Biodiversity Science ›› 2019, Vol. 27 ›› Issue (3): 249-256.doi: 10.17520/biods.2018195

• Special Feature: Analysis of Wildlife Camera-Trapping Data • Previous Article     Next Article

Using occupancy models in wildlife camera-trapping monitoring and the study case

Xiao Wenhong1, Shu Zufei2, Chen Lijun1, Yao Wutao3, Ma Yong3, Zhang Yingming2, Xiao Zhishu1, 4, *()   

  1. 1 State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101
    2 Guangdong Chebaling National Nature Reserve Administration Bureau, Shaoguan, Guangdong 512500
    3 Institute of Remote Sensing and Digital Earth, Chinese Academy of Sciences, Beijing 100094
    4 University of Chinese Academy of Sciences, Beijing 100049
  • Received:2018-07-16 Accepted:2018-12-19 Online:2019-03-20
  • Xiao Zhishu E-mail:xiaozs@ioz.ac.cn

Occupancy models have the advantage of accounting for imperfect detection, they have simple and flexible data requirements as we all high economic efficiency. For these reasons, occupancy models have been increasingly applied in wildlife research. In this paper, we introduced the basic principles and use of the occupancy models. Using camera trap data we outlined the operational procedures and considerations from field investigation to data analysis. Using the masked palm civet (Paguma larvata) in the Guangdong Chebaling National Nature Reserve as an example we demonstrate the basic steps of how estimate occupancy and detect probability. Finally, according to occupancy model research from recent years, we summarize use trends and main limitations in the research.

Key words: camera trap, wildlife, data analysis, occupancy models, detectability, masked palm civet

Table 1

Summary of model selection results for masked palm civet occupancy in the Guangdong Chebaling National Nature Reserve, showing estimated occupancy probability (ψ) and detectability (p) for the models with ΔAIC ≤ 2"

模型
Model
K AIC ΔAIC AIC权重
AIC weight
Ψ p
p(海拔范围)ψ(海拔范围) p(elevation range)ψ(elevation range) 4 267.61 0 0.30 0.55 0.13
p(海拔范围, EVI)ψ (海拔范围) p(elevation range, EVI)ψ(elevation range) 5 268.99 1.38 0.15 0.55 0.12
p(海拔范围)ψ(海拔范围, EVI) p(elevation range)ψ(elevation range, EVI) 5 269.11 1.51 0.14 0.58 0.13
模型平均 Model average 0.56 0.13

Table 2

Covariates influencing masked palm civet occupancy and detectability according to β-coefficients and associated standard errors (SE)"

模型成分 Model component 协变量 Covariates 估计值 Estimate 标准误 SE P
占域 Occupancy 截距 Intercept 0.38 0.85 0.66
海拔范围 Elevation range -1.82 1.02 0.07
EVI 0.06 0.23 0.78
探测 Detection 截距 Intercept -2.45 0.26 < 0.001
海拔范围 Elevation range 1.29 0.30 < 0.001
EVI 0.04 0.12 0.75

Fig. 1

The effect of covariates (elevation range, EVI) on masked palm civet occupancy probability and detectability under top models. EVI, Enhanced vegetation index."

