cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3520547.v1
title: Supplement 1. R code and the data set necessary to conduct the Random Forest analysis.

description: File List dreissena_in_lakes_of_belarus.csv (MD5: 3dc2d2f89af3064223358983c785771d) r_script_random_forest.R (MD5: af1295890d60bc832955e940889e4575) Description This Supplementary material contains two files necessary to fully reproduce the results obtained using the Random Forest classifier. The first of these files, dreissena_in_lakes_of_belarus.csv, is a plain text table that has 553 records, each described with the following variables: 1. Lake_Code: numeric codes uniquely identifying each lake (for reference only, not used in analysis explicitely). 2. ZMpresence: indicator of whether a lake is infested with zebra mussel (0 – for non-infested, 1 – for infested). 3. LAREA: lake area 4. LVOL: lake volume 5. MAXD: maximal depth 6. AVED: average depth 7. SPECWATSHED: specific watershed (i.e., drainage area) 8. TRANSP: Secci depth 9. COLOR: water color 10. pH: water pH 11. HCO3: HCO3 content 12. SO4: SO4 content 13. Cl: CL content 14. Ca: Ca content 15. Mg: Mg content 16. TDS: total dissolved solids 17: Fe: Fe content 18. Si: Si content 19. NH4: NH4 content 20. NO2: NO2 content 21. PO4: PO4 content 22. PermOx: permanganate oxydizability 23. N: latitude (decimal degree) 24: E: longitude (decimal degree) Missing values in the data set are denoted as NA. The second file, r_script_random_forest.R, loads the data into R (assuming that the file dreissena_in_lakes_of_belarus.csv is stored in the current R working directory), fits the Random Forest model, and plots the results. The analysis relies on three add-on packages: caret, geosphere, randomForest, and ggplot2. All these packages are assumed to be already installed on the user's computer (if not, they can be freely downloaded from the Comprehensive R Archive Network, cran.r-project.org, or installed directly from within R using the following command: install.packages(c("caret", "geosphere", "randomForest", "ggplot2"))).
DOI: 10.6084/m9.figshare.3520544
title: Appendix A. Theoretical basis for estimating rare-event bycatch using a Bayesian approach.

description: Theoretical basis for estimating rare-event bycatch using a Bayesian approach.
DOI: 10.6084/m9.figshare.3520541
title: Supplement 1. R code for estimating models of rare-event protected species bycatch using WinBUGS.

description: File List Supplement1_WinBUGS_code.R (MD5: 4d951eb09b779baaf882cef3df3d0993) Description Supplement1_WinBUGS_code.R – This R code specifies several different models of the bycatch rate for leatherback turtles and humpback whales in the California drift gillnet fishery. The code uses packages R2WinBUGS and Coda within R to communicate with the WinBUGS program and generate posterior distributions for the model parameters. The code includes the raw data on observed fishing sets and bycatch events (takes) of these species for 1990-2009 from the fisheries observer program administered by NOAA Fisheries. Therefore, other users can run the section of code for each model and species and reproduce our model estimation results.
DOI: 10.6084/m9.figshare.3520541.v1
title: Supplement 1. R code for estimating models of rare-event protected species bycatch using WinBUGS.

description: File List Supplement1_WinBUGS_code.R (MD5: 4d951eb09b779baaf882cef3df3d0993) Description Supplement1_WinBUGS_code.R – This R code specifies several different models of the bycatch rate for leatherback turtles and humpback whales in the California drift gillnet fishery. The code uses packages R2WinBUGS and Coda within R to communicate with the WinBUGS program and generate posterior distributions for the model parameters. The code includes the raw data on observed fishing sets and bycatch events (takes) of these species for 1990-2009 from the fisheries observer program administered by NOAA Fisheries. Therefore, other users can run the section of code for each model and species and reproduce our model estimation results.
DOI: 10.6084/m9.figshare.3520538
title: Supplement 2. R simulation code for predicting annual bycatch and mortality using WinBUGS model estimates.

