A Review of the Use of Conditional Likelihood in Capture‐Recapture Experiments

Resume Nous presentons une perspective moderne de l'approche par vraisemblances conditionnelles de l'analyse des experiences de capture-recapture. Nous montrons que ces vraisemblances conditionnelles relevent d'un modele lineaire generalise, ce qui permet l'application des nombreuses methodes elaborees dans ce cadre. Pour replacer ces applications dans leur contexte, nous passons en revue quelques-unes des approches existantes dans les modeles de capture-recapture avec probabilites de capture heterogenes au sein de populations fermees. Nous decrivons, en particulier, l'utilisation de modeles de melange parametriques et non parametriques, et examinons de facon plus detaillee le cas ou les probabilites de capture sont fonction de covariables. Summary We present a modern perspective of the conditional likelihood approach to the analysis of capture-recapture experiments, which shows the conditional likelihood to be a member of generalized linear model (GLM). Hence, there is the potential to apply the full range of GLM methodologies. To put this method in context, we first review some approaches to capture-recapture experiments with heterogeneous capture probabilities in closed populations, covering parametric and non-parametric mixture models and the use of covariates. We then review in more detail the analysis of capture-recapture experiments when the capture probabilities depend on a covariate.

[1]  Louis-Paul Rivest,et al.  Improved log‐linear model estimators of abundance in capture‐recapture experiments , 2001 .

[2]  G. Seber,et al.  Estimating Animal Abundance: Review III , 1999 .

[3]  R. Huggins Some practical aspects of a conditional likelihood approach to capture experiments , 1991 .

[4]  L. Rivest,et al.  Rcapture: Loglinear Models for Capture-Recapture in R , 2007 .

[5]  Richard M. Huggins,et al.  An examination of the effect of heterogeneity on the estimation of population size using capture-recapture data , 2005 .

[6]  Anders Hald,et al.  History of Probability and Statistics and Their Applications before 1750: Hald/History of Probability & Statistics , 2005 .

[7]  N. Beeching,et al.  Capture-recapture-adjusted prevalence rates of type 2 diabetes are related to social deprivation. , 1999, QJM : monthly journal of the Association of Physicians.

[8]  Paul S. F. Yip,et al.  Estimation in capture–recapture models when covariates are subject to measurement errors and missing data , 2009 .

[9]  Peter G M van der Heijden,et al.  The multiple‐record systems estimator when registrations refer to different but overlapping populations , 2004, Statistics in medicine.

[10]  I. Olkin,et al.  A Comparison of n Estimators for the Binomial Distribution , 1981 .

[11]  J. Nichols,et al.  ESTIMATING SPECIES RICHNESS: THE IMPORTANCE OF HETEROGENEITY IN SPECIES DETECTABILITY , 1998 .

[12]  K. Burnham,et al.  Estimation of the size of a closed population when capture probabilities vary among animals , 1978 .

[13]  Shirley Pledger,et al.  Using Mixtures to Model Heterogeneity in Ecological Capture‐Recapture Studies , 2008, Biometrical journal. Biometrische Zeitschrift.

[14]  A Chao,et al.  Estimating population size via sample coverage for closed capture-recapture models. , 1994, Biometrics.

[15]  A Chao,et al.  The applications of capture‐recapture models to epidemiological data , 2001, Statistics in medicine.

[16]  A. Chao,et al.  Estimating the Number of Classes via Sample Coverage , 1992 .

[17]  S E Fienberg,et al.  A three-sample multiple-recapture approach to census population estimation with heterogeneous catchability. , 1993, Journal of the American Statistical Association.

[18]  W. G. Cochran Laplace's Ratio Estimator , 1978 .

[19]  Robert K. Colwell,et al.  Estimating terrestrial biodiversity through extrapolation. , 1994, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[20]  Stephen V. Stehman,et al.  The Horvitz-Thompson Theorem as a Unifying Perspective for Probability Sampling: With Examples from Natural Resource Sampling , 1995 .

[21]  E. Ronchetti,et al.  Robust Inference for Generalized Linear Models , 2001 .

[22]  R R Regal,et al.  Capture-recapture methods in epidemiology: methods and limitations. , 1995, Epidemiologic reviews.

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

[24]  R. LaPorte Assessing the human condition: capture-recapture techniques , 1994, BMJ.

[25]  Louis-Paul Rivest,et al.  Why a time effect often has a limited impact on capture‐recapture estimates in closed populations , 2008 .

[26]  J. Norris,et al.  Non-parametric MLE for Poisson species abundance models allowing for heterogeneity between species , 1998, Environmental and Ecological Statistics.

