Likelihood analysis of spatial capture-recapture models for stratified or class structured populations

We develop a likelihood analysis framework for fitting spatial capture-recapture (SCR) models to data collected on class structured or stratified populations. Our interest is motivated by the necessity of accommodating the problem of missing observations of individual class membership. This is particularly problematic in SCR data arising from DNA analysis of scat, hair or other material, which frequently yields individual identity but fails to identify the sex. Moreover, this can represent a large fraction of the data and, given the typically small sample sizes of many capture-recapture studies based on DNA information, utilization of the data with missing sex information is necessary. We develop the class structured likelihood for the case of missing covariate values, and then we address the scaling of the likelihood so that models with and without class structured parameters can be formally compared regardless of missing values. We apply our class structured model to black bear data collected in New Yor...

[1]  J. Andrew Royle,et al.  Estimating abundance of mountain lions from unstructured spatial sampling , 2012 .

[2]  J. Andrew Royle,et al.  Spatial Capture-Recapture , 2013 .

[3]  Joseph E. Duchamp,et al.  Density and distribution of a colonizing front of the American black bear Ursus americanus , 2011 .

[4]  James E. Hines,et al.  ESTIMATION OF SEX-SPECIFIC SURVIVAL FROM CAPTURE-RECAPTURE DATA WHEN SEX IS NOT ALWAYS KNOWN , 2004 .

[5]  Michael S. Mitchell,et al.  Combined use of mark‐recapture and genetic analyses reveals response of a black bear population to changes in food productivity , 2013 .

[6]  J. Andrew Royle,et al.  Estimating Black Bear Density Using DNA Data From Hair Snares , 2010 .

[7]  J. Alho.  Logistic regression in capture-recapture models. , 1990, Biometrics.

[8]  Catherine C. Sun.  Estimating Black Bear Population Density In The Southern Black Bear Range Of New York With A Non-Invasive, Genetic, Spatial Capture-Recapture Study , 2014 .

[9]  J. Andrew Royle,et al.  Mixture Models for Estimating the Size of a Closed Population When Capture Rates Vary among Individuals , 2003, Biometrics.

[10]  David Borchers,et al.  A non-technical overview of spatially explicit capture–recapture models , 2012, Journal of Ornithology.

[11]  J Andrew Royle,et al.  Spatial capture--recapture models for jointly estimating population density and landscape connectivity. , 2013, Ecology.

[12]  J. Andrew Royle,et al.  Integrating resource selection information with spatial capture–recapture , 2012, Methods in Ecology and Evolution.

[13]  R. G. Anthony,et al.  Estimation of Black Bear Abundance Using a Discrete DNA Sampling Device , 2008 .

[14]  Roger Pradel,et al.  Estimation of sex‐specific survival with uncertainty in sex assessment , 2008 .

[15]  D. Borchers,et al.  Mark-Recapture Models for Line Transect Surveys , 1998 .

[16]  Jerrold L. Belant,et al.  American black bear population size and genetic diversity at Apostle Islands National Lakeshore , 2005 .

[17]  L. Waits,et al.  NONINVASIVE GENETIC SAMPLING TOOLS FOR WILDLIFE BIOLOGISTS: A REVIEW OF APPLICATIONS AND RECOMMENDATIONS FOR ACCURATE DATA COLLECTION , 2005 .

[18]  Gordon B. Stenhouse,et al.  An empirical test of DNA mark–recapture sampling strategies for grizzly bears , 2006 .

[19]  J. Andrew Royle,et al.  Modelling non‐Euclidean movement and landscape connectivity in highly structured ecological networks , 2015 .

[20]  Toshio Tsubota,et al.  Sex identification of Japanese black bear, Ursus thibetanus japonicus, by PCR based on amelogenin gene. , 2002, The Journal of veterinary medical science.

[21]  K. Pollock.  The use of auxiliary variables in capture-recapture modelling: An overview , 2002 .

[22]  David R. Anderson,et al.  Statistical inference from capture data on closed animal populations , 1980 .

[23]  David L. Borchers,et al.  Estimating Animal Abundance: Closed Populations , 2010 .

[24]  David Paetkau,et al.  Genetic tagging of free-ranging black and brown bears , 1999 .

[25]  M. Efford.  Density estimation in live‐trapping studies , 2004 .

[26]  R. Huggins.  On the statistical analysis of capture experiments , 1989 .

[27]  M. Efford,et al.  Compensatory heterogeneity in spatially explicit capture-recapture data. , 2014, Ecology.

[28]  J. Andrew Royle,et al.  Hierarchical spatial capture–recapture models: modelling population density in stratified populations , 2014 .

[29]  D L Borchers,et al.  Spatially Explicit Maximum Likelihood Methods for Capture–Recapture Studies , 2008, Biometrics.

[30]  G. Mowat,et al.  Estimating population size of grizzly bears using hair capture, DNA profiling, and mark-recapture analysis , 2000 .

[31]  J Andrew Royle,et al.  Analysis of Capture–Recapture Models with Individual Covariates Using Data Augmentation , 2008, Biometrics.

[32]  J Andrew Royle,et al.  A hierarchical model for spatial capture-recapture data. , 2008, Ecology.

[33]  M. Proctor,et al.  SAMPLING DESIGN AND BIAS IN DNA-BASED CAPTURE–MARK–RECAPTURE POPULATION AND DENSITY ESTIMATES OF GRIZZLY BEARS , 2004 .