description: File List Supplement2_RCode_PredictionByYears.R (MD5: ff27d3e2303bd8e670eea82b70f70780) Description Supplement2_RCode_PredictionByYears.R – This R code uses the posterior distributions for model parameters generated by WinBUGS in Supplement 1 to predict annual bycatch and mortality for leatherback turtles and humpback whales in the California drift gillnet fishery (1990–2009). For each species, we generated posterior distributions for <i>m<sub>i</sub></i>, expected annual mortality for year <i>i</i>. In the context of our fisheries bycatch problem, posterior <i>predictive</i> distributions (PPDs) are estimated distributions of unobserved bycatch or mortality counts given the estimated posterior for <i>Ɵ</i>, the bycatch rate per fishing set, and a specified number of sets fished, <i>n</i>. Using this code, we generated PPDs for <i>x<sub>i</sub></i> (observed takes), <i>y<sub>i</sub> - x<sub>i</sub></i> (unobserved takes), <i>y<sub>i</sub></i> (total takes), <i>w<sub>i</sub></i> (observed deaths), <i>z<sub>i</sub> - w<sub>i</sub></i> (unobserved deaths), and <i>z<sub>i</sub></i> (total deaths).
DOI: 10.6084/m9.figshare.3520538.v1
title: Supplement 2. R simulation code for predicting annual bycatch and mortality using WinBUGS model estimates.

description: File List Supplement2_RCode_PredictionByYears.R (MD5: ff27d3e2303bd8e670eea82b70f70780) Description Supplement2_RCode_PredictionByYears.R – This R code uses the posterior distributions for model parameters generated by WinBUGS in Supplement 1 to predict annual bycatch and mortality for leatherback turtles and humpback whales in the California drift gillnet fishery (1990–2009). For each species, we generated posterior distributions for <i>m<sub>i</sub></i>, expected annual mortality for year <i>i</i>. In the context of our fisheries bycatch problem, posterior <i>predictive</i> distributions (PPDs) are estimated distributions of unobserved bycatch or mortality counts given the estimated posterior for <i>Ɵ</i>, the bycatch rate per fishing set, and a specified number of sets fished, <i>n</i>. Using this code, we generated PPDs for <i>x<sub>i</sub></i> (observed takes), <i>y<sub>i</sub> - x<sub>i</sub></i> (unobserved takes), <i>y<sub>i</sub></i> (total takes), <i>w<sub>i</sub></i> (observed deaths), <i>z<sub>i</sub> - w<sub>i</sub></i> (unobserved deaths), and <i>z<sub>i</sub></i> (total deaths).
DOI: 10.6084/m9.figshare.3520535
title: Appendix A. The SAVANNA model structure and parameters used in this study.

description: The SAVANNA model structure and parameters used in this study.
DOI: 10.6084/m9.figshare.3520535.v1
title: Appendix A. The SAVANNA model structure and parameters used in this study.

description: The SAVANNA model structure and parameters used in this study.
DOI: 10.6084/m9.figshare.3520532
title: Appendix B. Simulated numbers of animals per species and region.

description: Simulated numbers of animals per species and region.
DOI: 10.6084/m9.figshare.3520532.v1
title: Appendix B. Simulated numbers of animals per species and region.

description: Simulated numbers of animals per species and region.
DOI: 10.6084/m9.figshare.3520529
title: Appendix C. Standardized beta coefficients between simulated animals species and plant groups.

description: Standardized beta coefficients between simulated animals species and plant groups.
DOI: 10.6084/m9.figshare.3520529.v1
title: Appendix C. Standardized beta coefficients between simulated animals species and plant groups.

description: Standardized beta coefficients between simulated animals species and plant groups.
DOI: 10.6084/m9.figshare.3520526
title: Appendix D. Results of simulations with and without buffalo, and with only wildebeest.

