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unmarked
aims to be a complete environment for the
statistical analysis of data from surveys of unmarked
animals. Currently, the focus is on hierarchical models that
separately model a latent state (or states) and an observation
process. This vignette provides a brief overview of the package -
for a more thorough treatment see @fiskeChandler_2011.
Unmarked provides methods to estimate site occupancy, abundance, and density of animals (or possibly other organisms/objects) that cannot be detected with certainty. Numerous models are available that correspond to specialized survey methods such as temporally replicated surveys, distance sampling, removal sampling, and double observer sampling. These data are often associated with metadata related to the design of the study. For example, in distance sampling, the study design (line- or point-transect), distance class break points, transect lengths, and units of measurement need to be accounted for in the analysis. Unmarked uses S4 classes to store data and metadata in a way that allows for easy data manipulation, summarization, and model specification. Table 1 lists the currently implemented models and their associated fitting functions and data classes.
tab1 <- data.frame( Model=c("Occupancy", "Royle-Nichols", "Point Count", "Distance-sampling", "Generalized distance-sampling", "Arbitrary multinomial-Poisson", "Colonization-extinction", "Generalized multinomial-mixture"), `Fitting Function`=c("occu","occuRN","pcount","distsamp","gdistsamp", "multinomPois","colext","gmultmix"), Data=c("unmarkedFrameOccu","unmarkedFrameOccu","unmarkedFramePCount", "unmarkedFrameDS","unmarkedFrameGDS","unmarkedFrameMPois", "unmarkedMultFrame","unmarkedFrameGMM"), Citation=c("@mackenzie_estimating_2002","@royle_estimating_2003", "@royle_n-mixture_2004","@royle_modeling_2004", "@chandlerEA_2011","@royle_generalized_2004", "@mackenzie_estimating_2003","@royle_generalized_2004"), check.names=FALSE) knitr::kable(tab1, format='markdown', align="lccc", caption="Table 1. Models handled by unmarked.")
Each data class can be created with a call to the constructor function of the same name as described in the examples below.
The first step is to import the data into R, which we do below using
the read.csv
function. Next, the data need to be formatted for
use with a specific model fitting function. This can be accomplished
with a call to the appropriate type of unmarkedFrame
. For
example, to prepare the data for a single-season site-occupancy
analysis, the function unmarkedFrameOccu
is used.
library(unmarked) wt <- read.csv(system.file("csv","widewt.csv", package="unmarked")) y <- wt[,2:4] siteCovs <- wt[,c("elev", "forest", "length")] obsCovs <- list(date=wt[,c("date.1", "date.2", "date.3")], ivel=wt[,c("ivel.1", "ivel.2", "ivel.3")]) wt <- unmarkedFrameOccu(y = y, siteCovs = siteCovs, obsCovs = obsCovs) summary(wt)
Alternatively, the convenience function csvToUMF
can be used
wt <- csvToUMF(system.file("csv","widewt.csv", package="unmarked"), long = FALSE, type = "unmarkedFrameOccu")
If not all sites have the same numbers of observations, then manual
importation of data in long format can be tricky. csvToUMF
seamlessly handles this situation.
pcru <- csvToUMF(system.file("csv","frog2001pcru.csv", package="unmarked"), long = TRUE, type = "unmarkedFrameOccu")
To help stabilize the numerical optimization algorithm, we recommend standardizing the covariates.
obsCovs(pcru) <- scale(obsCovs(pcru))
Occupancy models can then be fit with the occu() function:
fm1 <- occu(~1 ~1, pcru) fm2 <- occu(~ MinAfterSunset + Temperature ~ 1, pcru) fm2
Here, we have specified that the detection process is modeled with the
MinAfterSunset
and Temperature
covariates. No covariates are
specified for occupancy here. See ?occu
for more details.
unmarked
fitting functions return unmarkedFit
objects which can be
queried to investigate the model fit. Variables can be
back-transformed to the unconstrained scale using backTransform
.
Standard errors are computed using the delta method.
backTransform(fm2, 'state')
The expected probability that a site was
occupied is 0.823. This estimate applies to the hypothetical
population of all possible sites, not the sites found in our sample.
For a good discussion of population-level vs finite-sample inference,
see @royle_dorazio:2008 page 117. Note also that finite-sample
quantities can be computed in unmarked
using empirical Bayes
methods as demonstrated at the end of this document.
Back-transforming the estimate of $\psi$ was easy because there were no covariates. Because the detection component was modeled with covariates, $p$ is a function, not just a scalar quantity, and so we need to be provide values of our covariates to obtain an estimate of $p$. Here, we request the probability of detection given a site is occupied and all covariates are set to 0.
backTransform(linearComb(fm2, coefficients = c(1,0,0), type = 'det'))
Thus, we can say that the expected probability of detection was 0.552
when time of day and temperature are fixed at their mean value. A
predict
method also exists, which can be used to obtain estimates of
parameters at specific covariate values.
newData <- data.frame(MinAfterSunset = 0, Temperature = -2:2) round(predict(fm2, type = 'det', newdata = newData, appendData=TRUE), 2)
Confidence intervals are requested with confint
, using either the
asymptotic normal approximation or profiling.
confint(fm2, type='det') confint(fm2, type='det', method = "profile")
confint(fm2, type='det') nul <- capture.output(ci <- confint(fm2, type='det', method = "profile")) ci
Model selection and multi-model inference can be implemented after
organizing models using the fitList
function.
fms <- fitList('psi(.)p(.)' = fm1, 'psi(.)p(Time+Temp)' = fm2) modSel(fms) predict(fms, type='det', newdata = newData)
The parametric bootstrap can be used to check the adequacy of model fit. Here we use a $\chi^2$ statistic appropriate for binary data.
chisq <- function(fm) { umf <- fm@data y <- umf@y y[y>1] <- 1 sr <- fm@sitesRemoved if(length(sr)>0) y <- y[-sr,,drop=FALSE] fv <- fitted(fm, na.rm=TRUE) y[is.na(fv)] <- NA sum((y-fv)^2/(fv*(1-fv)), na.rm=TRUE) } (pb <- parboot(fm2, statistic=chisq, nsim=100, parallel=FALSE))
We fail to reject the null hypothesis, and conclude that the model fit is adequate.
The parboot
function can be also be used to compute confidence
intervals for estimates of derived parameters, such as the proportion
of $N$ sites occupied $\mbox{PAO} = \frac{\sum_i z_i}{N}$ where $z_i$ is the true
occurrence state at site $i$, which is unknown at sites where no individuals
were detected. The colext
vignette shows examples of using
parboot
to obtain confidence intervals for such derived
quantities. An alternative way achieving this goal is to use empirical Bayes
methods, which were introduced in unmarked
version 0.9-5. These methods estimate
the posterior distribution of the latent variable given the data and
the estimates of the fixed effects (the MLEs). The mean or the mode of
the estimated posterior distibution is referred to as the empirical
best unbiased predictor (EBUP), which in unmarked
can be
obtained by applying the bup
function to the estimates of the
posterior distributions returned by the ranef
function. The
following code returns an estimate of PAO using EBUP.
re <- ranef(fm2) EBUP <- bup(re, stat="mode") sum(EBUP) / numSites(pcru)
Note that this is similar, but slightly lower than the population-level estimate of $\psi$ obtained above.
A plot method also exists for objects returned by ranef
, but
distributions of binary variables are not so pretty. Try it out on a
fitted abundance model instead.
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