0% found this document useful (0 votes)
9 views6 pages

Occupancy Model Fact Sheet

The document discusses occupancy models used in wildlife studies to estimate the proportion of sites occupied by a species, addressing issues of imperfect detection. These models utilize detection/non-detection data to provide unbiased estimates of occupancy, which can be affected by various site and survey characteristics. The document also highlights the importance of assumptions in model accuracy and the need for careful data collection to avoid biases in occupancy estimates.

Uploaded by

SECIEM AC
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
0% found this document useful (0 votes)
9 views6 pages

Occupancy Model Fact Sheet

The document discusses occupancy models used in wildlife studies to estimate the proportion of sites occupied by a species, addressing issues of imperfect detection. These models utilize detection/non-detection data to provide unbiased estimates of occupancy, which can be affected by various site and survey characteristics. The document also highlights the importance of assumptions in model accuracy and the need for careful data collection to avoid biases in occupancy estimates.

Uploaded by

SECIEM AC
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
You are on page 1/ 6

Occupancy Models to Study Wildlife

Abstract areas and may be


appropriate for spe-
Many wildlife studies seek to
understand changes or differences in cies that exhibit wide
the proportion of sites occupied by population fluctua-
a species of interest. These studies tions over short time
are hampered by imperfect detection periods. For example,
of these species, which can result occupancy has been
in some sites appearing to be unoc- the most influential
cupied that are actually occupied. state variable in de-
Occupancy models solve this problem scribing world-wide
and produce unbiased estimates of amphibian declines
occupancy and related parameters. (Green 1997). Imitator Salamander
Required data (detection/non-detec-
tion information) are relatively simple The Problem The Solution
and inexpensive to collect. Software Wildlife species are rarely de-
is available free of charge to aid in- New classes of models, called
tected with perfect accuracy, regard- occupancy models, were developed to
vestigators in occupancy estimation. less of the technique employed. solve the problems created by imper-
Non-detection does not necessarily fect detectability (MacKenzie et al.
Response Variables in Wildlife mean that a species was absent unless 2002, 2003, 2004). These models use
Studies the probability of detecting the spe- information from repeated observa-
Studies of wildlife populations cies (detectability3) was 100%. This tions at each site to estimate detect-
often attempt to understand patterns leads to a fundamental problem: the ability. Detectability may vary with
of distribution and abundance. Es- measure of occupancy (presence/ab- site characteristics (e.g., habitat vari-
timating abundance can be a costly sence at a set of sites) is confounded4 ables) or survey characteristics (e.g.,
endeavor, and other state variables1 with the detectability of the spe- weather conditions), whereas occu-
like species richness or occupancy2 cies. More specifically, an observed pancy relates only to site characteris-
may be more appropriate and less “absence” occurs if either the species tics. Repeated observations can take
expensive. Occupancy is an alterna- was present at the site but not detect- many forms, but the most obvious is
tive that has a long history of use in ed, or the species was truly absent. simply surveying each site repeatedly.
ecological and wildlife studies. Two Detectability may vary among study In some cases, traps, coverboards,
of the most noticeable areas where oc- sites and may be related to character- transects, and surveys by independent
cupancy information is used include: istics of a survey on a particular day, observers can be treated as repeated
(1) studies of species distribution and such as weather conditions. Because observations for a local sample area
range where investigators seek to of this variation in detectability, it is or site. For example, data from 10
understand the factors that determine insufficient to simply analyze detec- minnow traps in each of 30 ponds
whether or not a species will exist at a tion/non-detection data as if they could be treated as 10 observations at
location (e.g., habitat modeling, Scott are truly presence/absence data. The each pond if there is some possibility
et al. 2002) and (2) metapopulation proportion of sites where a species is that the species of interest could be
dynamics (Hanski 1992) where site (or detected will always underestimate caught in each of the traps.
patch) occupancy is related to patch, the true occupancy level in the study
or site-specific, characteristics. For the area when detection is imperfect. How Does This Work?
latter case, extinction and colonization Therefore, inferences regarding the The technique is very similar to
probabilities can also be modeled in influences of site characteristics on estimating abundance from mark-
relation to patch characteristics. Moni- occupancy will be difficult or impos- recapture data but does not require
toring occupancy can reveal changes sible to discern reliably (e.g., Gu and any marking of animals. Necessary
in the status of a species over broad Swihart 2004). information for occupancy models is
U.S. Department of the Interior Fact Sheet 2005-3096
U.S. Geological Survey September 2005
simply a record of whether a species
was detected or not detected dur-
ing each survey of each site (Box Box 1: Details of occupancy estimation
1). These records, termed detection
histories, can be converted to math-
Parameters of interest:
ematical statements. Assuming the
sites are independent, the product of ψ is the probability a site is occupied by the target species.
all the mathematical statements (one pj is the probability of detecting the species during the jth survey,
for each possible detection history) given it is present (detectability).
forms the model likelihood5 for the
observed data, and maximum likeli- Necessary information: Detection histories
hood techniques are then used to Detection histories are just a record of whether or not the target spe-
estimate model parameters6. Param- cies was detected on each survey of each site. For example, suppose
eter estimates (occupancy or detect- 30 sites were each
ability) can be related to various site sampled four times Surveys
and survey characteristics using the within a season. The 1 2 3 4
logistic equation or logit-link func- following table could
Site 1 1 0 0 1
tion7. The details of this and other be the resulting detec-
variations on occupancy estimation Site 2 0 0 0 0
tion histories, where
are described in a series of journal each row represents a Site 3 1 1 0 0
articles (see MacKenzie et al. papers site and each column …
under Further Reading). represents one of the Site 30 0 0 0 0
Two software packages will four surveys:
help you do an occupancy analysis.
PRESENCE was created exclusively Each site has its own detection history that can be represented by an
for occupancy analysis and is avail- intuitive mathematical equation. In the above case, the target spe-
able at http://www.mbr-pwrc.usgs. cies was detected at Site 1 during the first and last survey occasions
gov/software.html. Occupancy analy- (1001). The site was occupied (ψ), and the species was detected on
sis has also been incorporated into the first and last surveys ( p1 and p4 ) and not detected on the second
MARK, which is available at http:// and third surveys. We can write the probability of this detection his-
www.cnr.colostate.edu/~gwhite/soft- tory as:
ware.html. Examples using occupan-
cy models include Corn et al. (2005), Pr(H i = 1001) = ψ × p1 (1 – p2)(1 – p3) p4
Olson et al. (2005), and O’Connell et
al. (2005). Sites 2 and 30 represent a case where the target species was never
detected (detection history = 0000). These sites could either be unoc-
Assumptions cupied, which mathematically is (1-ψ), or they could be occupied but
All models have assumptions, and we never detected the target species, which mathematically is:
occupancy models are no exception. 4
Critical assumptions for data collect-
ed during a single sampling season
ψ(1- p1)(1- p2)(1- p3)(1- p4) or ψ Π(1 – p )
j=1
j

