Accounting for Spatial Dependence in Ecological Data

The presence of spatial dependence can impair the statistical inference and subsequent ecological interpretation of the pattern(s) observed. It is important to understand how statistical biases due to spatially structured data can affect a wide array of ecological questions ranging from species–environment relationships to predicting the spread of invasive species. Consequently, there is an increasing emphasis on formally accounting for spatial dependence in inferential problems in ecology and conservation. We provide an overview regarding several ways in which spatial dependence has been addressed in regression-like models of species–environment relationships. Regression models are frequently used in ecology and conservation to address a variety of problems, ranging from interpreting habitat suitability to forecasting the effects of climate change. We first describe the problem of spatial dependence on inferences in ecology and conservation. Then, we discuss how to diagnose problems of spatial dependence in regression models. Finally, we illustrate new advances to addressing these statistical problems using a variety of approaches aimed at accounting for spatial dependence in statistical analyses, including trend surface analysis, eigenvector mapping, autocovariate and autoregressive models, multilevel models, generalized least squares, and spatial mixed models. We apply these models to understanding relationships of species occurrence of the varied thrush (Ixoreus naevius) to elevational gradients in the western USA. This example illustrates that each of these approaches varies in its ability to account for spatial dependence, depending on the scale at which spatial dependence occurs. Overall, autoregressive and spatial mixed models have beneficial attributes regarding obtaining appropriate inferences in the presence of spatial dependence. We end by providing guidance on accounting for spatial dependence in regression models used in ecology and conservation.

[1]  J. Guinan,et al.  Multiscale Terrain Analysis of Multibeam Bathymetry Data for Habitat Mapping on the Continental Slope , 2007 .

[2]  Erin E. Peterson,et al.  Spatial autoregressive models for statistical inference from ecological data , 2018 .

[3]  Ingolf Kühn,et al.  A Wavelet-Based Extension of Generalized Linear Models to Remove the Effect of Spatial Autocorrelation: Wavelet-based Extension of Generalized Linear Models , 2010 .

[4]  Res Altwegg,et al.  Spatial occupancy models applied to atlas data show Southern Ground Hornbills strongly depend on protected areas. , 2014, Ecological applications : a publication of the Ecological Society of America.

[5]  Stéphane Dray,et al.  Disentangling good from bad practices in the selection of spatial or phylogenetic eigenvectors , 2018 .

[6]  P. Legendre Spatial Autocorrelation: Trouble or New Paradigm? , 1993 .

[7]  Brendan A. Wintle,et al.  A new method for dealing with residual spatial autocorrelation in species distribution models , 2012 .

[8]  P. Dixon,et al.  Accounting for Spatial Pattern When Modeling Organism- Environment Interactions , 2022 .

[9]  R. Wolfinger,et al.  SAS for Mixed Models , 2018 .

[10]  Mike Rees,et al.  5. Statistics for Spatial Data , 1993 .

[11]  Rethinking the linear regression model for spatial ecological data: comment. , 2015, Ecology.

[12]  W. Cleveland Robust Locally Weighted Regression and Smoothing Scatterplots , 1979 .

[13]  M. Cameletti,et al.  Spatial and Spatio-temporal Bayesian Models with R - INLA , 2015 .

[14]  Roger Bivand,et al.  Community ecology in the age of multivariate multiscale spatial analysis , 2012 .

[15]  Richard Field,et al.  Coefficient shifts in geographical ecology: an empirical evaluation of spatial and non-spatial regression , 2009 .

[16]  R. Fletcher Multiple edge effects and their implications in fragmented landscapes , 2005 .

[17]  Marie-Josée Fortin,et al.  SPATIAL ANALYSIS OF LANDSCAPES: CONCEPTS AND STATISTICS , 2005 .

[18]  J. Andrew Royle,et al.  Hierarchical Modeling and Inference in Ecology: The Analysis of Data from Populations, Metapopulations and Communities , 2008 .

[19]  R. Tibshirani,et al.  Generalized additive models for medical research , 1986, Statistical methods in medical research.

[20]  Andrew O. Finley,et al.  spBayes for Large Univariate and Multivariate Point-Referenced Spatio-Temporal Data Models , 2013, 1310.8192.

[21]  Berthold K. P. Horn,et al.  Hill shading and the reflectance map , 1981, Proceedings of the IEEE.

[22]  Jack J. Lennon,et al.  Red-shifts and red herrings in geographical ecology , 2000 .

