cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3512243.v1
title: Supplement 1. S-Plus code used to fit life history (LH) and Hallock and Fisher (HF) hidden process models, along with data files.

description: File List hfmax.apf - S-Plus code for auxiliary particle filter for H&F model <br> lhmax.apf - S-Plus code for auxiliary particle filter for LH model <br> hfmax.call - S-Plus code that calls hfmax.apf and loads data <br> lhmax.call - S-Plus code that calls lhmax.apf and loads data <br> Utilities - S-Plus code with miscellaneous functions used by the .apf pgms <br> est.counts - data file for juvenile and adult data (1996–2001) <br> rbdd.adult - data file for adult returns to Redd Bluff Diversion Dam (1967–2001) <br> hpmall.tar - tar file of all the above files Description All the above files can be put into the default working directory for S-Plus (Version 6.1.2 Release 2 for Linux 2.2.12: 2002) and then sourcing the .call files will run the .apf files. Alternate storage locations can be used but then the .call files will need to be edited for the alternate locations. Alternate output locations can be created, also, by editing the write() lines in hfmax.apf and lhmax.apf. These files currently assume that output directories named HFOUT and LHOUT exist. The number of particles generated is set by the object labelled <i>N.opt</i>. <br> The degree of kernel smoothing is set by the object <i>discount.opt</i>; it must be between 0 and 1 (values close to 1 are generally preferred; 0.9 is used in the paper).
DOI: 10.6084/m9.figshare.3512240.v1
title: Appendix A. A table of the parameter values used to generate hypothetical data sets A–F.

description: A table of the parameter values used to generate hypothetical data sets A–F.
DOI: 10.6084/m9.figshare.3512237
title: Appendix B. Results of a reanalysis of patterns of seedling dispersion for five tree species originally reported by LePage et al. (2000).

description: Results of a reanalysis of patterns of seedling dispersion for five tree species originally reported by LePage et al. (2000).
DOI: 10.6084/m9.figshare.3512237.v1
title: Appendix B. Results of a reanalysis of patterns of seedling dispersion for five tree species originally reported by LePage et al. (2000).

description: Results of a reanalysis of patterns of seedling dispersion for five tree species originally reported by LePage et al. (2000).
DOI: 10.6084/m9.figshare.3512234
title: Appendix C. The estimated parameters for dispersal functions using different neighborhood search distances and functional forms of the dispersal kernel.

description: The estimated parameters for dispersal functions using different neighborhood search distances and functional forms of the dispersal kernel.
DOI: 10.6084/m9.figshare.3512234.v1
title: Appendix C. The estimated parameters for dispersal functions using different neighborhood search distances and functional forms of the dispersal kernel.

description: The estimated parameters for dispersal functions using different neighborhood search distances and functional forms of the dispersal kernel.
DOI: 10.6084/m9.figshare.3512231
title: Supplement 1. Delphi source code and compiled program for nonstationary matrix model projection.

description: File List MarixGrowthProject.exe- stand-alone executable version of nonstationary matrix growth model<br> MatrixGrowth.zip- Delphi source code for nonstationary matrix growth model<br> Description The MatrixGrowthProject.exe iterates population growth and population size structure, for either stationary or nonstationary matrix models. In a series of tabbed input screens, the user supplies an initial transition matrix and size vector, with an optional variance-covariance matrix and regression parameters an external environmental driver. The MatrixGrowth.zip file contains 35 Delphi files that contain the source code for the components of this program. The source code is compiled in Delphi 6.0.
DOI: 10.6084/m9.figshare.3512228
title: Appendix A. Environmental data layers.

description: Environmental data layers.
DOI: 10.6084/m9.figshare.3512231.v1
title: Supplement 1. Delphi source code and compiled program for nonstationary matrix model projection.

description: File List MarixGrowthProject.exe- stand-alone executable version of nonstationary matrix growth model<br> MatrixGrowth.zip- Delphi source code for nonstationary matrix growth model<br> Description The MatrixGrowthProject.exe iterates population growth and population size structure, for either stationary or nonstationary matrix models. In a series of tabbed input screens, the user supplies an initial transition matrix and size vector, with an optional variance-covariance matrix and regression parameters an external environmental driver. The MatrixGrowth.zip file contains 35 Delphi files that contain the source code for the components of this program. The source code is compiled in Delphi 6.0.
DOI: 10.6084/m9.figshare.3512225
title: Supplement 1. Model code for WinBUGS.

description: File List models1and2.odc -- WinBUGS Code for Models 1 and 2, with explanation and sample data (in WinBUGS .odc format) <br> models1and2.html -- WinBUGS Code for Models 1 and 2, with explanation and sample data (in .html format) Description The WinBUGS compound document models1and2.odc contains code that implements Models 1 and 2, as well as introductory material that explains the data format and reviews the structure of the models. This compound document also integrates sample data and suggested initial values for initializing the model. This same material is also provided as models1and2.html for viewing in a web browser. Pictures of the environmental data layers included in these models, as well as additional data layers, are provided in Appendix A.
DOI: 10.6084/m9.figshare.3512228.v1
title: Appendix A. Environmental data layers.