include: Thus, we can write the probability of detection history (0000) as:
(1) Occupancy state is “closed.”
4
Species are present at occupied
sites for the duration of the sam-
Pr(H i = 0000) = ψ Π (1 – p ) + (1-ψ)
j=1
j

pling season. Occupancy does not


change at a site within the sam- Mathematical statements of all detection histories are combined into
pling season, but it can change model likelihood, such as:
between sampling seasons. 30
(2) Sites are independent. Detection
of the target species at one site is
L(ψ, p H 1,…, H 30) = Π Pr( H )
i=1
i

independent of detecting the spe- Maximum likelihood methods incorporated in program PRESENCE
cies at other sites. This might be or program MARK are used to obtain estimates of occupancy and
a problem if your sites are closely detectability (see MacKenzie et al. 2002).
spaced, allowing animals to move
Biases Caused by Assumption
Violations
If the assumptions mentioned
above are not met, estimates of oc-
cupancy and detectability can be
biased10 and inferences about fac-
tors that influence these parameters
may be flawed (e.g., Gu and Swihart
2004). If the target species is not
present at sites throughout the entire
study season, then estimates of oc-
cupancy may still be unbiased if the
species moves randomly in and out
of a sampling unit. Interestingly, the
interpretation of occupancy changes
to the proportion of sites used by the
Kenai National Wildlife Refuge
target species in this case. Likewise
the probability of detecting the spe-
cies at occupied sites is now a combi-
nation of two different components:
among sites and be detected at Sites should be chosen according the probability that the species was
multiple sites. to some type of probability-based present at the sampling unit and the
(3) No unexplained heterogene- sampling9 (e.g., simple-random probability of detecting the species
ity8 in occupancy. Probability of sample, stratified-random sample, given it was present. If movement in
occupancy is the same across sites etc.) to ensure that estimates of oc- and out of the sampling unit is not
or differences in occupancy can be cupancy apply to the area of interest. random, the occupancy estimator
explained with site characteristics Sampling may be standardized to try will likely be biased. For example,
(covariates) that have been quanti- to minimize differences in detection non-random movement occurs if the
fied for inclusion in the model. probability caused by variation in target species was not initially at the
(4) No unexplained heterogeneity in site when sampling commenced, then
environmental conditions or time of
detectability. Detectability at oc- moves into the sample unit and stays
day. Unfortunately, it is impossible
cupied sites is the same across all for the duration of the season. The di-
to control for all possible factors that
surveys and sites, or differences in rection of the occupancy bias depends
can affect detectability or occupancy.
detectability can be explained with on the direction of the movement (see
When design-based approaches
site or survey characteristics that Kendall 1999 for more details and
cannot reduce all of the variation
have been quantified for inclusion possible solutions).
(sometimes termed heterogeneity)
Little work has been done involv-
in the model. in either occupancy or detectability,
ing the impact of variation in occu-
model-based approaches might help.
pancy probability among sites that
Approaches to Meeting Investigators should collect informa-
cannot be associated with covariates
Assumptions tion about factors they believe could (occupancy heterogeneity). It is pos-
Investigators can use design- cause heterogeneity in either of these sible that the overall average occu-
based or model-based approaches to two parameters and then incorporate pancy estimate may still be unbiased,
meet these assumptions. A design- these covariates into the estimation but more research on the impacts of
based approach involves collecting process. For example, it may be im- occupancy heterogeneity is needed.
