cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3530249
title: Supplement 2. Python and WinBUGS model code for simulation study.

description: File List bugs_sim.py -- Python code to simulate data for input into WINBUGS. Program calls WINBUGS in a DOS command and sends summary output to a storage file. def_sim.py -- Python code (called by bugs_sim.py) specifying input parameters for simulations. oarunscript.txt -- WINBUGS script file for batch execution. oa_model.txt -- WINBUGS model file for batch execution. oa_data.txt -- WINBUGS data file (replaced at each simulation iteration). oa_inits.txt -- WINBUGS initial parameter value file (replaced at each simulation iteration). Description To execute program in WINDOWS operating systems, place all files in /Program Files/ WINBUGS14 and open the file "bugs_sim.py". This file references the "def_sim.py" and simulates data and initial values, replacing oa_data.txt and oa_intis.txt. The program then executes WINBUGS as a DOS command, with parameters contained in "oa_runscript.txt", using the simulated model specified in "oa_model.txt" and current data and initial values. Summary output is sent to two comma-delimited files: "sim_params.csv" and "sim_summary.csv", which keep track of parameter values and model estimates, respectively, for each simulation, and from which estimator performance (e.g., bias, MSE, and interval coverage) can be evaluated. <i>Note</i>: Execution of "bugs_sim.py" and "def_sim.py" requires installation of Python; we recommend ActiveState ActivePython 2.5 (http://www.activestate.com), and numpy numeric Python (http://www.scipy.org/Download). Installation of pymc (http://pymc.googlecode.com/files/pymc-2.0.win32-py2.5.exe) is required to access the likelihood objects in "bugs_sim.py"; alternatively users may code their own likelihood functions directly in Python.
DOI: 10.6084/m9.figshare.3530249.v1
title: Supplement 2. Python and WinBUGS model code for simulation study.

description: File List bugs_sim.py -- Python code to simulate data for input into WINBUGS. Program calls WINBUGS in a DOS command and sends summary output to a storage file. def_sim.py -- Python code (called by bugs_sim.py) specifying input parameters for simulations. oarunscript.txt -- WINBUGS script file for batch execution. oa_model.txt -- WINBUGS model file for batch execution. oa_data.txt -- WINBUGS data file (replaced at each simulation iteration). oa_inits.txt -- WINBUGS initial parameter value file (replaced at each simulation iteration). Description To execute program in WINDOWS operating systems, place all files in /Program Files/ WINBUGS14 and open the file "bugs_sim.py". This file references the "def_sim.py" and simulates data and initial values, replacing oa_data.txt and oa_intis.txt. The program then executes WINBUGS as a DOS command, with parameters contained in "oa_runscript.txt", using the simulated model specified in "oa_model.txt" and current data and initial values. Summary output is sent to two comma-delimited files: "sim_params.csv" and "sim_summary.csv", which keep track of parameter values and model estimates, respectively, for each simulation, and from which estimator performance (e.g., bias, MSE, and interval coverage) can be evaluated. <i>Note</i>: Execution of "bugs_sim.py" and "def_sim.py" requires installation of Python; we recommend ActiveState ActivePython 2.5 (http://www.activestate.com), and numpy numeric Python (http://www.scipy.org/Download). Installation of pymc (http://pymc.googlecode.com/files/pymc-2.0.win32-py2.5.exe) is required to access the likelihood objects in "bugs_sim.py"; alternatively users may code their own likelihood functions directly in Python.
DOI: 10.6084/m9.figshare.3530246
title: Appendix A. Lavielle's (2005) model selection procedure.

description: Lavielle's (2005) model selection procedure.
DOI: 10.6084/m9.figshare.3530246.v1
title: Appendix A. Lavielle's (2005) model selection procedure.

description: Lavielle's (2005) model selection procedure.
DOI: 10.6084/m9.figshare.3530243
title: Supplement 1. Pascal program for computing the residence time.

