unmarked (version 0.11-0)

occuPEN_CV: Fit the MacKenzie et al. (2002) Occupancy Model with the penalized likelihood methods of Hutchinson et al. (2015) using cross-validation

Description

This function fits the occupancy model of MacKenzie et al (2002) with the penalized methods of Hutchinson et al (2015) using k-fold cross-validation to choose the penalty weight.

Usage

occuPEN_CV(formula, data, knownOcc=numeric(0), starts, method="BFGS", engine=c("C", "R"), lambdaVec=c(0,2^seq(-4,4)), pen.type = c("Bayes","Ridge"), k = 5, foldAssignments = NA, ...)

Arguments

formula

Double right-hand side formula describing covariates of detection and occupancy in that order.

data

An unmarkedFrameOccu object

knownOcc

Vector of sites that are known to be occupied. These should be supplied as row numbers of the y matrix, eg, c(3,8) if sites 3 and 8 were known to be occupied a priori.

starts

Vector of parameter starting values.

method

Optimization method used by optim.

engine

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

lambdaVec

Vector of values to try for lambda.

pen.type

Which form of penalty to use.

k

Number of folds for k-fold cross-validation.

foldAssignments

Vector containing the number of the fold that each site falls into. Length of the vector should be equal to the number of sites, and the vector should contain k unique values. E.g. for 9 sites and 3 folds, c(1,2,3,1,2,3,1,2,3) or c(1,1,1,2,2,2,3,3,3).

...

Additional arguments to optim, such as lower and upper bounds

Value

Details

See unmarkedFrame and unmarkedFrameOccu for a description of how to supply data to the data argument.

This function wraps k-fold cross-validation around occuPEN_CV for the "Bayes" and "Ridge" penalties of Hutchinson et al. (2015). The user may specify the number of folds (k), the values to try (lambdaVec), and the assignments of sites to folds (foldAssignments). If foldAssignments is not provided, the assignments are done pseudo-randomly, and the function attempts to put some sites with and without positive detections in each fold. This randomness introduces variability into the results of this function across runs; to eliminate the randomness, supply foldAssignments.

References

Hutchinson, R. A., J. V. Valente, S. C. Emerson, M. G. Betts, and T. G. Dietterich. 2015. Penalized Likelihood Methods Improve Parameter Estimates in Occupancy Models. Methods in Ecology and Evolution. DOI: 10.1111/2041-210X.12368

MacKenzie, D. I., J. D. Nichols, G. B. Lachman, S. Droege, J. Andrew Royle, and C. A. Langtimm. 2002. Estimating Site Occupancy Rates When Detection Probabilities Are Less Than One. Ecology 83: 2248-2255.

See Also

unmarked, unmarkedFrameOccu, occu, occuPEN, nonparboot

Examples

# Simulate occupancy data
set.seed(646)
nSites <- 60
nReps <- 2
covariates <- data.frame(veght=rnorm(nSites),
    habitat=factor(c(rep('A', 30), rep('B', 30))))

psipars <- c(-1, 1, -1)
ppars <- c(1, -1, 0)
X <- model.matrix(~veght+habitat, covariates) # design matrix
psi <- plogis(X %*% psipars)
p <- plogis(X %*% ppars)

y <- matrix(NA, nSites, nReps)
z <- rbinom(nSites, 1, psi)       # true occupancy state
for(i in 1:nSites) {
    y[i,] <- rbinom(nReps, 1, z[i]*p[i])
    }

# Organize data and look at it
umf <- unmarkedFrameOccu(y = y, siteCovs = covariates)
obsCovs(umf) <- covariates
head(umf)
summary(umf)

## Not run: 
# 
# # Fit some models
# fmMLE <- occu(~veght+habitat ~veght+habitat, umf)
# fmMLE@estimates
# 
# fm1penCV <- occuPEN_CV(~veght+habitat ~veght+habitat,
#  umf,pen.type="Ridge", foldAssignments=rep(1:5,ceiling(nSites/5))[1:nSites])
# fm1penCV@lambdaVec
# fm1penCV@chosenLambda
# fm1penCV@estimates
# 
# fm2penCV <- occuPEN_CV(~veght+habitat ~veght+habitat,
# umf,pen.type="Bayes",foldAssignments=rep(1:5,ceiling(nSites/5))[1:nSites])
# fm2penCV@lambdaVec
# fm2penCV@chosenLambda
# fm2penCV@estimates
# 
# # nonparametric bootstrap for uncertainty analysis:
# # bootstrap is wrapped around the cross-validation
# fm2penCV <- nonparboot(fm2penCV,B=10) # should use more samples
# vcov(fm2penCV,method="nonparboot")
# 
# # Mean squared error of parameters:
# mean((c(psipars,ppars)-c(fmMLE[1]@estimates,fmMLE[2]@estimates))^2)
# mean((c(psipars,ppars)-c(fm1penCV[1]@estimates,fm1penCV[2]@estimates))^2)
# mean((c(psipars,ppars)-c(fm2penCV[1]@estimates,fm2penCV[2]@estimates))^2)
# ## End(Not run)