1 Ahumada JA, Silva CE, Gajapersad K, Hallam C, Hurtado J, Martin E, McWilliam A, Mugerwa B, O’Brien T, Rovero F ( 2011) Community structure and diversity of tropical forest mammals: Data from a global camera trap network. Philosophical Transactions of the Royal Society B: Biological Sciences, 366, 2703-2711.
doi: 10.1098/rstb.2011.0115 pmid: 21844049
2 Alexander JS, Shi K, Tallents LA, Riordan P ( 2015) On the high trail: Examining determinants of site use by the endangered snow leopard Panthera uncia in Qilianshan, China. Oryx, 50, 231-238.
doi: 10.1017/s0030605315001027
3 Bailey LL, Simons TR, Pollock KH ( 2004) Spatial and temporal variation in detection probability of Plethodon salamanders using the robust capture-recapture design. Journal of Wildlife Management, 68, 14-24.
doi: 10.2193/0022-541X(2004)068[0014:SATVID]2.0.CO;2
4 Bu HL, Wang F, McShea WJ, Lu Z, Wang DJ, Li S ( 2016) Spatial co-occurrence and activity patterns of mesocarnivores in the temperate forests of Southwest China. PLoS ONE, 11, e0164271.
doi: 10.1371/journal.pone.0164271 pmid: 5056745
5 Burnham KP, Anderson DR ( 2004) Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach, 2nd edn. Springer, New York.
6 Burton AC, Neilson E, Moreira D, Ladle A, Steenweg R, Fisher JT, Bayne E, Boutin S, Stephens P ( 2015) Wildlife camera trapping: A review and recommendations for linking surveys to ecological processes. Journal of Applied Ecology, 52, 675-685.
doi: 10.1111/1365-2664.12432
7 Clare JDJ, Anderson EM, Macfarland DM ( 2015) Predicting bobcat abundance at a landscape scale and evaluating occupancy as a density index in central Wisconsin. Journal of Wildlife Management, 79, 469-480.
doi: 10.1002/jwmg.844
8 Dorazio RM, Royle JA ( 2005) Estimating size and composition of biological communities by modeling the occurrence of species. Journal of the American Statistical Association, 100, 389-398.
doi: 10.1198/016214505000000015
9 Dorazio RM, Royle JA, Soderstrom B, Glimskar A ( 2006) Estimating species richness and accumulation by modeling species occurrence and detectability. Ecology, 87, 842-854.
doi: 10.1890/0012-9658(2006)87[842:ESRAAB]2.0.CO;2 pmid: 16676528
10 Efford MG, Dawson DK ( 2012) Occupancy in continuous habitat. Ecosphere, 3, 1-15.
11 Eraud C, Boutin JM, Roux D, Faivre B ( 2007) Spatial dynamics of an invasive bird species assessed using robust design occupancy analysis: The case of the Eurasian collared dove (Streptopelia decaocto) in France. Journal of Biogeography, 34, 1077-1086.
doi: 10.1111/j.1365-2699.2006.01673.x
12 Falke JA, Bailey LL, Fausch KD, Bestgen KR ( 2012) Colonization and extinction in dynamic habitats: An occupancy approach for a Great Plains stream fish assemblage. Ecology, 93, 858-867.
doi: 10.1890/11-1515.1 pmid: 22690636
13 Ferraz G, Nichols JD, Hines JE, Stouffer PC, Bierregaard RO, Lovejoy TE ( 2007) A large-scale deforestation experiment: Effects of patch area and isolation on Amazon birds. Science, 315, 238-241.
doi: 10.1126/science.1133097
14 Fiske IJ, Chandler RB ( 2011) Unmarked: An R package for fitting hierarchical models of wildlife occurrence and abundance. Journal of Statistical Software, 43, 1-23.
15 Guillera-Arroita G ( 2011) Impact of sampling with replacement in occupancy studies with spatial replication. Methods in Ecology and Evolution, 2, 401-406.
doi: 10.1111/j.2041-210X.2011.00089.x pmid: 00009799
16 Karanth KU, Gopalaswamy AM, Kumar NS, Vaidyanathan S, Nichols JD, MacKenzie DI ( 2011) Monitoring carnivore populations at the landscape scale: Occupancy modelling of tigers from sign surveys. Journal of Applied Ecology, 48, 1048-1056.
doi: 10.1111/j.1365-2664.2011.02002.x
17 Kéry M, Guillera-Arroita G, Lahoz-Monfort JJ ( 2013) Analysing and mapping species range dynamics using occupancy models. Journal of Biogeography, 40, 1463-1474.
doi: 10.1111/jbi.12087
18 Kéry M, Royle JA ( 2008) Hierarchical Bayes estimation of species richness and occupancy in spatially replicated surveys. Journal of Applied Ecology, 45, 589-598.
doi: 10.1111/j.1365-2664.2007.01441.x
