolution 4: 45-52.

Kery, Marc, and J. Andrew Royle. 2016. Applied Hierarchical Modeling in Ecology, Volume 1. Academic Press.

See Also

unmarked, unmarkedFrameOccuTTD

Examples

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## Not run: 

### Single season model
N <- 500; J <- 1

#Simulate occupancy
scovs <- data.frame(elev=c(scale(runif(N, 0,100))),
                    forest=runif(N,0,1),
                    wind=runif(N,0,1))

beta_psi <- c(-0.69, 0.71, -0.5)
psi <- plogis(cbind(1, scovs$elev, scovs$forest) %*% beta_psi)
z <- rbinom(N, 1, psi)

#Simulate detection
Tmax <- 10 #Same survey length for all observations
beta_lam <- c(-2, -0.2, 0.7)
rate <- exp(cbind(1, scovs$elev, scovs$wind) %*% beta_lam)
ttd <- rexp(N, rate)
ttd[z==0] <- Tmax #Censor at unoccupied sites
ttd[ttd>Tmax] <- Tmax #Censor when ttd was greater than survey length

#Build unmarkedFrame
umf <- unmarkedFrameOccuTTD(y=ttd, surveyLength=Tmax, siteCovs=scovs)

#Fit model
fit <- occuTTD(psiformula=~elev+forest, detformula=~elev+wind, data=umf)

#Predict psi values
predict(fit, type='psi', newdata=data.frame(elev=0.5, forest=1))

#Predict lambda values
predict(fit, type='det', newdata=data.frame(elev=0.5, wind=0))

#Calculate p, probability species is detected at a site given it is present
#for a value of lambda. This is equivalent to eq 4 of Garrard et al. 2008
lam <- predict(fit, type='det', newdata=data.frame(elev=0.5, wind=0))$Predicted
pexp(Tmax, lam)

#Estimated p for all observations
head(getP(fit))

### Dynamic model

N <- 1000; J <- 2; T <- 2
scovs <- data.frame(elev=c(scale(runif(N, 0,100))),
                    forest=runif(N,0,1),
                    wind=runif(N,0,1))

beta_psi <- c(-0.69, 0.71, -0.5)
psi <- plogis(cbind(1, scovs$elev, scovs$forest) %*% beta_psi)
z <- matrix(NA, N, T)
z[,1] <- rbinom(N, 1, psi)

#Col/ext process
ysc <- data.frame(forest=rep(scovs$forest, each=T), 
                  elev=rep(scovs$elev, each=T))
c_b0 <- -0.4; c_b1 <- 0.3
gam <- plogis(c_b0 + c_b1 * scovs$forest)
e_b0 <- -0.7; e_b1 <- 0.4
ext <- plogis(e_b0 + e_b1 * scovs$elev)

for (i in 1:N){
  for (t in 1:(T-1)){
    if(z[i,t]==1){
      #ext
      z[i,t+1] <- rbinom(1, 1, (1-ext[i]))
    } else {
      #col
      z[i,t+1] <- rbinom(1,1, gam[i])
    }
  }
}

#Simulate detection
ocovs <- data.frame(obs=rep(c('A','B'),N*T))
Tmax <- 10
beta_lam <- c(-2, -0.2, 0.7)
rate <- exp(cbind(1, scovs$elev, scovs$wind) %*% beta_lam)
#Add second observer at each site
rateB <- exp(cbind(1, scovs$elev, scovs$wind) %*% beta_lam - 0.5)
#Across seasons
rate2 <- as.numeric(t(cbind(rate, rateB, rate, rateB)))
ttd <- rexp(N*T*2, rate2)
ttd <- matrix(ttd, nrow=N, byrow=T)
ttd[ttd>Tmax] <- Tmax
ttd[z[,1]==0,1:2] <- Tmax
ttd[z[,2]==0,3:4] <- Tmax
  
umf <- unmarkedFrameOccuTTD(y = ttd, surveyLength = Tmax, 
                            siteCovs = scovs, obsCovs=ocovs,
                            yearlySiteCovs=ysc, numPrimary=2) 

dim(umf@y) #num sites, (num surveys x num primary periods)

fit <- occuTTD(psiformula=~elev+forest,detformula=~elev+wind+obs,
               gammaformula=~forest, epsilonformula=~elev, 
               data=umf,se=T,engine="C")

truth <- c(beta_psi, c_b0, c_b1, e_b0, e_b1, beta_lam, -0.5)

#Compare to truth
cbind(coef(fit), truth)


## End(Not run)

unmarked documentation built on May 27, 2021, 5:07 p.m.