description: File List Residence_time.txt -- PASCAL CODE Description This program can run with any Pascal compiler (a free compiler working on most operating systems can be downloaded at www.freepascal.org). It works from an input file in plain text where the two first columns are Cartesian coordinates (<em>x</em>, <em>y</em>) of the successive locations, and the third column is the associated time <em>t</em>. Georeferenced data (i.e., expressed in latitudeand longitude) must be first converted in Cartesian coordinates, by using an appropriate projection system. Nevertheless, if the movement was restricted to a relatively small area (a few degrees in both latitude and longitude) that is not too close to the poles (i.e., below 70°N and above 70°S), approximate but reliable Cartesian coordinates, expressed in km, can be obtained from latitude, <em>lat</em>, and longitude, <em>long</em>, expressed in degrees, as: <em>x</em> = 111.12 (<em>long</em> - <em>long0</em>) cos(<em>lat0</em> -- IMAGE: Please see in attached file. --/180), <em>y</em> = 111.12 (<em>lat</em> - <em>lat0</em>), where <em>lat0</em> and <em>long0</em> are the latitude and the longitude of the first location. The name of the input and output files should include the whole directory path (e.g., C:\data\input_file.txt on a DOS or Windows operating system). The radius of the virtual circle and the step length (if the movement should be spatially rediscretized) must be expressed in the same unit as Cartesian coordinates <em>x</em> and <em>y</em>; the step duration (if the movement should be temporally rediscretized) must be expressed in the same unit as time <em>t</em>.
DOI: 10.6084/m9.figshare.3530243.v1
title: Supplement 1. Pascal program for computing the residence time.

description: File List Residence_time.txt -- PASCAL CODE Description This program can run with any Pascal compiler (a free compiler working on most operating systems can be downloaded at www.freepascal.org). It works from an input file in plain text where the two first columns are Cartesian coordinates (<em>x</em>, <em>y</em>) of the successive locations, and the third column is the associated time <em>t</em>. Georeferenced data (i.e., expressed in latitudeand longitude) must be first converted in Cartesian coordinates, by using an appropriate projection system. Nevertheless, if the movement was restricted to a relatively small area (a few degrees in both latitude and longitude) that is not too close to the poles (i.e., below 70°N and above 70°S), approximate but reliable Cartesian coordinates, expressed in km, can be obtained from latitude, <em>lat</em>, and longitude, <em>long</em>, expressed in degrees, as: <em>x</em> = 111.12 (<em>long</em> - <em>long0</em>) cos(<em>lat0</em> -- IMAGE: Please see in attached file. --/180), <em>y</em> = 111.12 (<em>lat</em> - <em>lat0</em>), where <em>lat0</em> and <em>long0</em> are the latitude and the longitude of the first location. The name of the input and output files should include the whole directory path (e.g., C:\data\input_file.txt on a DOS or Windows operating system). The radius of the virtual circle and the step length (if the movement should be spatially rediscretized) must be expressed in the same unit as Cartesian coordinates <em>x</em> and <em>y</em>; the step duration (if the movement should be temporally rediscretized) must be expressed in the same unit as time <em>t</em>.
DOI: 10.6084/m9.figshare.3530240
title: Appendix A. Comparisons among four age and sex classes in the percentage of time spent torpid, average torpor bout length, and the average torpor bout minimum skin temperature in three 20-day windows within the low-food year (2005–2006) and the high-food year (2006–2007).

description: Comparisons among four age and sex classes in the percentage of time spent torpid, average torpor bout length, and the average torpor bout minimum skin temperature in three 20-day windows within the low-food year (2005–2006) and the high-food year (2006–2007).
DOI: 10.6084/m9.figshare.3530240.v1
title: Appendix A. Comparisons among four age and sex classes in the percentage of time spent torpid, average torpor bout length, and the average torpor bout minimum skin temperature in three 20-day windows within the low-food year (2005–2006) and the high-food year (2006–2007).

description: Comparisons among four age and sex classes in the percentage of time spent torpid, average torpor bout length, and the average torpor bout minimum skin temperature in three 20-day windows within the low-food year (2005–2006) and the high-food year (2006–2007).
DOI: 10.6084/m9.figshare.3530237
title: Appendix B. Mixed model repeated-measures analysis of Tsk-m for all observed torpor bouts including a random effect of individual and a fixed effect of year interacting with burrow soil temperature (Tsoil; average during a given torpor bout).

description: Mixed model repeated-measures analysis of Tsk-m for all observed torpor bouts including a random effect of individual and a fixed effect of year interacting with burrow soil temperature (Tsoil; average during a given torpor bout).
DOI: 10.6084/m9.figshare.3530237.v1
title: Appendix B. Mixed model repeated-measures analysis of Tsk-m for all observed torpor bouts including a random effect of individual and a fixed effect of year interacting with burrow soil temperature (Tsoil; average during a given torpor bout).

description: Mixed model repeated-measures analysis of Tsk-m for all observed torpor bouts including a random effect of individual and a fixed effect of year interacting with burrow soil temperature (Tsoil; average during a given torpor bout).
DOI: 10.6084/m9.figshare.3530234
title: Appendix A. Natural enemies of EPN at Bodega Marine Reserve.

description: Natural enemies of EPN at Bodega Marine Reserve.
DOI: 10.6084/m9.figshare.3530234.v1
title: Appendix A. Natural enemies of EPN at Bodega Marine Reserve.