description: Environmental data layers.
DOI: 10.6084/m9.figshare.3512225.v1
title: Supplement 1. Model code for WinBUGS.

description: File List models1and2.odc -- WinBUGS Code for Models 1 and 2, with explanation and sample data (in WinBUGS .odc format) <br> models1and2.html -- WinBUGS Code for Models 1 and 2, with explanation and sample data (in .html format) Description The WinBUGS compound document models1and2.odc contains code that implements Models 1 and 2, as well as introductory material that explains the data format and reviews the structure of the models. This compound document also integrates sample data and suggested initial values for initializing the model. This same material is also provided as models1and2.html for viewing in a web browser. Pictures of the environmental data layers included in these models, as well as additional data layers, are provided in Appendix A.
DOI: 10.6084/m9.figshare.3512222
title: Supplement 1. Annotated computer code in Matlab and SAS for performing the simulations and analyses in examples 1–4.

description: File List <b><i>Text file</i></b> fullV.txt <b><i>Matlab executable files</i></b> IZ_GLSeg.m IZ_SPACEeg.m Space_MLfunct.m IZ_TIMEeg.m Time_MLfunct.m IZ_MIXEDeg.m IZ_MIXEDegRep.m <b><i>SAS executable files</i></b> SASMIXEDeg.sas SASMIXEDegREG.sas <b><i>File descriptions</i></b> IZ_GLSeg.m – Matlab code simulating and analyzing phylogenetic data as in example #1 fullV.txt – Text file containing covariance matrix needed for IZ_GLSeg.m IZ_SPACEeg.m – Matlab code simulating and analyzing spatial data as in example #2 Space_MLfunct.m – Matlab function giving the likelihood function called by IZ_SPACEeg.m IZ_TIMEeg.m – Matlab code simulating and analyzing time-series data as in example #3 Time_MLfunct.m – Matlab function giving the likelihood function called by IZ_TIMEeg.m IZ_MIXEDeg.m – Matlab code simulating a single data set with spatial and temporal corelations as in example #4 IZ_MIXEDegRep.m – Matlab code simulating multiple data sets with spatial and temporal corelations as in example #4 SASMIXEDeg.sas – SAS code using REML to analyze a single data set produced by IZ_MIXEDeg.m SASMIXEDegREG.sas – SAS code using REML to analyze multiple data sets produced by IZ_MIXEDegRep.m Description Matlab ".m" files are text files that should run under Matlab version 5.0 and 6.5 (MathWorks 1996). The two programs used for example #4, IZ_MIXEDeg.m and IZ_MIXEDegRep.m, generate text files called 'mixedeg.txt'and 'mixedegrep.txt', respecitvely. These text files are then analyzed by the two SAS programs, SASMIXEDeg.sas and SASMIXEDegREG.sas, respectively, which are written in SAS version 6.12 (SAS 1996). To run the SAS programs, the infile line will have to be changed to set the path to the files mixedeg.txt and mixedegrep.txt. The current infile line in SASMIXEDeg.sas is infile 'Macintosh HD:mixedeg.txt'; which finds the file mixedeg.txt on the hard drive 'Macintosh HD'. All files should run under Macintosh, Windows, and Unix operating systems.
DOI: 10.6084/m9.figshare.3512222.v1
title: Supplement 1. Annotated computer code in Matlab and SAS for performing the simulations and analyses in examples 1–4.

description: File List <b><i>Text file</i></b> fullV.txt <b><i>Matlab executable files</i></b> IZ_GLSeg.m IZ_SPACEeg.m Space_MLfunct.m IZ_TIMEeg.m Time_MLfunct.m IZ_MIXEDeg.m IZ_MIXEDegRep.m <b><i>SAS executable files</i></b> SASMIXEDeg.sas SASMIXEDegREG.sas <b><i>File descriptions</i></b> IZ_GLSeg.m – Matlab code simulating and analyzing phylogenetic data as in example #1 fullV.txt – Text file containing covariance matrix needed for IZ_GLSeg.m IZ_SPACEeg.m – Matlab code simulating and analyzing spatial data as in example #2 Space_MLfunct.m – Matlab function giving the likelihood function called by IZ_SPACEeg.m IZ_TIMEeg.m – Matlab code simulating and analyzing time-series data as in example #3 Time_MLfunct.m – Matlab function giving the likelihood function called by IZ_TIMEeg.m IZ_MIXEDeg.m – Matlab code simulating a single data set with spatial and temporal corelations as in example #4 IZ_MIXEDegRep.m – Matlab code simulating multiple data sets with spatial and temporal corelations as in example #4 SASMIXEDeg.sas – SAS code using REML to analyze a single data set produced by IZ_MIXEDeg.m SASMIXEDegREG.sas – SAS code using REML to analyze multiple data sets produced by IZ_MIXEDegRep.m Description Matlab ".m" files are text files that should run under Matlab version 5.0 and 6.5 (MathWorks 1996). The two programs used for example #4, IZ_MIXEDeg.m and IZ_MIXEDegRep.m, generate text files called 'mixedeg.txt'and 'mixedegrep.txt', respecitvely. These text files are then analyzed by the two SAS programs, SASMIXEDeg.sas and SASMIXEDegREG.sas, respectively, which are written in SAS version 6.12 (SAS 1996). To run the SAS programs, the infile line will have to be changed to set the path to the files mixedeg.txt and mixedegrep.txt. The current infile line in SASMIXEDeg.sas is infile 'Macintosh HD:mixedeg.txt'; which finds the file mixedeg.txt on the hard drive 'Macintosh HD'. All files should run under Macintosh, Windows, and Unix operating systems.
DOI: 10.6084/m9.figshare.3512219
title: Appendix A. An example calculation of likelihood.