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

[28]  A. Agresti Simple capture-recapture models permitting unequal catchability and variable sampling effort. , 1994, Biometrics.

[29]  Peter G M van der Heijden,et al.  Point and Interval Estimation of the Population Size Using a Zero‐Truncated Negative Binomial Regression Model , 2008, Biometrical journal. Biometrische Zeitschrift.

[30]  E. N. Zwane,et al.  Semiparametric models for capture-recapture studies with covariates , 2004, Comput. Stat. Data Anal..

[31]  Roderick J. A. Little,et al.  Statistical Analysis with Missing Data: Little/Statistical Analysis with Missing Data , 2002 .

[32]  Wen-Han Hwang,et al.  Estimation in capture-recapture models when covariates are subject to measurement errors. , 2003, Biometrics.

[33]  Richard M. Huggins,et al.  APPLICATION OF SEMIPARAMETRIC REGRESSION MODELS IN THE ANALYSIS OF CAPTURE-RECAPTURE EXPERIMENTS , 2007 .

[34]  D. Lin,et al.  Inference for capture-recapture experiments in continuous time with variable capture rates , 1996 .

[35]  B. Lindsay,et al.  A Penalized Nonparametric Maximum Likelihood Approach to Species Richness Estimation , 2005 .

[36]  G. Seber A Review of Estimating Animal Abundance II , 1992 .

[37]  D. Böhning,et al.  Nonparametric maximum likelihood estimation of population size based on the counting distribution , 2005 .

[38]  I. Good THE POPULATION FREQUENCIES OF SPECIES AND THE ESTIMATION OF POPULATION PARAMETERS , 1953 .

[39]  P. Jupp,et al.  Inference for Poisson and multinomial models for capture-recapture experiments , 1991 .

[40]  S. Pledger Unified Maximum Likelihood Estimates for Closed Capture–Recapture Models Using Mixtures , 2000, Biometrics.

[41]  D. Böhning,et al.  Estimating the number of drug users in Bangkok 2001: A capture–recapture approach using repeated entries in one list , 2004, European Journal of Epidemiology.

[42]  A. Chao,et al.  A Sample Coverage Approach to Multiple-System Estimation with Application to Census Undercount , 1998 .

[43]  Chang Xuan Mao,et al.  On Comparison of Mixture Models for Closed Population Capture–Recapture Studies , 2009, Biometrics.

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

[45]  P. Yip,et al.  Estimating Population Size for a Continuous Time Frailty Model with Covariates in a Capture–Recapture Study , 2007, Biometrics.

[46]  S. Fienberg The multiple recapture census for closed populations and incomplete 2k contingency tables , 1972 .

[47]  E. Zwane,et al.  Implementing the Parametric Bootstrap in Capture-Recapture Models with Continuous Covariates , 2002 .

[48]  T. Yee The VGAM Package for Categorical Data Analysis , 2010 .

[49]  K. Tilling,et al.  Capture-recapture models including covariate effects. , 1999, American journal of epidemiology.

[50]  Anne Chao,et al.  An overview of closed capture-recapture models , 2001 .

[51]  Hans C van Houwelingen,et al.  Point and interval estimation of the population size using the truncated Poisson regression model , 2003 .

[52]  K. Burnham,et al.  Program MARK: survival estimation from populations of marked animals , 1999 .

[53]  K. Burnham,et al.  Robust Estimation of Population Size When Capture Probabilities Vary Among Animals , 1979 .

[54]  J. Nichols,et al.  The Use of Auxiliary Variables in Capture-Recapture and Removal Experiments , 1984 .

[55]  L. Sanathanan Models and Estimation Methods in Visual Scanning Experiments , 1972 .

[56]  B. Silverman,et al.  Nonparametric regression and generalized linear models , 1994 .

[57]  Wen-Han Hwang,et al.  Measurement errors in continuous-time capture–recapture models , 2007 .

[58]  A. Chao Estimating the population size for capture-recapture data with unequal catchability. , 1987, Biometrics.

[59]  Cormack Rm,et al.  Problems with using capture-recapture in epidemiology: an example of a measles epidemic. , 1999 .

[60]  A Chao,et al.  Estimating population size for capture-recapture data when capture probabilities vary by time and individual animal. , 1992, Biometrics.

[61]  Dankmar Böhning,et al.  Mixture models for capture-recapture count data , 2005, Stat. Methods Appl..

[62]  Lalitha Sanathanan,et al.  ESTIMATING THE SIZE OF A MULTINOMIAL POPULATION , 1972 .