data in a way that assures the as- practical and wasteful to only sample Heterogeneity in detection prob-
sumptions will be met. For example, amphibian breeding ponds during ability will often result in occupancy
natural history information may aid sunny days, but larvae are more estimates that are low (negatively
in scheduling surveys during times difficult to see on cloudy days; thus, biased). This problem is further exac-
when the closure assumption is most investigators should record weather erbated in studies involving a small
likely to hold. In addition, a scientist conditions during each survey. The number of sites, few repeated surveys
may use existing movement informa- variation in detection probabilities at each site, or species with excep-
tion to ensure that sample sites are caused by cloud cover can easily tionally low detection probabilities.
dispersed across the sample area in a be incorporated to obtain unbiased Anticipating variation and minimiz-
manner that maintains independence. estimates of occupancy. ing its effects either through study
design or collecting relevant covari-
ates to model it is essential for good
performance of these methods. Box 2: Results of model selection for salamanders of
Finally, if detection is not inde- the Desmognathus imitator complex in Great Smoky
pendent among sites, the standard Mountains National Park
error estimates are usually too low. In
these instances, the number of inde- The models we considered assume occupancy was either
pendent sites is actually smaller than constant across sites ψ (.), or varied according to the sites’
the total number of sites surveyed. previous disturbance history, ψ (dist). Detectability was either
There are existing model-based constant across all surveys and sites p(.), or it varied among
methods that aid in detecting and cor- surveys p(t), or across sites according to previous disturbance
recting this problem (MacKenzie and history p(dist), or both p(dist+t). Model selection was based
on Akaike’s Information Criteria for small sample size (AICc),
Bailey 2004).
which selects the most parsimonious model, balancing model
Occupancy and Terrestrial fit and parameter precision. Models with lower AICc are con-
Salamanders sidered best. AICc is the difference between the AICc of the
best model and a subsequent model. As a general rule, models
Approximately 10% of the with AICc<2.0 have substantial support and should be consid-
world’s salamander species are found ered when making inferences or reporting parameter estimates.
in the southern Appalachian region, Another way of assessing model support is with Akaike weight
with 31 species occurring inside the (w), which can be interpreted as the weight of evidence for a
boundaries of Great Smoky Moun- particular model. All weights sum to 1.
tains National Park (GSMNP; Dodd
2003). Despite this rich diversity,
large-scale or long-term studies of Model Parameters AICc AICc Weight (w)
terrestrial salamanders in this re- ψ (dist) p (dist + t) 7 89.68 0.00 0.32
gion are almost nonexistent (but see ψ (dist) p (t) 6 90.27 0.59 0.24
Hairston and Wiley 1993). An area of ψ (dist) p (dist) 4 91.03 1.35 0.16
interest involves the impact of vari- ψ (dist) p (.) 3 91.47 1.78 0.13
ous forms of disturbance on terrestrial ψ (.) p (dist + t) 6 92.25 2.57 0.09
salamander populations (Petranka et ψ (.) p (dist) 3 93.54 3.86 0.05
al. 1993, Ash 1997, Petranka 1999, ψ (.) p (t) 5 100.36 10.68 0.00
Ash and Pollock 1999). Some areas ψ (.) p (.) 2 102.01 12.33 0.00
within GSMNP incurred heavy hu-
man use in the form of logging or
settlement prior to the park’s estab-
lishment in 1934. In this example 1.0
analysis, we ask if previous distur-
bance history affects the probability 0.8
of occurrence for salamanders of the
Desmognathus imitator complex in
Detectability

0.6
GSMNP. We caution that this analysis
is meant as an example only, and we 0.4
remind readers that there is always an
inherent danger in inferring biological 0.2 Undisturbed

process from spatial patterns.