description: Results of simulations with and without buffalo, and with only wildebeest.
DOI: 10.6084/m9.figshare.3520526.v1
title: Appendix D. Results of simulations with and without buffalo, and with only wildebeest.

description: Results of simulations with and without buffalo, and with only wildebeest.
DOI: 10.6084/m9.figshare.3520523
title: Appendix E. The influence of elephant density for all water scenarios.

description: The influence of elephant density for all water scenarios.
DOI: 10.6084/m9.figshare.3520523.v1
title: Appendix E. The influence of elephant density for all water scenarios.

description: The influence of elephant density for all water scenarios.
DOI: 10.6084/m9.figshare.3520520
title: Appendix A. Raven Pro v1.4 band-limited energy detector parameters used for automated call detection.

description: Raven Pro v1.4 band-limited energy detector parameters used for automated call detection.
DOI: 10.6084/m9.figshare.3520520.v1
title: Appendix A. Raven Pro v1.4 band-limited energy detector parameters used for automated call detection.

description: Raven Pro v1.4 band-limited energy detector parameters used for automated call detection.
DOI: 10.6084/m9.figshare.3520517
title: Appendix B. Animal flight traffic rate estimates, by decile periods of the night, derived from observations by weather surveillance radar (mean linear reflectivity (Z) by height above ground in 100-m intervals), thermal infrared camera (detections per hour), and acoustic recorder (calls per hour) during the fall of 2012. Only complete nights are presented. Note that scales vary among nights.

description: Animal flight traffic rate estimates, by decile periods of the night, derived from observations by weather surveillance radar (mean linear reflectivity (Z) by height above ground in 100-m intervals), thermal infrared camera (detections per hour), and acoustic recorder (calls per hour) during the fall of 2012. Only complete nights are presented. Note that scales vary among nights.
DOI: 10.6084/m9.figshare.3520517.v1
title: Appendix B. Animal flight traffic rate estimates, by decile periods of the night, derived from observations by weather surveillance radar (mean linear reflectivity (Z) by height above ground in 100-m intervals), thermal infrared camera (detections per hour), and acoustic recorder (calls per hour) during the fall of 2012. Only complete nights are presented. Note that scales vary among nights.

description: Animal flight traffic rate estimates, by decile periods of the night, derived from observations by weather surveillance radar (mean linear reflectivity (Z) by height above ground in 100-m intervals), thermal infrared camera (detections per hour), and acoustic recorder (calls per hour) during the fall of 2012. Only complete nights are presented. Note that scales vary among nights.
DOI: 10.6084/m9.figshare.3520514
title: Appendix A. Marine mammal abundance estimation summarized from Link et al. 2006.

description: Marine mammal abundance estimation summarized from Link et al. 2006.
DOI: 10.6084/m9.figshare.3520514.v1
title: Appendix A. Marine mammal abundance estimation summarized from Link et al. 2006.

description: Marine mammal abundance estimation summarized from Link et al. 2006.
DOI: 10.6084/m9.figshare.3520511
title: Appendix A. Tables showing Pearson product-moment correlations between explanatory variables, coefficients and hypothesis testing from best-fitting model using all trees and using all larger trees, and the management model using the coefficients from the all-tree analysis, and a figure depicting a model planting plan that achieves zero canopy cover and yet three to four neighboring shade trees (within 10 meters) for each cocoa tree, with very few exceptions.

description: Tables showing Pearson product-moment correlations between explanatory variables, coefficients and hypothesis testing from best-fitting model using all trees and using all larger trees, and the management model using the coefficients from the all-tree analysis, and a figure depicting a model planting plan that achieves zero canopy cover and yet three to four neighboring shade trees (within 10 meters) for each cocoa tree, with very few exceptions.
DOI: 10.6084/m9.figshare.3520508
title: Appendix A. Appropriateness of plot sizes used.

