unmarked: gmultmix – R documentation

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gmultmix

Generalized multinomial N-mixture model

Description

A three level hierarchical model for designs involving repeated counts that yield multinomial outcomes. Possible data collection methods include repeated removal sampling and double observer sampling. The three model parameters are abundance, availability, and detection probability.

Usage

gmultmix(lambdaformula, phiformula, pformula, data, mixture = c("P", "NB"), K, 
         starts, method = "BFGS", se = TRUE, engine=c("C","R"), threads=1, ...)

Arguments

`lambdaformula`	Righthand side (RHS) formula describing abundance covariates
`phiformula`	RHS formula describing availability covariates
`pformula`	RHS formula describing detection covariates
`data`	An object of class unmarkedFrameGMM
`mixture`	Either "P" or "NB" for Poisson and Negative Binomial mixing distributions.
`K`	The upper bound of integration
`starts`	Starting values
`method`	Optimization method used by `optim`
`se`	Logical. Should standard errors be calculated?
`engine`	Either "C" to use fast C++ code or "R" to use native R code during the optimization.
`threads`	Set the number of threads to use for optimization in C++, if OpenMP is available on your system. Increasing the number of threads may speed up optimization in some cases by running the likelihood calculation in parallel. If `threads=1` (the default), OpenMP is disabled.
`...`	Additional arguments to optim, such as lower and upper bounds

Details

The latent transect-level super-population abundance distribution f(M | theta) can be set as either a Poisson or a negative binomial random variable, depending on the setting of the mixture argument. mixture = "P" or mixture = "NB" select the Poisson or negative binomial distribution respectively. The mean of M_i is lambda_i. If M_i ~ NB, then an additional parameter, alpha, describes dispersion (lower alpha implies higher variance).

The number of individuals available for detection at time j is a modeled as binomial: N(i,j) ~ Binomial(M(i), phi(i,j)).

The detection process is modeled as multinomial: y(i,1:J,t) ~ Multinomial(N(i,t), pi(i,1,t), pi(i,2,t), ..., pi(i,J,t)), where pi(ijt) is the multinomial cell probability for plot i at time t on occasion j.

Cell probabilities are computed via a user-defined function related to the sampling design. Alternatively, the default functions removalPiFun or doublePiFun can be used for equal-interval removal sampling or double observer sampling. Note that the function for computing cell probabilites is specified when setting up the data using unmarkedFrameGMM.

Parameters lambda, phi and p can be modeled as linear functions of covariates using the log, logit and logit links respectively.

Value

An object of class unmarkedFitGMM.

Note

In the case where availability for detection is due to random temporary emigration, population density at time j, D(i,j), can be estimated by N(i,j)/plotArea.

This model is also applicable to sampling designs in which the local population size is closed during the J repeated counts, and availability is related to factors such as the probability of vocalizing. In this case, density can be estimated by M(i)/plotArea.

If availability is a function of both temporary emigration and other processess such as song rate, then density cannot be directly estimated, but inference about the super-population size, M(i), is possible.

Three types of covariates can be supplied, site-level, site-by-year-level, and observation-level. These must be formatted correctly when organizing the data with unmarkedFrameGPC

Author(s)

Richard Chandler rbchan@uga.edu and Andy Royle

References

Royle, J. A. (2004) Generalized estimators of avian abundance from count survey data. Animal Biodiversity and Conservation 27, pp. 375–386.

Chandler, R. B., J. A. Royle, and D. I. King. 2011. Inference about density and temporary emigration in unmarked populations. Ecology 92:1429-1435.

Examples

# Simulate data using the multinomial-Poisson model with a
# repeated constant-interval removal design.

n <- 100  # number of sites
T <- 4    # number of primary periods
J <- 3    # number of secondary periods

lam <- 3
phi <- 0.5
p <- 0.3

#set.seed(26)
y <- array(NA, c(n, T, J))
M <- rpois(n, lam)          # Local population size
N <- matrix(NA, n, T)       # Individuals available for detection

for(i in 1:n) {
    N[i,] <- rbinom(T, M[i], phi)
    y[i,,1] <- rbinom(T, N[i,], p)    # Observe some
    Nleft1 <- N[i,] - y[i,,1]         # Remove them
    y[i,,2] <- rbinom(T, Nleft1, p)   # ...
    Nleft2 <- Nleft1 - y[i,,2]
    y[i,,3] <- rbinom(T, Nleft2, p)
    }

y.ijt <- cbind(y[,1,], y[,2,], y[,3,], y[,4,])


umf1 <- unmarkedFrameGMM(y=y.ijt, numPrimary=T, type="removal")

(m1 <- gmultmix(~1, ~1, ~1, data=umf1, K=30))

backTransform(m1, type="lambda")        # Individuals per plot
backTransform(m1, type="phi")           # Probability of being avilable
(p <- backTransform(m1, type="det"))    # Probability of detection
p <- coef(p)

# Multinomial cell probabilities under removal design
c(p, (1-p) * p, (1-p)^2 * p)

# Or more generally:
head(getP(m1))

# Empirical Bayes estimates of super-population size
re <- ranef(m1)
plot(re, layout=c(5,5), xlim=c(-1,20), subset=site%in%1:25)

unmarked

Models for Data from Unmarked Animals

v1.1.0

GPL (>= 3)

Authors

Richard Chandler [aut], Ken Kellner [aut], Ian Fiske [aut], David Miller [aut], Andy Royle [cre, aut], Jeff Hostetler [aut], Rebecca Hutchinson [aut], Adam Smith [aut], Marc Kery [ctb], Mike Meredith [ctb], Auriel Fournier [ctb], Ariel Muldoon [ctb], Chris Baker [ctb]

Initial release

2021-05-05