19 Kéry M, Royle JA ( 2009) Inference about species richness and community structure using species-specific occupancy models in the national Swiss breeding bird survey MHB. In: Demographic Processes in Marked Populations (eds Thomson DL, Cooch EG, Conroy MJ), pp. 639-656. Springer, New York.
doi: 10.1007/978-0-387-78151-8_28
20 Li S, Wang DJ, Xiao ZS, Li XH, Wang TM, Feng LM, Wang Y ( 2014) Camera-trapping in wildlife research and conservation in China: Review and outlook. Biodiversity Science, 22, 685-695. (in Chinese with English abstract)
doi: 10.3724/SP.J.1003.2014.14203
[ 李晟, 王大军, 肖治术, 李欣海, 王天明, 冯利民, 王云 ( 2014) 红外相机技术在我国野生动物研究与保护中的应用与前景. 生物多样性, 22, 685-695.]
doi: 10.3724/SP.J.1003.2014.14203
21 Linden DW, Fuller AK, Royle JA, Hare MP ( 2017) Examining the occupancy-density relationship for a low-density carnivore. Journal of Applied Ecology, 54, 2043-2052.
doi: 10.1111/1365-2664.12883
22 Linkie M, Dinata Y, Nugroho A, Haidir IA ( 2007) Estimating occupancy of a data deficient mammalian species living in tropical rainforests: Sun bears in the Kerinci Seblat region, Sumatra. Biological Conservation, 137, 20-27.
doi: 10.1016/j.biocon.2007.01.016
23 MacKenzie DI, Nichols JD, Royle JA, Pollock KH, Bailey LL, Hines JE ( 2006) Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence. Academic Press, San Diego.
24 MacKenzie DI, Bailey LL ( 2004) Assessing the fit of site-occupancy models. Journal of Agricultural Biological and Environmental Statistics, 9, 300-318.
doi: 10.2307/1400484
25 MacKenzie DI, Bailey LL, Nichols JD ( 2004) Investigating species co-occurrence patterns when species are detected imperfectly. Journal of Animal Ecology, 73, 546-555.
doi: 10.1111/jae.2004.73.issue-3
26 MacKenzie DI, Nichols JD, Hines JE, Knutson MG, Franklin AB ( 2003) Estimating site occupancy, colonization, and local extinction when a species is detected imperfectly. Ecology, 84, 2200-2207.
doi: 10.1890/02-3090
27 MacKenzie DI, Nichols JD, Lachman GB, Droege S, Royle JA, Langtimm CA ( 2002) Estimating site occupancy rates when detection probabilities are less than one. Ecology, 83, 2248-2255.
doi: 10.2307/3072056
28 MacKenzie DI, Nichols JD, Royle JA, Pollock KH, Bailey LL, Hines JE ( 2017) Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence, 2nd edn. Academic Press, San Diego.
29 MacKenzie DI, Royle JA ( 2005) Designing occupancy studies: General advice and allocating survey effort. Journal of Applied Ecology, 42, 1105-1114.
doi: 10.1111/j.1365-2664.2005.01098.x
30 Miller DA, Brehme CS, Hines JE, Nichols JD, Fisher RN ( 2012) Joint estimation of habitat dynamics and species interactions: Disturbance reduces co-occurrence of non-native predators with an endangered toad. Journal of Animal Ecology, 81, 1288-1297.
doi: 10.1111/j.1365-2656.2012.02001.x pmid: 22702337
31 Miller DA, Nichols JD, McClintock BT, Grant EHC, Bailey LL, Weir LA ( 2011) Improving occupancy estimation when two types of observational error occur: Non-detection and species misidentification. Ecology, 92, 1422-1428.
doi: 10.1890/10-1396.1 pmid: 21870616
32 Nichols JD, Bailey LL, Talancy NW, Grant EHC, Gilbert AT, Annand EM, Husband TP, Hines JE ( 2008) Multi-scale occupancy estimation and modelling using multiple detection methods. Journal of Applied Ecology, 45, 1321-1329.
doi: 10.1111/jpe.2008.45.issue-5
33 O’Connell AF, Talancy NW, Bailey LL, Sauer JR, Cook R, Gilbert AT ( 2006) Estimating site occupancy and detection probability parameters for meso- and large mammals in a coastal ecosystem. Journal of Wildlife Management, 70, 1625-1633.
doi: 10.2193/0022-541X(2006)70[1625:ESOADP]2.0.CO;2
34 Peterman WE, Rittenhouse TAG, Earl JE, Semlitsch RD ( 2013) Demographic network and multi-season occupancy modeling of Rana sylvatica reveal spatial and temporal patterns of population connectivity and persistence. Landscape Ecology, 28, 1601-1613.
doi: 10.1007/s10980-013-9906-9
35 Pilliod DS, Goldberg CS, Arkle RS, Waits LP ( 2013) Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples. Canadian Journal of Fisheries and Aquatic Sciences, 70, 1123-1130.
doi: 10.1139/cjfas-2013-0047