description: Appropriateness of plot sizes used.
DOI: 10.6084/m9.figshare.3520508.v1
title: Appendix A. Appropriateness of plot sizes used.

description: Appropriateness of plot sizes used.
DOI: 10.6084/m9.figshare.3520505
title: Appendix B. Camera trapping validation of dung surveys.

description: Camera trapping validation of dung surveys.
DOI: 10.6084/m9.figshare.3520505.v1
title: Appendix B. Camera trapping validation of dung surveys.

description: Camera trapping validation of dung surveys.
DOI: 10.6084/m9.figshare.3520502
title: Appendix C. NMDS correlations for environmental factors and mammal subfamilies.

description: NMDS correlations for environmental factors and mammal subfamilies.
DOI: 10.6084/m9.figshare.3520502.v1
title: Appendix C. NMDS correlations for environmental factors and mammal subfamilies.

description: NMDS correlations for environmental factors and mammal subfamilies.
DOI: 10.6084/m9.figshare.3520499
title: Appendix D. Effects of rainfall on small mammal abundance.

description: Effects of rainfall on small mammal abundance.
DOI: 10.6084/m9.figshare.3520499.v1
title: Appendix D. Effects of rainfall on small mammal abundance.

description: Effects of rainfall on small mammal abundance.
DOI: 10.6084/m9.figshare.3520496
title: Appendix E. Mammal survey list by habitat.

description: Mammal survey list by habitat.
DOI: 10.6084/m9.figshare.3520496.v1
title: Appendix E. Mammal survey list by habitat.

description: Mammal survey list by habitat.
DOI: 10.6084/m9.figshare.3520493
title: Appendix F. Proximate drivers of species richness and diversity.

description: Proximate drivers of species richness and diversity.
DOI: 10.6084/m9.figshare.3520493.v1
title: Appendix F. Proximate drivers of species richness and diversity.

description: Proximate drivers of species richness and diversity.
DOI: 10.6084/m9.figshare.3520490
title: Appendix A. Detailed model selection for modeling Ovenbird nonbreeding abundance from eBird data and apparent survival.

description: Detailed model selection for modeling Ovenbird nonbreeding abundance from eBird data and apparent survival.
DOI: 10.6084/m9.figshare.3520487
title: Appendix A. Detailed description of sample preparation, satellite transmitter attachment and foraging area determination, as well as assignment methods.

description: Detailed description of sample preparation, satellite transmitter attachment and foraging area determination, as well as assignment methods.
DOI: 10.6084/m9.figshare.3520487.v1
title: Appendix A. Detailed description of sample preparation, satellite transmitter attachment and foraging area determination, as well as assignment methods.

description: Detailed description of sample preparation, satellite transmitter attachment and foraging area determination, as well as assignment methods.
DOI: 10.6084/m9.figshare.3520484
title: Appendix B. Stable isotope data and foraging locations for all loggerheads in this study.

description: Stable isotope data and foraging locations for all loggerheads in this study.
DOI: 10.6084/m9.figshare.3520484.v1
title: Appendix B. Stable isotope data and foraging locations for all loggerheads in this study.

description: Stable isotope data and foraging locations for all loggerheads in this study.
DOI: 10.6084/m9.figshare.3520481
title: Appendix C. Validation individual assignment maps.

description: Validation individual assignment maps.
DOI: 10.6084/m9.figshare.3520481.v1
title: Appendix C. Validation individual assignment maps.

description: Validation individual assignment maps.
DOI: 10.6084/m9.figshare.3520472
title: Supplement 1. Raster format of loggerhead δ13C and δ15N isoscapes and associated standard deviation.

