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

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

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

Relationship between total defoliation by <i>Dryocosmus kuriphilus</i> and tree species richness at the plot level.

<p>Dots represent the mean percentage of total defoliation per plot. The solid line and the shaded area represent predictions from linear mixed models and corresponding confidence interval.</p

Relationship between total defoliation by <i>Dryocosmus kuriphilus</i> and chestnut tree apparency at the neighborhood level.

<p>Dots represent the percentage of total tree defoliation. The solid line and shaded area represent predictions by linear mixed models and corresponding confidence intervals. Dots on the left hand side and right hand side represent chestnut trees that were on average shorter and taller than their neighbors, respectively.</p

Results of model selection for the analyses of total defoliation by <i>Dryocosmus kuriphilus</i> on chestnut trees in forests with increasing tree species diversity.

<p>All models include plot identity as random factor. Univariate and multivariate models are shown, including their number of estimable parameters (<i>K</i>) and their Akaike’s weights (<i>w</i>_<i>i</i>). Models within 2 AICc units (<i>Δ</i>_<i>i</i>) of the model with the lowest AICc are in <i>italics</i>. Estimated parameter values and standard deviations are indicated for these models with <i>Δ</i>_<i>i</i> < 2. Variables in bold are at the plot level and normal typeface variables are at the neighborhood level.</p><p><i>Null</i> = Null model; <i>Richness</i> = tree species richness; <i>Shannon’s diversity index</i> = Shannon index of tree diversity; C. sativa <i>proportion =</i> proportion of <i>Castanea sativa</i>; <i>Taxonomic diversity</i> = Taxonomic diversity index; <i>Oak galls</i> = Mean percentage of oak leaves with presence of Cynipid galls; <i>Tree apparency</i> = Tree apparency index.</p><p>Results of model selection for the analyses of total defoliation by <i>Dryocosmus kuriphilus</i> on chestnut trees in forests with increasing tree species diversity.</p

Additional file 7: Figure S1. of Habitat properties are key drivers of Borrelia burgdorferi (s.l.) prevalence in Ixodes ricinus populations of deciduous forest fragments

Flow chart of the overall data processing procedure. (PDF 46 kb

Les drames de l'adultère ou Le mari de Marguerite : roman parisien / par Xavier de Montépin

Contient une table des matièresAvec mode text

Additional file 3: Text 1. of Habitat properties are key drivers of Borrelia burgdorferi (s.l.) prevalence in Ixodes ricinus populations of deciduous forest fragments

Methods: technical details. (DOCX 16 kb

Additional file 2: Table S5. of Habitat properties are key drivers of Borrelia burgdorferi (s.l.) prevalence in Ixodes ricinus populations of deciduous forest fragments

Meta-data on study setup. Outline of the most important meta-data, such as center of each studied landscape window, dates of sampling, number of forest patches and a couple of landscape metrics to characterize the respective landscapes. (XLSX 26 kb