Disturbed

Data: Salamanders were sampled 0


2 3 4 5
using two methods: an area-con-
strained natural-cover transect (50 x Survey
3 m) and a 50 m coverboard transect,
consisting of 5 coverboard stations
spaced at 10 m intervals. The two Figure 1. Model-averaged estimates of detectability across surveys and among
transects were parallel to one another sites with different disturbance histories.
and separated by approximately 10 m.
Together, the area sampled by these
transects constituted a site or sample
unit. Sample units were near trails and
located approximately 250 m apart
Glossary:
to ensure independence among sites.
Thirty-nine sites were sampled once 1. State variable: variable used to characterize the status of the wild-
every two weeks from April to mid- life system of interest; the system being studied.
June when salamanders were believed 2. Occupancy: the proportion of sites, patches, or habitat units oc-
to be most active and near the surface. cupied by a species.
However, we detected no salaman-
3. Detectability: the probability of detecting a species during a single
ders of the Desmognathus imitator
survey, given it is present at the site.
Coverboards 4. Confounded: an inability to separate multiple factors potentially
contributing to an observed pattern.
5. Likelihood function: a functional expression of unknown param-
eters, given observed data and an assumed model structure.
6. Parameters: quantities to be estimated, such as occupancy or de-
tectability, under an assumed model structure.
7. Logit function: an equation that converts a sigmoid relationship
(logistic) between two factors to a linear relationship. The logit
function involving detectability may be: logit(p)=ln(p/(1-p))= y.
complex during the first survey. Thus, 8. Heterogeneity: Often used synonymously with variation. Here, it is
we eliminated this survey from the used to refer to unexplained variation in the parameters of interest.
analysis because we assume the sala- 9. Probability-based sampling: a sampling scheme in which every
manders had not emerged from their sample unit (site) has a known probability of being selected (see
winter retreats and were unavailable Thompson et al. 1998).
for capture during this survey occa-
sion. This left a total of four surveys 10.Biased: describes an estimator that, over repeated trials, exhibits
a non-random (directional) difference from the true value being
for the analysis.
estimated.
Analysis, Model Selection, and
Interpretation: Salamanders of the 11.Parsimonious model selection: given a set of candidate models,
Desmognathus imitator complex selecting those model(s) that describe the information content of
were detected at 10 of the 39 sites, the data adequately with the fewest number of parameters pos-
yielding a naïve occupancy estimate sible.
of 0.26; however, we suspected that 12.Weighted average: an average where the contribution of the values
salamanders may be more likely to being averaged is unequal. For example, the unweighted average
occupy undisturbed sites compared of 5, 3, and 9 is (5+3+9)/3=(0.33(5)+0.33(3)+0.33(9))=5.7. How-
to disturbed sites. In addition, we ever, if we wanted the contribution of those three values to be 0.1,
thought detectability might vary 0.4, and 0.5 respectively, we would calculate a weighted average
among surveys due to environmental of (0.1(5)+0.4(3)+0.5(9))=6.2.
conditions such as rainfall or temper-
ature. Thus, we consider all combina-
tions of models in which occupancy
probability is assumed to be constant ous process of model selection,11 but indeed differs between previously
for all sites (denoted as ψ (.)) or Burnham and Anderson (2002) have disturbed and undisturbed sites; all of
varied among sites according to the written a comprehensive book on the the top models include previous dis-
site’s previous disturbance history (ψ subject. Using the software PRES- turbance history as a covariate in the
(dist)); detection probability was ei- ENCE and methods they describe, occupancy estimate. Model-averaged
ther constant ( p (.)), different among our analysis highlighted four models occupancy estimates were 0.19 (SE =
surveys (p (t)), or varied among sites as the best models representing our 0.15) and 0.70 (SE = 0.15) for previ-
according to previous disturbance his- salamander data (see Box 2). There is ously disturbed and undisturbed sites,
