Supplement 1. MATLAB simulation.

<h2>File List</h2><blockquote> <p><a href="Evans_Collinearity_Supplement.m">Evans_Collinearity_Supplement.m</a></p> <p><a href="read me.txt">read me.txt</a></p> </blockquote><h2>Description</h2><blockquote> <p>The MATLAB script Evans_Collinearity_Supplement.m generates two random normal variables <i>x</i> and <i>y</i> with the correlation between them specified by the user. It then creates a third ‘response’ variable <i>z</i> that is a function of <i>x</i> and <i>y</i>. The exact function used to create <i>z</i> can be chosen by the user. Finally, it runs a set of linear regressions of <i>z</i> vs. various combinations of <i>x</i>, <i>y</i>, and their interactions. The regressions are used to demonstrate how using <i>P</i> values to select variables in a regression model can lead to retaining falsely significant parameters, resulting in an incorrect interpretation of the data. Model selection using Akaike’s ‘An Information Criterion’ (AIC) is illustrated as an alternative method. More complete details are given in <a href="appendix-B.htm">Appendix B</a> and in the comments of the file itself.</p> </blockquote

Appendix C. Winter density dependence.

Winter density dependence

Appendix B. Collinearity and parameter bias.

Collinearity and parameter bias

Code and Data Supplement

This supplement contains all the code and data necessary to reproduce the full results and figures from the paper. Users will need to install R version 1.1.3 and follow the instructions in the README file. -Jeff Evan

Supplement 1. MATLAB and SAS code necessary to replicate the simulation models and other demographic analyses presented in the paper.

<h2>File List</h2><p> <a href="Code_and_Data_Supplement.zip">Code_and_Data_Supplement.zip</a> (md5: dea8636b921f39c9d3fd269e44b6228c) </p><h2>Description</h2><p> The supplementary material provided includes all code and data files necessary to replicate the simulation models other demographic analyses presented in the paper. MATLAB code is provided for the simulations, and SAS code is provided to show how model parameters (vital rates) were estimated. </p> <p> The principal programs are Figure_3_4_5_Elasticity_Contours.m and Figure_6_Contours_Stochastic_Lambda.m which perform the elasticity analyses and run the stochastic simulation, respectively. </p> <p> The files are presented in a zipped folder called Code_and_Data_Supplement. When uncompressed, users may run the MATLAB programs by opening them from within this directory. Subdirectories contain the data files and supporting MATLAB functions necessary to complete execution. The programs are written to find the necessary supporting functions in the Code_and_Data_Supplement directory. If users copy these MATLAB files to a different directory, they must add the Code_and_Data_Supplement directory and its subdirectories to their search path to make the supporting files available. </p> <p> More details are provided in the README.txt file included in the supplement. </p> <p> The file and directory structure of entire zipped supplement is shown below. </p> <pre>Folder PATH listing Code_and_Data_Supplement | Figure_3_4_5_Elasticity_Contours.m | Figure_6_Contours_Stochastic_Lambda.m | Figure_A1_RefitG2.m | Figure_A2_PlotFecundityRegression.m | README.txt | +---FinalDataFiles +---Make Tables | README.txt | Table_lamANNUAL.csv | Table_mgtProbPredicted.csv | +---ParameterEstimation | | Categorical Model output.xls | | | +---Fecundity | | Appendix_A3_Fecundity_Breakpoint.sas | | fec_Cat_Indiv.sas | | Mean_Fec_Previous_Study.m | | | +---G1 | | G1_Cat.sas | | | +---G2 | | G2_Cat.sas | | | +---Model Ranking | | Categorical Model Ranking.xls | | | +---Seedlings | | sdl_Cat.sas | | | +---SS | | SS_Cat.sas | | | +---SumSrv | | sum_Cat.sas | | | \---WinSrv | modavg.m | winCatModAvgfitted.m | winCatModAvgLinP.m | winCatModAvgMu.m | win_Cat.sas | +---ProcessedDatafiles | fecdat_gm_param_est_paper.mat | hierarchical_parameters.mat | refitG2_param_estimation.mat | \---Required_Functions | hline.m | hmstoc.m | Jeffs_Figure_Settings.m | Jeffs_startup.m | newbootci.m | sem.m | senstuff.m | vline.m | +---export_fig | change_value.m | eps2pdf.m | export_fig.m | fix_lines.m | ghostscript.m | license.txt | pdf2eps.m | pdftops.m | print2array.m | print2eps.m | +---lowess | license.txt | lowess.m | +---Multiprod_2009 | | Appendix A - Algorithm.pdf | | Appendix B - Testing speed and memory usage.pdf | | Appendix C - Syntaxes.pdf | | license.txt | | loc2loc.m | | MULTIPROD Toolbox Manual.pdf | | multiprod.m | | multitransp.m | | | \---Testing | | arraylab13.m | | arraylab131.m | | arraylab132.m | | arraylab133.m | | genop.m | | multiprod13.m | | readme.txt | | sysrequirements_for_testing.m | | testing_memory_usage.m | | testMULTIPROD.m | | timing_arraylab_engines.m | | timing_matlab_commands.m | | timing_MX.m | | | \---Data | Memory used by MATLAB statements.xls | Timing results.xlsx | timing_MX.txt | +---province | PROVINCE.DBF | province.prj | PROVINCE.SHP | PROVINCE.SHX | README.txt | +---SubAxis | parseArgs.m | subaxis.m | +---suplabel | license.txt | suplabel.m | suplabel_test.m | \---tight_subplot license.txt tight_subplot.m </pre

Appendix B. Six figures, including a map of study sites, data distributions, temporal, and annual results.

Six figures, including a map of study sites, data distributions, temporal, and annual results

Appendix A. Detailed documentation of field data collection, model selection and parameter estimation, and matrix model construction.

Detailed documentation of field data collection, model selection and parameter estimation, and matrix model construction