description: File List loggerhead_d13C_isoscape.txt (md5: 75d5be745e2018c1fbf639224e598736) loggerhead_d15N_isoscape.txt (md5: d76570667098245e4102e8380b588324) loggerhead_d13C_error.txt (md5: 7f8bb3cc91d34eb8ad033942bd2f93cf) loggerhead_d15N_error.txt (md5:995ce245c4e066001d6f8322e33038ef ) Description loggerhead_d13C_isoscape.txt – krigged surface of <i>δ</i><sup>13</sup>C values from 41 calibration loggerhead sea turtles in coastal waters &lt; 200m depth of the Gulf of Mexico and Greater Caribbean loggerhead_d15N_isoscape.txt – krigged surface of <i>δ</i><sup>15</sup>N values from 41 calibration loggerhead sea turtles in coastal waters &lt; 200m depth of the Gulf of Mexico and Greater Caribbean loggerhead_d13C_error.txt – standard deviation of the kriging prediction of<i>δ</i><sup>13</sup>C values loggerhead_d15N_error.txt – standard deviation of the kriging prediction of<i>δ</i><sup>15</sup>N values These four files are the<i>δ</i><sup>13</sup>C and<i>δ</i><sup>15</sup>N isoscapes and standard deviation rasters that are depicted in Fig. 1 of the main text. They are ASCII-formatted text files and contain a header to identify the structure of the file. They can be opened in ArcGIS by using the ASCII to Raster conversion tool or in R with the raster() function using the Raster package and then assigned a spatial reference within the program used. Resolution of each of the files is 0.0572 degrees.
DOI: 10.6084/m9.figshare.3520472.v1
title: Supplement 1. Raster format of loggerhead δ13C and δ15N isoscapes and associated standard deviation.

description: File List loggerhead_d13C_isoscape.txt (md5: 75d5be745e2018c1fbf639224e598736) loggerhead_d15N_isoscape.txt (md5: d76570667098245e4102e8380b588324) loggerhead_d13C_error.txt (md5: 7f8bb3cc91d34eb8ad033942bd2f93cf) loggerhead_d15N_error.txt (md5:995ce245c4e066001d6f8322e33038ef ) Description loggerhead_d13C_isoscape.txt – krigged surface of <i>δ</i><sup>13</sup>C values from 41 calibration loggerhead sea turtles in coastal waters &lt; 200m depth of the Gulf of Mexico and Greater Caribbean loggerhead_d15N_isoscape.txt – krigged surface of <i>δ</i><sup>15</sup>N values from 41 calibration loggerhead sea turtles in coastal waters &lt; 200m depth of the Gulf of Mexico and Greater Caribbean loggerhead_d13C_error.txt – standard deviation of the kriging prediction of<i>δ</i><sup>13</sup>C values loggerhead_d15N_error.txt – standard deviation of the kriging prediction of<i>δ</i><sup>15</sup>N values These four files are the<i>δ</i><sup>13</sup>C and<i>δ</i><sup>15</sup>N isoscapes and standard deviation rasters that are depicted in Fig. 1 of the main text. They are ASCII-formatted text files and contain a header to identify the structure of the file. They can be opened in ArcGIS by using the ASCII to Raster conversion tool or in R with the raster() function using the Raster package and then assigned a spatial reference within the program used. Resolution of each of the files is 0.0572 degrees.
DOI: 10.6084/m9.figshare.3520469
title: Appendix A. Qualitative analysis of model stability and predictions of press perturbation response.

description: Qualitative analysis of model stability and predictions of press perturbation response.
DOI: 10.6084/m9.figshare.3520466
title: Appendix A. Map of wildfire scars from 1972–2011 within the Murray Sunset National Park.

description: Map of wildfire scars from 1972–2011 within the Murray Sunset National Park.
DOI: 10.6084/m9.figshare.3520466.v1
title: Appendix A. Map of wildfire scars from 1972–2011 within the Murray Sunset National Park.

description: Map of wildfire scars from 1972–2011 within the Murray Sunset National Park.
DOI: 10.6084/m9.figshare.3520463
title: Appendix B. Annual probability of wildfire in Triodia scariosa mallee vegetation, within the Murray Sunset National Park.

