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

doi:10.17520/biods.2018195

Abstract

Abstract:

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

Xiao Wenhong,Shu Zufei,Chen Lijun,Yao Wutao,Ma Yong,Zhang Yingming,Xiao Zhishu. Using occupancy models in wildlife camera-trapping monitoring and the study case[J]. Biodiv Sci, 2019, 27(3): 249-256.

Add to citation manager EndNote|Ris|BibTeX

URL: https://www.biodiversity-science.net/EN/10.17520/biods.2018195

https://www.biodiversity-science.net/EN/Y2019/V27/I3/249

Figures/Tables 3

References 52

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 URL PMID
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 URL
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 URL
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 URL PMID
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 URL
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 URL
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 URL
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 URL PMID
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 URL
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 URL PMID
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 URL
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 URL PMID
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 URL
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 URL
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 URL
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 URL
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 URL
	[ 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 URL
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 URL
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 URL
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 URL
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 URL
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 URL
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 URL
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 URL
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 URL PMID
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 URL PMID
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 URL
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 URL
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 URL
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 URL
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 URL PMID
37	Royle JA, Kéry M ( 2007) A Bayesian state-space formulation of dynamic occupancy models. Ecology, 88, 1813-1823. DOI URL
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 URL
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 URL PMID
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 URL
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 URL
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 URL PMID
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 URL
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 URL PMID
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 URL
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 URL
	[ 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 URL
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 URL
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 URL
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 URL
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 URL
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 URL

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

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

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

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

[1]	Min Luo, Yongchuan Yang, Cheng Jin, Lihua Zhou, Yuxiao Long. Composition profile and response to human activity of mammals in the urban forests of central Chongqing [J]. Biodiv Sci, 2025, 33(5): 24402-.
[2]	Fu Mengdi, Zhu Yanpeng, Ren Yueheng, Li Shuang, Qin Le, Xie Zhengjun, Wang Qingchun, Zhang Libo. Research on the optimization of wildlife passage spatial layout in Xinjiang [J]. Biodiv Sci, 2025, 33(3): 24346-.
[3]	Gong Cuifeng, Wei Wei, Luo Gai, Han Yimin, Wu Pengcheng, He Mengnan, Min Qingyue, Fu Qiang, Chen Peng. Spatial distribution and coexistence of ungulates in Chongzhou Area of Giant Panda National Park [J]. Biodiv Sci, 2025, 33(3): 24260-.
[4]	Wang Dawei, Cheng Shuai, Feng Jiawei, Wang Tianming. The wildlife camera-trapping dataset of Zhangguangcai Mountains in Northeast China (2015-2020) [J]. Biodiv Sci, 2025, 33(2): 24384-.
[5]	Sicheng Han, Daowei Lu, Yuchen Han, Ruohan Li, Jing Yang, Ge Sun, Lu Yang, Junwei Qian, Xiang Fang, Shu-Jin Luo. Distribution of leopard cats in the nearest mountains to urban Beijing and its affecting environmental factors [J]. Biodiv Sci, 2024, 32(8): 24138-.
[6]	Jiayu Lu, Xiaoyi Shi, Li’an Duo, Tianming Wang, Zhilin Li. Circadian rhythms of urban terrestrial mammals in Tianjin based on camera trapping method [J]. Biodiv Sci, 2024, 32(8): 23369-.
[7]	Rongfei Su, Ruishan Chen, Linlin Yu, Jingbin Wu, Yan Kang. Biodiversity in community habitat gardens in Changning District, Shanghai based on camera trapping [J]. Biodiv Sci, 2024, 32(8): 24068-.
[8]	Mingjun Zhang, Hesheng Wang, Wenbo Yan, Yunnan Fu, Qi Wang, Zhigao Zeng. Diel activity and habitat selection of small Indian civets (Viverricula indica) in Hainan Datian National Nature Reserve [J]. Biodiv Sci, 2024, 32(6): 23420-.
[9]	Binyue Lu, Kun Li, Chenxi Wang, Sheng Li. The application and outlook of wildlife tracking using sensor-based tags in China [J]. Biodiv Sci, 2024, 32(5): 23497-.
[10]	Qifan Wang, Xiaohui Liu, Ziwei Zhu, Lei Liu, Xinxue Wang, Xuyang Ji, Shaochun Zhou, Zidong Zhang, Hongyu Dong, Minghai Zhang. Mammal and avian diversity in Beijicun National Nature Reserve, Heilongjiang Province, China [J]. Biodiv Sci, 2024, 32(4): 24024-.
[11]	Xiaotong Mai, Jia Kang, Zichen Li, Tianming Wang. Assessing activity pattern of sika deer (Cervus nippon) and their response to roads in the Northeast China Tiger and Leopard National Park [J]. Biodiv Sci, 2024, 32(11): 24178-.
[12]	Jinfeng Chen, Xinjing Wu, Hai Lin, Guofa Cui. A comparative analysis of the List of State Key Protected Wild Animals and other wildlife protection lists [J]. Biodiv Sci, 2023, 31(6): 22639-.
[13]	Kunming Zhao, Shengbin Chen, Xifu Yang. Investigation of the diversity of mammals and birds and the activity rhythm of dominant species using camera trapping in a fragmented forest in the Dujiangyan region, Sichuan Province [J]. Biodiv Sci, 2023, 31(6): 22529-.
[14]	Benping Chen, Jianwu Chen, Zhengwen Ling, Xu Yang, Xin Chen, Shengqiang Li, Biao Yang. Developing a dataset on the diversity and dynamic changes of mammals and birds recorded using camera traps in Laojun Mountain National Nature Reserve, Sichuan, China [J]. Biodiv Sci, 2023, 31(5): 22566-.
[15]	Zhenzhen Li, Mengtian Du, Yuanxin Zhu, Dawei Wang, Zhilin Li, Tianming Wang. A practical guide for estimating the density of unmarked populations using camera traps [J]. Biodiv Sci, 2023, 31(3): 22422-.