Supplement 1. Model implementation detail, R ,and WinBUGS code, and data for the Wood Thrush example presented in the paper.

<h2>File List</h2><blockquote> <a href="carCJS.r">carCJS.r</a> - R script used to read in wood thrush data, create data objects for the spatial CJS model, specify the model in WinBUGS, call WinBUGS to run model and save output, and create ASCII grids for mapping ouput<br> <a href="woth.txt">woth.txt</a> - Capture history file for wood thrush example</blockquote><h2>Description</h2><blockquote> <p>The 'carCJS.r' script requires the following R packages: boot, coda, deldir, gpclib, maptools, Matrix, R2WinBUGS, spam, spatstat, spdep, and tripack. The script reads in data; and creates a base 1-degree ASCII grid ('MAPSgrid.txt'), a model file for WinBUGS ('spatialcjs.txt'), and objects needed to run the model in WinBUGS. The script calls WinBUGS and stores output in an R list called 'out'. The script also creates objects for creating spatial maps of survival and residency (as in Fig. 3) within R and writes ASCII grids for making maps with GIS software outside of R. </p> <p>The data in 'woth.txt' are capture histories derived from the Monitoring Avian Productivity and Survivorship (MAPS) program. Included are all records of adult birds (i.e., ‘after-hatch-year’) of both sexes at stations where the species is known to breed. Fields in ‘woth.txt’ include:</p> <ol> <li>SPEC – Species 4-letter code. WOTH = wood thrush (<i>Hylocichla mustelina</i>)</li> <li>STA2 – MAPS station 4-character code. Stations consist of about 10 mist nets that sample an area of approximately 20 ha. Multiple stations < 1 km apart were considered a single station</li> <li>BAND – USGS Bird Banding Laboratory band number</li> <li>R – Indicates whether predetermined resident (M) or not (U)</li> <li>Y1 – Indicator variable denoting whether captured (1) or not captured (0) in year 1. Y1 corresponds to 1992, the first year of the study (first year of standardized MAPS protocol)</li> <li>Y2 – Indicator variable denoting whether captured (1) or not captured (0) in year 2 (1993)</li> <li>Y3 – Indicator variable denoting whether captured (1) or not captured (0) in year 3 (1994)</li> <li>Y4 – Indicator variable denoting whether captured (1) or not captured (0) in year 4 (1995)</li> <li>Y5 – Indicator variable denoting whether captured (1) or not captured (0) in year 5 (1996)</li> <li>Y6 – Indicator variable denoting whether captured (1) or not captured (0) in year 6 (1997)</li> <li>Y7 – Indicator variable denoting whether captured (1) or not captured (0) in year 7 (1998)</li> <li>Y8 – Indicator variable denoting whether captured (1) or not captured (0) in year 8 (1999)</li> <li>Y9 – Indicator variable denoting whether captured (1) or not captured (0) in year 9 (2000)</li> <li>Y10 – Indicator variable denoting whether captured (1) or not captured (0) in year 10 (2001)</li> <li>Y11 – Indicator variable denoting whether captured (1) or not captured (0) in year 11 (2002)</li> <li>Y12 – Indicator variable denoting whether captured (1) or not captured (0) in year 12 (2003)</li> <li>LAT – Latitude of the MAPS station in decimal degrees</li> <li>LONG – Longitude of the MAPS station in decimal degrees</li> <li>CAP – Mean no. of within-year captures per individual at the station</li> </ol> <p>Note that although 6,645 birds are included in the woth.txt, only 6,241 of these birds that were captured for the first time prior to the last year of the study are read into the data object used in the model.</p> </blockquote

Input files for capture histories of individuals

These are basic input files without station or covariate information, for each of the species in the manuscript

Appendix A. Description of stable isotope analysis methods.

Description of stable isotope analysis methods

Appendix C. The δ²H isoscape, feather sampling locations (bird icons) and the quadrants used in validation and to quantifying range wide migratory connectivity for Wood Thrush.

The δ²H isoscape, feather sampling locations (bird icons) and the quadrants used in validation and to quantifying range wide migratory connectivity for Wood Thrush

Saipan bird, rainfall, and EVI data and analysis code

7 data files and 3 R workspaces (for survival analyses) are included to reproduce results reported in the paper. Individual files and R code are included in the README.pdf file

Locations of the Mariana Archipelago (top right), Saipan (left), and bird-banding stations operated as part of this study (bottom right).

<p>Station codes are defined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148570#pone.0148570.t001" target="_blank">Table 1</a>. The Saipan International Airport, where rainfall data were collected, is also shown.</p

EVI-avian productivity relationships.

<p>Predicted productivity (probability of capturing a hatching-year bird; <i>p</i>[<i>Y</i>]_<i>st</i> ± 95% confidence intervals) in relation to deviation of the enhanced vegetation index (EVI) from 5-year mean values during the late dry season (Mar-May; <i>evi</i>.<i>d</i>.<i>dev</i>_<i>st</i>) at three levels of late wet season EVI deviation values (from previous Sep-Nov; <i>evi</i>.<i>w</i>.<i>dev</i>_<i>st-1</i>). Predictions are based on top-performing (lowest AIC_<i>c</i>) models for the three target species using capture data collected during the 10 periods (11 April-19 July) sampled in each of the five years (2008–2012).</p

EVI-avian survival relationships.

<p>Predicted adult apparent survival probability (<math><mi>S</mi><mo>^</mo></math>) in relation to: (top and middle panels) deviation of the enhanced vegetation index (EVI) from 5-year mean values during the late dry (Mar-May; <i>evi</i>.<i>d</i>.<i>dev</i>_<i>st</i>) and late wet (Sep-Nov; <i>evi</i>.<i>w</i>.<i>dev</i>_<i>st</i>) seasons from best (lowest AIC_<i>c</i>) model (<i>evi</i>.<i>d</i>.<i>dev</i>_<i>st</i>+<i>evi</i>.<i>w</i>.<i>dev</i>_<i>st</i>); and (bottom panel) annual mean EVI during dry (<i>evi</i>.<i>d</i>_<i>st</i>) and wet (<i>evi</i>.<i>w</i>_<i>st</i>) seasons for bridled white-eye based on models with similar support to the top model.</p

EVI-rainfall patterns.

<p>(A) Time series showing seasonal and annual variation in monthly rainfall recorded at the Saipan International Airport and average monthly EVI values at the six mist-netting stations on Saipan during Jul 2007-Dec 2012 and (B) Relationship between monthly mean EVI and rainfall. Curve shows log-linear model fit; red dots represent dry-season means for the six mist-netting stations and blue dots represent wet-season means.</p

Station-scale MODIS-derived enhanced vegetation index (EVI) values.

<p>EVI values represent interpolated monthly EVI values over the four 1-km² pixels closest to station coordinates. EVI values are plotted (A) by month (individual points represent year-specific values for each station; boxplots delineate quartiles with whiskers bounding the 95^th percentile) and (B-C) by year during the late dry (B: Mar-May) and wet (C: Sep-Nov) seasons.</p