description: Annual probability of wildfire in Triodia scariosa mallee vegetation, within the Murray Sunset National Park.
DOI: 10.6084/m9.figshare.3520463.v1
title: Appendix B. Annual probability of wildfire in Triodia scariosa mallee vegetation, within the Murray Sunset National Park.

description: Annual probability of wildfire in Triodia scariosa mallee vegetation, within the Murray Sunset National Park.
DOI: 10.6084/m9.figshare.3520460
title: Appendix C. Optimal strategy and expected value of the reserve for the bird-only analysis.

description: Optimal strategy and expected value of the reserve for the bird-only analysis.
DOI: 10.6084/m9.figshare.3520457
title: Appendix D. Optimal strategy and expected value of the reserve for the reptile-only analysis.

description: Optimal strategy and expected value of the reserve for the reptile-only analysis.
DOI: 10.6084/m9.figshare.3520457.v1
title: Appendix D. Optimal strategy and expected value of the reserve for the reptile-only analysis.

description: Optimal strategy and expected value of the reserve for the reptile-only analysis.
DOI: 10.6084/m9.figshare.3520454
title: Appendix E. Relative performance of the objective functions, through time, when adhering to the optimal strategy for each of the alternate objective functions. Data is for all 22 species combined.

description: Relative performance of the objective functions, through time, when adhering to the optimal strategy for each of the alternate objective functions. Data is for all 22 species combined.
DOI: 10.6084/m9.figshare.3520454.v1
title: Appendix E. Relative performance of the objective functions, through time, when adhering to the optimal strategy for each of the alternate objective functions. Data is for all 22 species combined.

description: Relative performance of the objective functions, through time, when adhering to the optimal strategy for each of the alternate objective functions. Data is for all 22 species combined.
DOI: 10.6084/m9.figshare.3520451
title: Appendix F. Optimal strategy and expected value of the reserve when constraining the solution to achieve a 3% annual fuel reduction target.

description: Optimal strategy and expected value of the reserve when constraining the solution to achieve a 3% annual fuel reduction target.
DOI: 10.6084/m9.figshare.3520451.v1
title: Appendix F. Optimal strategy and expected value of the reserve when constraining the solution to achieve a 3% annual fuel reduction target.

description: Optimal strategy and expected value of the reserve when constraining the solution to achieve a 3% annual fuel reduction target.
DOI: 10.6084/m9.figshare.3520448
title: Appendix A. An examination of the distribution of North American fishes within the 3-point life-history continuum and an evaluation of differences between trait values for lotic and lentic fish.

description: An examination of the distribution of North American fishes within the 3-point life-history continuum and an evaluation of differences between trait values for lotic and lentic fish.
DOI: 10.6084/m9.figshare.3520448.v1
title: Appendix A. An examination of the distribution of North American fishes within the 3-point life-history continuum and an evaluation of differences between trait values for lotic and lentic fish.

description: An examination of the distribution of North American fishes within the 3-point life-history continuum and an evaluation of differences between trait values for lotic and lentic fish.
DOI: 10.6084/m9.figshare.3520445
title: Appendix B. Justification for inclusion and methods for summarizing landscape variables for use in predicting fish traits, summary of correlations among predictors and trait-frequencies, and an assessment of redundancy in predictors.

description: Justification for inclusion and methods for summarizing landscape variables for use in predicting fish traits, summary of correlations among predictors and trait-frequencies, and an assessment of redundancy in predictors.
DOI: 10.6084/m9.figshare.3520445.v1
title: Appendix B. Justification for inclusion and methods for summarizing landscape variables for use in predicting fish traits, summary of correlations among predictors and trait-frequencies, and an assessment of redundancy in predictors.

description: Justification for inclusion and methods for summarizing landscape variables for use in predicting fish traits, summary of correlations among predictors and trait-frequencies, and an assessment of redundancy in predictors.