36 Rovero F, Martin E, Rosa M, Ahumada JA, Spitale D ( 2014) Estimating species richness and modelling habitat preferences of tropical forest mammals from camera trap data. PLoS ONE, 9, e103300.
doi: 10.1371/journal.pone.0103300 pmid: 4108438
37 Royle JA, Kéry M ( 2007) A Bayesian state-space formulation of dynamic occupancy models. Ecology, 88, 1813-1823.
doi: 10.1890/06-0669.1
38 Ruiz-Gutiérrez V, Zipkin EF, Dhondt AA ( 2010) Occupancy dynamics in a tropical bird community: Unexpectedly high forest use by birds classified as non-forest species. Journal of Applied Ecology, 47, 621-630.
doi: 10.1111/j.1365-2664.2010.01811.x
39 Russell RE, Royle JA, Saab VA, Lehmkuhl JF, Block WM, Sauer JR ( 2009) Modeling the effects of environmental disturbance on wildlife communities: Avian responses to prescribed fire. Ecological Applications, 19, 1253-1263.
doi: 10.1890/08-0910.1 pmid: 19688932
40 Santulli G, Palazon S, Melero Y, Gosalbez J, Lambin X ( 2014) Multi-season occupancy analysis reveals large scale competitive exclusion of the critically endangered European mink by the invasive non-native American mink in Spain. Biological Conservation, 176, 21-29.
doi: 10.1016/j.biocon.2014.05.002
41 Scotson L, Johnston LR, Iannarilli F, Wearn OR, Mohd-Azlan J, Wong WM, Gray TNE, Dinata Y, Suzuki A, Willard CE, Frechette J, Loken B, Steinmetz R, MoΒbrucker AM, Clements GR, Fieberg J, Rowcliffe M, De Angelo C ( 2017) Best practices and software for the management and sharing of camera trap data for small and large scales studies. Remote Sensing in Ecology and Conservation, 3, 158-172.
doi: 10.1002/rse2.54
42 Shannon G, Lewis JS, Gerber BD ( 2014) Recommended survey designs for occupancy modelling using motion-activated cameras: Insights from empirical wildlife data. PeerJ, 2, e532.
doi: 10.7717/peerj.532 pmid: 25210658
43 Sollmann R, Furtado MM, Hofer H, Jacomo ATA, Torres NM, Silveira L ( 2012) Using occupancy models to investigate space partitioning between two sympatric large predators, the jaguar and puma in central Brazil. Mammalian Biology, 77, 41-46.
doi: 10.1016/j.mambio.2011.06.011
44 Steenweg R, Hebblewhite M, Whittington J, Mckelvey K, Lukacs P ( 2018) Sampling scales define occupancy and the occupancy-abundance relationship in animals. Ecology, 99, 172-183.
doi: 10.1002/ecy.2054 pmid: 29065232
45 Tobler MW, Zúñiga A, Carrillo-Percastegui SE, Powell GVN, Lukacs P ( 2015) Spatiotemporal hierarchical modelling of species richness and occupancy using camera trap data. Journal of Applied Ecology, 52, 413-421.
doi: 10.1111/1365-2664.12399
46 Wan YQ, Wu J, Mo YM, Wu ZJ, Li GF, Xu HG ( 2017) Distribution and site occupancy analysis of 11 species of amphibians in Guangxi. Journal of Ecology and Rural Environment, 33, 281-287. (in Chinese with English abstract)
doi: 10.11934/j.issn.1673-4831.2017.03.013
[ 万雅琼, 吴军, 莫运明, 武正军, 李桂芬, 徐海根 ( 2017) 广西11种两栖动物的分布及占域分析. 生态与农村环境学报, 33, 281-287.]
doi: 10.11934/j.issn.1673-4831.2017.03.013
47 Wang F, McShea WJ, Wang DJ, Li S ( 2015 a) Shared resources between giant panda and sympatric wild and domestic mammals. Biological Conservation, 186, 319-325.
doi: 10.1016/j.biocon.2015.03.032
48 Wang TM, Royle JA, Smith JLD, Zou L, Lu XY, Li T, Yang HT, Li ZL, Feng RN, Bian YJ, Feng LM, Ge JP ( 2018) Living on the edge: Opportunities for Amur tiger recovery in China. Biological Conservation, 217, 269-279.
doi: 10.1016/j.biocon.2017.11.008
49 Wang Y, Allen ML, Wilmers CC ( 2015 b) Mesopredator spatial and temporal responses to large predators and human development in the Santa Cruz Mountains of California. Biological Conservation, 190, 23-33.
doi: 10.1016/j.biocon.2015.05.007
50 Wearn OR, Glover-Kapfer P ( 2017) Camera-trapping for Conservation: A Guide to Best-Practices. WWF-UK, Woking, United Kingdom.
51 White GC, Burnham KP ( 1999) Program MARK: Survival estimation from populations of marked animals. Bird Study, 46, 120-139.
doi: 10.1080/00063659909477239
52 Zipkin EF, DeWan A, Royle JA ( 2009) Impacts of forest fragmentation on species richness: A hierarchical approach to community modelling. Journal of Applied Ecology, 46, 815-822.
doi: 10.1111/j.1365-2664.2009.01664.x
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