description: Natural enemies of EPN at Bodega Marine Reserve.
DOI: 10.6084/m9.figshare.3530231
title: Appendix B. Description of sites and BML habitats.

description: Description of sites and BML habitats.
DOI: 10.6084/m9.figshare.3530231.v1
title: Appendix B. Description of sites and BML habitats.

description: Description of sites and BML habitats.
DOI: 10.6084/m9.figshare.3530228
title: Appendix C. Average long-term incidence from 1993–2006.

description: Average long-term incidence from 1993–2006.
DOI: 10.6084/m9.figshare.3530228.v1
title: Appendix C. Average long-term incidence from 1993–2006.

description: Average long-term incidence from 1993–2006.
DOI: 10.6084/m9.figshare.3530225
title: Appendix D. The effect of rhizosphere and site on EPN survival.

description: The effect of rhizosphere and site on EPN survival.
DOI: 10.6084/m9.figshare.3530225.v1
title: Appendix D. The effect of rhizosphere and site on EPN survival.

description: The effect of rhizosphere and site on EPN survival.
DOI: 10.6084/m9.figshare.3530222
title: Appendix E. Mortality estimates by site and rhizosphere type.

description: Mortality estimates by site and rhizosphere type.
DOI: 10.6084/m9.figshare.3530222.v1
title: Appendix E. Mortality estimates by site and rhizosphere type.

description: Mortality estimates by site and rhizosphere type.
DOI: 10.6084/m9.figshare.3530219
title: Appendix A. Views of neighborhood-reduced and fenced plots in the transplant and seed-addition experiments.

description: Views of neighborhood-reduced and fenced plots in the transplant and seed-addition experiments.
DOI: 10.6084/m9.figshare.3530219.v1
title: Appendix A. Views of neighborhood-reduced and fenced plots in the transplant and seed-addition experiments.

description: Views of neighborhood-reduced and fenced plots in the transplant and seed-addition experiments.
DOI: 10.6084/m9.figshare.3530216
title: Appendix B. Native and nonnative extant species in experimental plots in Garry oak meadows on Salt Spring Island, British Columbia (BC), Canada.

description: Native and nonnative extant species in experimental plots in Garry oak meadows on Salt Spring Island, British Columbia (BC), Canada.
DOI: 10.6084/m9.figshare.3530213
title: Appendix C. Characteristics and measures of the focal plant species measured in the transplant experiment.

description: Characteristics and measures of the focal plant species measured in the transplant experiment.
DOI: 10.6084/m9.figshare.3530213.v1
title: Appendix C. Characteristics and measures of the focal plant species measured in the transplant experiment.

description: Characteristics and measures of the focal plant species measured in the transplant experiment.
DOI: 10.6084/m9.figshare.3530210
title: Appendix D. Species added to each plot in the seed-addition experiment, their plant type, and the number of seeds per plot.

description: Species added to each plot in the seed-addition experiment, their plant type, and the number of seeds per plot.
DOI: 10.6084/m9.figshare.3530210.v1
title: Appendix D. Species added to each plot in the seed-addition experiment, their plant type, and the number of seeds per plot.

description: Species added to each plot in the seed-addition experiment, their plant type, and the number of seeds per plot.
DOI: 10.6084/m9.figshare.3530207
title: Appendix E. Tables of the results of all mixed models for two-level, two-factor competition and herbivory transplant and seed-addition experiments in Garry oak meadows and Salt Spring Island, British Columbia, Canada.

description: Tables of the results of all mixed models for two-level, two-factor competition and herbivory transplant and seed-addition experiments in Garry oak meadows and Salt Spring Island, British Columbia, Canada.
DOI: 10.6084/m9.figshare.3530207.v1
title: Appendix E. Tables of the results of all mixed models for two-level, two-factor competition and herbivory transplant and seed-addition experiments in Garry oak meadows and Salt Spring Island, British Columbia, Canada.

description: Tables of the results of all mixed models for two-level, two-factor competition and herbivory transplant and seed-addition experiments in Garry oak meadows and Salt Spring Island, British Columbia, Canada.
DOI: 10.6084/m9.figshare.3530204
title: Appendix A. Hydrological indices for the disturbed and undisturbed reach for the three diverted streams.

description: Hydrological indices for the disturbed and undisturbed reach for the three diverted streams.
DOI: 10.6084/m9.figshare.3530204.v1
title: Appendix A. Hydrological indices for the disturbed and undisturbed reach for the three diverted streams.