[23]  Stéphane Dray,et al.  Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbour matrices (PCNM) , 2006 .

[24]  Jason M. Evans,et al.  Does accounting for imperfect detection improve species distribution models , 2011 .

[25]  Helene H. Wagner,et al.  DIRECT MULTI‐SCALE ORDINATION WITH CANONICAL CORRESPONDENCE ANALYSIS , 2004 .

[26]  Andrew Gelman,et al.  Data Analysis Using Regression and Multilevel/Hierarchical Models , 2006 .

[27]  Marie-Josée Fortin,et al.  Spatial Analysis by Mark R. T. Dale , 2014 .

[28]  A. Zuur,et al.  Mixed Effects Models and Extensions in Ecology with R , 2009 .

[29]  S. T. Buckland,et al.  An autologistic model for the spatial distribution of wildlife , 1996 .

[30]  L. A. Brand,et al.  RESPONSE OF PASSERINE BIRDS TO FOREST EDGE IN COAST REDWOOD FOREST FRAGMENTS , 2001 .

[31]  Walter Krämer,et al.  Review of Modern applied statistics with S, 4th ed. by W.N. Venables and B.D. Ripley. Springer-Verlag 2002 , 2003 .

[32]  P. McCullagh,et al.  Generalized Linear Models , 1984 .

[33]  J. Andrew Royle,et al.  Applied Hierarchical Modeling in Ecology: Analysis of Distribution, Abundance and Species Richness in R and BUGS , 2015 .

[34]  Daniel A Griffith,et al.  Spatial modeling in ecology: the flexibility of eigenfunction spatial analyses. , 2006, Ecology.

[35]  J. Diniz‐Filho,et al.  Red herrings revisited: spatial autocorrelation and parameter estimation in geographical ecology , 2007 .

[36]  M. Wall A close look at the spatial structure implied by the CAR and SAR models , 2004 .

[37]  Benjamin M. Bolker,et al.  Ecological Models and Data in R , 2008 .

[38]  J. Andrew Royle,et al.  ESTIMATING SITE OCCUPANCY RATES WHEN DETECTION PROBABILITIES ARE LESS THAN ONE , 2002, Ecology.

[39]  B A Wintle,et al.  Modeling species-habitat relationships with spatially autocorrelated observation data. , 2006, Ecological applications : a publication of the Ecological Society of America.

[40]  Richard L. Hutto,et al.  Regional landbird monitoring: perspectives from the Northern Rocky Mountains , 2002 .

[41]  C. Dormann Response to Comment on “Methods to account for spatial autocorrelation in the analysis of species distributional data: a review” , 2009 .

[42]  W. D. Kissling,et al.  Spatial autocorrelation and the selection of simultaneous autoregressive models , 2007 .

[43]  William N. Venables,et al.  Modern Applied Statistics with S , 2010 .

[44]  Robert Haining,et al.  Spatial Data Analysis: Theory and Practice , 2003 .

[45]  Robert R. Sokal,et al.  Spatial autocorrelation in biology: 2. Some biological implications and four applications of evolutionary and ecological interest , 1978 .

[46]  Håvard Rue,et al.  Hierarchical analysis of spatially autocorrelated ecological data using integrated nested Laplace approximation , 2012 .

[47]  Jennifer A. Miller,et al.  Incorporating spatial dependence in predictive vegetation models , 2007 .

[48]  T. Simons,et al.  Spatial autocorrelation and autoregressive models in ecology , 2002 .

[49]  M. Araújo,et al.  Consequences of spatial autocorrelation for niche‐based models , 2006 .

[50]  Matthew G. Betts,et al.  The importance of spatial autocorrelation, extent and resolution in predicting forest bird occurrence , 2006 .

[51]  François Rousset,et al.  Testing environmental and genetic effects in the presence of spatial autocorrelation , 2014 .

[52]  Robert J Fletcher,et al.  Predicting Species Distributions from Samples Collected along Roadsides , 2012, Conservation biology : the journal of the Society for Conservation Biology.

[53]  José Alexandre Felizola Diniz-Filho,et al.  A review of techniques for spatial modeling in geographical, conservation and landscape genetics , 2009, Genetics and molecular biology.

[54]  Edzer Pebesma,et al.  Applied Spatial Data Analysis with R. Springer , 2008 .

[55]  Mollie E. Brooks,et al.  Generalized linear mixed models: a practical guide for ecology and evolution. , 2009, Trends in ecology & evolution.