[63]  B. Lindsay,et al.  Estimating the number of classes , 2007, 0708.2153.

[64]  R. L. Sandland,et al.  Statistical inference for Poisson and multinomial models for capture-recapture experiments , 1984 .

[65]  Chang Xuan Mao,et al.  Estimating population sizes for capture-recapture sampling with binomial mixtures , 2007, Comput. Stat. Data Anal..

[66]  Hsin-Chou Yang,et al.  Modeling Animals' Behavioral Response by Markov Chain Models for Capture–Recapture Experiments , 2005, Biometrics.

[67]  J. R. Cook,et al.  Simulation-Extrapolation Estimation in Parametric Measurement Error Models , 1994 .

[68]  Lionel C. Briand,et al.  A Comprehensive Evaluation of Capture-Recapture Models for Estimating Software Defect Content , 2000, IEEE Trans. Software Eng..

[69]  Anne Chao,et al.  Estimating population size for sparse data in capture-recapture experiments , 1989 .

[70]  J. Norris,et al.  NONPARAMETRIC MLE UNDER TWO CLOSED CAPTURE-RECAPTURE MODELS WITH HETEROGENEITY , 1996 .

[71]  G. Seber A review of estimating animal abundance. , 1986, Biometrics.

[72]  A Semiparametric Method for Estimating Population Size for Capture–Recapture Experiments with Random Covariates in Continuous Time , 2005, Biometrics.

[73]  A. Munk,et al.  On Identifiability in Capture–Recapture Models , 2006, Biometrics.

[74]  R E LaPorte,et al.  Ascertainment corrected rates: applications of capture-recapture methods. , 1993, International journal of epidemiology.

[75]  A. Chao,et al.  Stopping rules and estimation for recapture debugging with unequal failure rates , 1993 .

[76]  D. Bőhning,et al.  A covariate adjustment for zero-truncated approaches to estimating the size of hidden and elusive populations , 2009, 0908.2296.

[77]  Anne Chao,et al.  Population size estimation based on estimating functions for closed capture–recapture models ☆ , 2001 .

[78]  Paul S. F. Yip,et al.  A Martingale Estimating Equation for a Capture-Recapture Experiment in Discrete Time , 1991 .

[79]  Ganapati P. Patil Maximum likelihood estimation for generalized power series distributions and its application to a truncated binomial distribution , 1962 .

[80]  R. Huggins,et al.  Non‐parametric estimation of population size from capture–recapture data when the capture probability depends on a covariate , 2007 .

[81]  Richard Huggins,et al.  Heterogeneous Capture–Recapture Models with Covariates: A Partial Likelihood Approach for Closed Populations , 2011, Biometrics.

[82]  Kani Chen,et al.  Parametric and semiparametric models for recapture and removal studies: a likelihood approach , 2001 .

[83]  R. Cormack Log-linear models for capture-recapture , 1989 .

[84]  A. Chao,et al.  ASYMPTOTIC PROPERTIES OF AN OPTIMAL ESTIMATING FUNCTION APPROACH TO THE ANALYSIS OF MARK RECAPTURE DATA , 2002 .

[85]  Peter G. M. van der Heijden,et al.  Estimating the Size of a Criminal Population from Police Records Using the Truncated Poisson Regression Model , 2003 .

[86]  A. Agresti,et al.  The Use of Mixed Logit Models to Reflect Heterogeneity in Capture‐Recapture Studies , 1999, Biometrics.

[87]  Raymond J. Carroll,et al.  Conditional scores and optimal scores for generalized linear measurement-error models , 1987 .

[88]  Martin Fox,et al.  Estimation of the Parameter n in the Binomial Distribution , 1968 .

[89]  Yan Wang,et al.  The Application of Capture-Recapture Methods in Reliability Studies , 2003 .

[90]  T. Mastro,et al.  Estimating the number of HIV-infected injection drug users in Bangkok: a capture--recapture method. , 1994, American journal of public health.

[91]  F. Simondon,et al.  Capture-recapture method for estimating misclassification errors: application to the measurement of vaccine efficacy in randomized controlled trials. , 1999, International journal of epidemiology.

[92]  Juni Palmgren,et al.  The Fisher information matrix for log linear models arguing conditionally on observed explanatory variable , 1981 .

[93]  H. Rubin,et al.  Estimation of binomial parameters when both n, p are unknown , 2005 .

[94]  W. Link Nonidentifiability of Population Size from Capture‐Recapture Data with Heterogeneous Detection Probabilities , 2003, Biometrics.