description: Hydrological indices for the disturbed and undisturbed reach for the three diverted streams.
DOI: 10.6084/m9.figshare.3530201
title: Appendix B. Community richness values for all stream sites.

description: Community richness values for all stream sites.
DOI: 10.6084/m9.figshare.3530201.v1
title: Appendix B. Community richness values for all stream sites.

description: Community richness values for all stream sites.
DOI: 10.6084/m9.figshare.3530198
title: Appendix C. Trophic position statistics.

description: Trophic position statistics.
DOI: 10.6084/m9.figshare.3530198.v1
title: Appendix C. Trophic position statistics.

description: Trophic position statistics.
DOI: 10.6084/m9.figshare.3530195
title: A1_TableA1

description: Species list with traits.
DOI: 10.6084/m9.figshare.3530195.v1
title: A1_TableA1

description: Species list with traits.
DOI: 10.6084/m9.figshare.3530192
title: Supplement 1. Original data used for analyzing relationships between species richness and chlorophyll a by linear and polynomial regression.

description: File List supplement.txt Description The file is a tab-separated ascii file. The file contains values of chlorophyll <i>a</i> (x) and species richness (y) used for linear and polynomial regression analysis. Data presented here are log10 transformed as in the published analyses. Column headings indicate the figure the data correspond to and are labeled either as Log 10 Species richness or Log 10 Mean Chl (Chlorophyll) <i>a</i>. Units are identified as number of species for species richness or mg L<sup>-1</sup> for chlorophyll <i>a</i>.
DOI: 10.6084/m9.figshare.3530189
title: Appendix A. Additional information on CORONA, including verbatim minutes of the meetings.

description: Additional information on CORONA, including verbatim minutes of the meetings.
DOI: 10.6084/m9.figshare.3530192.v1
title: Supplement 1. Original data used for analyzing relationships between species richness and chlorophyll a by linear and polynomial regression.

description: File List supplement.txt Description The file is a tab-separated ascii file. The file contains values of chlorophyll <i>a</i> (x) and species richness (y) used for linear and polynomial regression analysis. Data presented here are log10 transformed as in the published analyses. Column headings indicate the figure the data correspond to and are labeled either as Log 10 Species richness or Log 10 Mean Chl (Chlorophyll) <i>a</i>. Units are identified as number of species for species richness or mg L<sup>-1</sup> for chlorophyll <i>a</i>.
DOI: 10.6084/m9.figshare.3530189.v1
title: Appendix A. Additional information on CORONA, including verbatim minutes of the meetings.

description: Additional information on CORONA, including verbatim minutes of the meetings.
DOI: 10.6084/m9.figshare.3530183
title: Appendix A. A table of comparisons of predator treatments where no significant interaction terms were found between a treatment and population predation risk.

description: A table of comparisons of predator treatments where no significant interaction terms were found between a treatment and population predation risk.
DOI: 10.6084/m9.figshare.3530183.v1
title: Appendix A. A table of comparisons of predator treatments where no significant interaction terms were found between a treatment and population predation risk.

description: A table of comparisons of predator treatments where no significant interaction terms were found between a treatment and population predation risk.
DOI: 10.6084/m9.figshare.3530180
title: Appendix A. A table showing the 20 octocoral families and 73 genera recorded in shallow waters of coral reefs of the Great Barrier Reef and their relative frequency and trophic group, and a figure of partial dependency plots from the boosted tree analysis showing the interactions between the spatial factors affecting the richness of phototrophic and heterotrophic octocoral assemblages on the Great Barrier Reef.

description: A table showing the 20 octocoral families and 73 genera recorded in shallow waters of coral reefs of the Great Barrier Reef and their relative frequency and trophic group, and a figure of partial dependency plots from the boosted tree analysis showing the interactions between the spatial factors affecting the richness of phototrophic and heterotrophic octocoral assemblages on the Great Barrier Reef.
DOI: 10.6084/m9.figshare.3530180.v1
title: Appendix A. A table showing the 20 octocoral families and 73 genera recorded in shallow waters of coral reefs of the Great Barrier Reef and their relative frequency and trophic group, and a figure of partial dependency plots from the boosted tree analysis showing the interactions between the spatial factors affecting the richness of phototrophic and heterotrophic octocoral assemblages on the Great Barrier Reef.

description: A table showing the 20 octocoral families and 73 genera recorded in shallow waters of coral reefs of the Great Barrier Reef and their relative frequency and trophic group, and a figure of partial dependency plots from the boosted tree analysis showing the interactions between the spatial factors affecting the richness of phototrophic and heterotrophic octocoral assemblages on the Great Barrier Reef.
DOI: 10.6084/m9.figshare.3530177
title: Appendix A. Photographs of feeding fronts of Oreaster reticulatus and Strongylocentrotus droebachiensis.