tory (p (dist)). some uncertainly as to which model respectively. Detectability also varied
Models that fit the data best with is the best, so our parameter estimates among surveys and possibly among
the least number of parameters are are essentially a weighted average12 sites with different disturbance histo-
favored. We do not have room to among all four models. Together ries (Figure 1, Box 2).
explain the details of this parsimoni- these models suggest that occupancy
Further Reading Caudata) populations: a twenty-year and dynamics of species occurance.
study in the southern Appalachians. Academic Press.
Ash, A. N. 1997. Disappearance and Brimleyana 18: 59-64.
return of salamanders to clearcut plots O’Connell, A. F., N. W. Talancy, L.
in the southern Blue Ridge Mountains. Hanski, I. 1992. Inferences from eco- L. Bailey, J. R. Sauer, R. Cook and
Conservation Biology 11: 983-989. logical incidence functions. American A. T. Gilbert. 2005. Estimating site
Naturalist 139: 657-662. occupancy and detection probability
Ash, A. N. and K. H. Pollock. 1999.
parameters for mammals in a coastal
Clearcuts, salamanders and field stud- Kendall, W. L. 1999. Robustness of ecosystem. Journal of Wildlife Man-
ies. Conservation Biology 13: 206- closed capture–recapture methods to agement 69: in press.
208. violations of the closure assumption.
Ecology 80: 2517–2525. Olson, G. A., R. G. Anthony, E. E.
Burnham, K. P. and D. R. Anderson.
Forsman, S. H. Ackers, P. J. Los-
2002. Model selection and multimodel MacKenzie, D. I., J. D. Nichols, G. B. chl, J. A. Reid, K. M. Dugger, E.
inference. Springer-Verlag, New York, Lachman, S. Droege, J. A. Royle and M. Glenn and W. J. Ripple. 2005.
New York, USA. C. A. Langtimm. 2002. Estimating site Modeling of site occupancy dynam-
occupancy rates when detection prob- ics for Northern Spotted Owls, with
Corn, P. S., B. R. Hossack, E. Muths,
abilities are less than one. Ecology 83: emphasis on the effects of Barred
D. A. Patla, C. R. Peterson and A. L.
2248-2255. Owls. Journal of Wildlife Manage-
Gallant. 2005. Status of amphibians
on the Continental Divide: surveys on ment 69: in press.
MacKenzie, D. I., J. D. Nichols, J.
a transect from Montana to Colorado, E. Hines, M. G. Knutson and A. Petranka, J. W., M. E. Eldridge and K.
USA. Alytes 22: 85-94. B. Franklin. 2003. Estimating site E. Haley. 1993. Effects of timber
Dodd, C. K. 2003. Monitoring amphib- occupancy, colonization and local harvesting on southern Appalachian
ians in Great Smoky Mountains extinction probabilities when a species salamanders. Conservation Biology 7:
National Park. U.S. Geological Survey is detected imperfectly. Ecology 84: 363-377.
Circular 1258. 117p. 2200-2207.
Petranka, J. W. 1999. Recovery of
Green, D. M. 1997. Perspectives on MacKenzie, D. I., L. L. Bailey and J. D. salamanders after clearcutting in the
amphibian population decline: defin- Nichols. 2004. Investigating species southern Appalachians: a critique of
ing the problem and searching for co-occurrence patterns when species Ash’s estimates. Conservation Biology
answers. In: Green D. M. (ed.) Am- are detected imperfectly. Journal of 13: 203-205.
phibians in decline: Canadian studies Animal Ecology 73: 546-555.
Scott, J. M., P. J. Heglund, M. L. Mor-
of a global problem. Herpetological
MacKenzie, D. I. and L. L. Bailey. 2004. rison, J. B. Haufler, M. G. Raphael, W.
Conservation 1: 291-308.
Assessing the fit of site occupancy A. Wall and F. B. Samson (eds). 2002.
Gu, W. and R. K. Swihart. 2004. Absent models. Journal of Agricultural, Bio- Predicting species occurrence: issues
or undetected? Effects of non-detec- logical and Environmental Statistics 9: of accuracy and scale. Island Press,
tion of species occurrence on wildlife- 300-318. Washington, D.C.
habitat models. Biological Conserva-
tion 116: 195-203. MacKenzie, D. I., J. D. Nichols, J. A. Ro- Thompson, W. L., G. C. White and C.
yle, K. H. Pollock, L. L. Bailey and J. Gowan. 1998. Monitoring vertebrate
Hairston, N. G. and R. H. Wiley. 1993. E. Hines. In press. Occupancy estima- populations. Academic Press, San
No decline in salamander (Amphibia: tion and modeling: inferring patterns Diego, CA.

Larissa Bailey, USGS Patuxent Wildlife


Research Center, [email protected]
301-497-5637

And

Michael Adams, USGS Forest and


Rangeland Ecosystem Science Center,
[email protected]
541-758-8857

Photo: Bufo boreas, Susanne L. Collins

You might also like