Appendix B. Details on the autoregressive component accounting for nonindependent temporal replicates when modeling detection probability.

Details on the autoregressive component accounting for nonindependent temporal replicates when modeling detection probability

Appendix A. List of species included and excluded from the analyses, sample sizes, and posterior summaries of estimated detection probabilities.

List of species included and excluded from the analyses, sample sizes, and posterior summaries of estimated detection probabilities

Supplement 1. Script for the hierarchical model coded in BUGS language and technical specifications.

<h2>File List</h2><div> <p><a href="hierarchical_model_NZ_birds.r">hierarchical_model_NZ_birds.r</a> (MD5: eeeb5ac11c7e8ceacd5bd6fc67d14473)</p> <p>Script for the hierarchical model coded in BUGS language.</p> </div><h2>Description</h2><div> <p>This supplement provides the code of the hierarchical model used in the main analyses. This code can be directly implemented in any BUGS software, although JAGS has proved the most efficient. The code is intended to be easily transferable to similar data sets.</p> <p>Technical specifications for the main text analyses: three chains of 250 000 iterations were run, plus an adaptation period of 1000 iterations. A burnin period of 125 000 iterations was discarded, the remaining 125 000 were used for inference after thinning by 100. These chains took 15 days to run on a server with the following characteristics:</p> <p>CPU: 2 x Intel Xeon X5670 2.93 GHz<br> RAM: 48 GB<br> Operating system: Microsoft Server 2008 - 64bit<br> Disk-capacity: 3.63 TB ( 2 x 2 TB disks in RAID-0 configuration) </p> <p>The data need to be formatted as follows: </p> <p>obs: a three-dimensional array [sites, replicates, species] for bird counts;</p> <p>FOR, NATFOR, ALT, YR, VH, HOUR, HOUR2, HDET, SUBZON, TYH, OBSERV , ST: vectors for covariates, each with one value per site. HOUR2 corresponds to HOUR*HOUR. All continuous variables should be centered and scaled to improve convergence;</p> <p>S: the number of species;</p> <p>R: the number of sites;</p> <p>K: the number of replicates;</p> <p>nobs: the number of different observers;</p> <p>nsubzone: the number of regions;</p> <p>nyear: the number of survey years;</p> <p>NST: the number of guilds (here two, exotic and natives);</p> <p>NTYH: the number of different local habitats.</p> </div

Definition of the ecological niche used in this article.

<p>(<b>A</b>) The environmental space can be represented as a set of axes (here, two: <i>X</i>, <i>Y</i>), each representing a gradient of resource or condition. A species' niche is defined as the range of each of these gradients that the species can exploit/occupy/cope with (yellow ellipse). The projection of the niche on each gradient is defined by a position (<i>P_x</i>, <i>P_y</i>) and a breadth (red solid lines). In our analyses, we consider two axes: (<b>B</b>) <b>a thermal axis</b> (referred to in the text as ‘thermal niche’) corresponds to a gradient of temperature; (<b>C</b>) <b>a habitat axis</b> (‘habitat niche’) refers to a gradient of vegetation structure ranging from mature forest to grasslands and open fields (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032819#pone-0032819-t001" target="_blank">Table 1</a>).</p

Relationship between thermal and habitat niches for 74 European bird species.

<p>(<b>A</b>) Relationship between niche positions; (<b>B</b>) relationship between niche breadths. The linear relationships (dashed lines) and their confidence intervals (dotted lines) are derived from averaged coefficients resulting from phylogenetic generalized least square regressions, after AICc-based model selection. Thermal positions and breadths are log transformed to approach a normal distribution. Both thermal and habitat positions are scaled to mean = 0, SD = 1. DELURB: <i>Delichon urbicum</i>, HIRRUS: <i>Hirundo rustica</i>. MOTALB: <i>Motacilla alba</i>. MOTFLA: <i>Motacilla flava</i>, PASDOM: <i>Passer domesticus</i>. PICPIC: <i>Pica pica</i>. STRDEC: <i>Streptopelia decaocto</i>. STRTUR: <i>Streptopelia turtur</i>.</p

Results of the model selection process.

<p>Models are phylogenetic generalized least square regressions with either climatic niche position or breadth as the response variable. Fixed predictors included migratory status (migr), age of first breeding (AFB), and either habitat niche position (HPI) or breadth (SSI) according to the model. The intercept is noted <i>γ</i>; <i>k</i> corresponds to the number of model parameters. The ΔAICc refers to the difference between the AICc of model <i>i</i> and that of the model with the lowest AICc value. The column “weight” refers to AICc weights, which were used to compute the averaged coefficients of the fixed effects.</p