description: Photographs of feeding fronts of Oreaster reticulatus and Strongylocentrotus droebachiensis.
DOI: 10.6084/m9.figshare.3530177.v1
title: Appendix A. Photographs of feeding fronts of Oreaster reticulatus and Strongylocentrotus droebachiensis.

description: Photographs of feeding fronts of Oreaster reticulatus and Strongylocentrotus droebachiensis.
DOI: 10.6084/m9.figshare.3530174
title: Appendix B. Details of the von Mises distribution of turning angles for Oreaster reticulatus.

description: Details of the von Mises distribution of turning angles for Oreaster reticulatus.
DOI: 10.6084/m9.figshare.3530174.v1
title: Appendix B. Details of the von Mises distribution of turning angles for Oreaster reticulatus.

description: Details of the von Mises distribution of turning angles for Oreaster reticulatus.
DOI: 10.6084/m9.figshare.3530171
title: Appendix C. Initial conditions of Model 1 (for Oreaster reticulatus) and Model 2 (for Strongylocentrotus droebachiensis).

description: Initial conditions of Model 1 (for Oreaster reticulatus) and Model 2 (for Strongylocentrotus droebachiensis).
DOI: 10.6084/m9.figshare.3530171.v1
title: Appendix C. Initial conditions of Model 1 (for Oreaster reticulatus) and Model 2 (for Strongylocentrotus droebachiensis).

description: Initial conditions of Model 1 (for Oreaster reticulatus) and Model 2 (for Strongylocentrotus droebachiensis).
DOI: 10.6084/m9.figshare.3530168
title: Appendix D. Simulations of Model 1 (for Oreaster reticulatus) and Model 2 (for Strongylocentrotus droebachiensis) with different gradients in food distribution.

description: Simulations of Model 1 (for Oreaster reticulatus) and Model 2 (for Strongylocentrotus droebachiensis) with different gradients in food distribution.
DOI: 10.6084/m9.figshare.3530168.v1
title: Appendix D. Simulations of Model 1 (for Oreaster reticulatus) and Model 2 (for Strongylocentrotus droebachiensis) with different gradients in food distribution.

description: Simulations of Model 1 (for Oreaster reticulatus) and Model 2 (for Strongylocentrotus droebachiensis) with different gradients in food distribution.
DOI: 10.6084/m9.figshare.3530165
title: Appendix E. Details of the procedures used in uncertainty and elasticity analyses.

description: Details of the procedures used in uncertainty and elasticity analyses.
DOI: 10.6084/m9.figshare.3530165.v1
title: Appendix E. Details of the procedures used in uncertainty and elasticity analyses.

description: Details of the procedures used in uncertainty and elasticity analyses.
DOI: 10.6084/m9.figshare.3530162
title: Appendix F. Fit of the Gaussian distribution to daily displacement distance measured for Strongylocentrotus droebachiensis.

description: Fit of the Gaussian distribution to daily displacement distance measured for Strongylocentrotus droebachiensis.
DOI: 10.6084/m9.figshare.3530162.v1
title: Appendix F. Fit of the Gaussian distribution to daily displacement distance measured for Strongylocentrotus droebachiensis.

description: Fit of the Gaussian distribution to daily displacement distance measured for Strongylocentrotus droebachiensis.
DOI: 10.6084/m9.figshare.3530159
title: Appendix G. List of parameter values used in Model 2 for sea urchins Strongylocentrotus droebachiensis.

description: List of parameter values used in Model 2 for sea urchins Strongylocentrotus droebachiensis.
DOI: 10.6084/m9.figshare.3530159.v1
title: Appendix G. List of parameter values used in Model 2 for sea urchins Strongylocentrotus droebachiensis.

description: List of parameter values used in Model 2 for sea urchins Strongylocentrotus droebachiensis.
DOI: 10.6084/m9.figshare.3530156
title: Appendix A. Location of study sites.

description: Location of study sites.
DOI: 10.6084/m9.figshare.3530156.v1
title: Appendix A. Location of study sites.

description: Location of study sites.
DOI: 10.6084/m9.figshare.3530153
title: Appendix B. Statistical analysis (ANOVA) of 33-year time series of barnacle abundance.

description: Statistical analysis (ANOVA) of 33-year time series of barnacle abundance.
DOI: 10.6084/m9.figshare.3530153.v1
title: Appendix B. Statistical analysis (ANOVA) of 33-year time series of barnacle abundance.

description: Statistical analysis (ANOVA) of 33-year time series of barnacle abundance.