[56]  Norman A. Slade,et al.  Testing For Independence of Observations in Animal Movements , 1985 .

[57]  Mevin B. Hooten,et al.  Spatial occupancy models for large data sets , 2013 .

[58]  J. Diniz‐Filho,et al.  Spatial autocorrelation and red herrings in geographical ecology , 2003 .

[59]  D. Bates,et al.  Fitting Linear Mixed-Effects Models Using lme4 , 2014, 1406.5823.

[60]  David A. W. Miller,et al.  Improving occupancy estimation when two types of observational error occur: non-detection and species misidentification. , 2011, Ecology.

[61]  C. Carroll,et al.  The Importance of Being Spatial (and Reserved): Assessing Northern Spotted Owl Habitat Relationships with Hierarchical Bayesian Models , 2008, Conservation biology : the journal of the Society for Conservation Biology.

[62]  W. Falck,et al.  Nonparametric spatial covariance functions: Estimation and testing , 2001, Environmental and Ecological Statistics.

[63]  James T. Thorson,et al.  Mixed effects: a unifying framework for statistical modelling in fisheries biology , 2015 .

[64]  Colin M Beale,et al.  Regression analysis of spatial data. , 2010, Ecology letters.

[65]  Philip A. Stephens,et al.  Inference in ecology and evolution. , 2007, Trends in ecology & evolution.

[66]  P. McCullagh,et al.  Generalized Linear Models , 1972, Predictive Analytics.

[67]  Shuqing N. Teng,et al.  Effects of intrinsic sources of spatial autocorrelation on spatial regression modelling , 2017 .

[68]  Eric Young,et al.  Predicting the future of species diversity: macroecological theory, climate change, and direct tests of alternative forecasting methods , 2009 .

[69]  T. Garland,et al.  Procedures for the Analysis of Comparative Data Using Phylogenetically Independent Contrasts , 1992 .

[70]  Carlos Carroll,et al.  Hierarchical Bayesian Spatial Models for Multispecies Conservation Planning and Monitoring , 2010, Conservation biology : the journal of the Society for Conservation Biology.

[71]  B. Wintle,et al.  Incorporating spatial autocorrelation into species distribution models alters forecasts of climate‐mediated range shifts , 2014, Global change biology.

[72]  Roger Bivand,et al.  Comparing Implementations of Estimation Methods for Spatial Econometrics , 2015 .

[73]  A. Getis,et al.  Comparative Spatial Filtering in Regression Analysis , 2002 .

[74]  J. Andrew Royle,et al.  Tigers on trails: occupancy modeling for cluster sampling. , 2009, Ecological applications : a publication of the Ecological Society of America.

[75]  Nunzio Knerr,et al.  A comparison of network and clustering methods to detect biogeographical regions , 2018 .

[76]  S. Hurlbert Pseudoreplication and the Design of Ecological Field Experiments , 1984 .

[77]  Koenig,et al.  Spatial autocorrelation of ecological phenomena. , 1999, Trends in ecology & evolution.

[78]  Antoine Guisan,et al.  Predictive habitat distribution models in ecology , 2000 .

[79]  M. Fortin,et al.  Spatial statistics, spatial regression, and graph theory in ecology , 2012 .

[80]  M. Boyce,et al.  Evaluating resource selection functions , 2002 .

[81]  Marie-Josée Fortin,et al.  Expanding northward: influence of climate change, forest connectivity, and population processes on a threatened species' range shift , 2011 .

[82]  S. Wood Generalized Additive Models: An Introduction with R , 2006 .

[83]  Jennifer A. Miller Species distribution models , 2012 .

[84]  Zhiqiang Yang,et al.  Old‐growth forests buffer climate‐sensitive bird populations from warming , 2018 .

[85]  Helene H. Wagner,et al.  SPATIAL COVARIANCE IN PLANT COMMUNITIES: INTEGRATING ORDINATION, GEOSTATISTICS, AND VARIANCE TESTING , 2003 .

[86]  R. G. Davies,et al.  Methods to account for spatial autocorrelation in the analysis of species distributional data : a review , 2007 .

[87]  J. Andrew Royle,et al.  Hierarchical Spatiotemporal Matrix Models for Characterizing Invasions , 2007, Biometrics.

[88]  Brendan A. Wintle,et al.  Valid auto‐models for spatially autocorrelated occupancy and abundance data , 2015, 1501.06529.