description: An example calculation of likelihood.
DOI: 10.6084/m9.figshare.3512216
title: Appendix B. A discussion regarding what likelihood to use.

description: A discussion regarding what likelihood to use.
DOI: 10.6084/m9.figshare.3512213
title: Appendix C. A discussion on how to use likelihood and information theoretics to evaluate support in data for competing models.

description: A discussion on how to use likelihood and information theoretics to evaluate support in data for competing models.
DOI: 10.6084/m9.figshare.3512210
title: Appendix D. A further discussion on the concept of likelihood.

description: A further discussion on the concept of likelihood.
DOI: 10.6084/m9.figshare.3512204
title: Appendix A. A description of heuristic algorithms, species data, and landscape data.

description: A description of heuristic algorithms, species data, and landscape data.
DOI: 10.6084/m9.figshare.3512204.v1
title: Appendix A. A description of heuristic algorithms, species data, and landscape data.

description: A description of heuristic algorithms, species data, and landscape data.
DOI: 10.6084/m9.figshare.3512201
title: Appendix A. Maps of Nova Scotia showing distribution of (Fig. A1) moose populations and protected areas; (Fig. A2) moose habitat suitability values; (Fig. A3) road density and moose pellet presence/absence; (Fig. A4) contiguous areas of natural cover 10,000 ha; (Fig. A5) roadless areas; (Fig. A6) uneven-aged forest stands; (Fig. A7) combined cover for contiguous natural cover 10,000 ha, roadless areas, and uneven-aged forest stands; (Fig. A8) areas of primary priority combining natural...

description: Maps of Nova Scotia showing distribution of (Fig. A1) moose populations and protected areas; (Fig. A2) moose habitat suitability values; (Fig. A3) road density and moose pellet presence/absence; (Fig. A4) contiguous areas of natural cover 10,000 ha; (Fig. A5) roadless areas; (Fig. A6) uneven-aged forest stands; (Fig. A7) combined cover for contiguous natural cover 10,000 ha, roadless areas, and uneven-aged forest stands; (Fig. A8) areas of primary priority combining natural areas, 10,000 ha, uneven-aged forest stands, and roadless areas; (Fig. A9) species at risk globally or provincially; (Fig. A10) highest rarity-weighted richness values; (Fig. A11) significant ecosites; (Fig. A12) signigficant old and unique forest stands; (Fig. A13) areas of primary priority for special elements; highest habitat suitability and population densities for (Fig. A14) American moose, (Fig. A15) American marten, and (Fig. A16) Northern Goshawk; (Fig. A17) 47 core areas selected by priority sites for representation, special elements, and focal species; (Fig. A18) cost-surface for American marten; and (Fig. A19) least-cost paths for American marten.
DOI: 10.6084/m9.figshare.3512201.v1
title: Appendix A. Maps of Nova Scotia showing distribution of (Fig. A1) moose populations and protected areas; (Fig. A2) moose habitat suitability values; (Fig. A3) road density and moose pellet presence/absence; (Fig. A4) contiguous areas of natural cover 10,000 ha; (Fig. A5) roadless areas; (Fig. A6) uneven-aged forest stands; (Fig. A7) combined cover for contiguous natural cover 10,000 ha, roadless areas, and uneven-aged forest stands; (Fig. A8) areas of primary priority combining natural...

description: Maps of Nova Scotia showing distribution of (Fig. A1) moose populations and protected areas; (Fig. A2) moose habitat suitability values; (Fig. A3) road density and moose pellet presence/absence; (Fig. A4) contiguous areas of natural cover 10,000 ha; (Fig. A5) roadless areas; (Fig. A6) uneven-aged forest stands; (Fig. A7) combined cover for contiguous natural cover 10,000 ha, roadless areas, and uneven-aged forest stands; (Fig. A8) areas of primary priority combining natural areas, 10,000 ha, uneven-aged forest stands, and roadless areas; (Fig. A9) species at risk globally or provincially; (Fig. A10) highest rarity-weighted richness values; (Fig. A11) significant ecosites; (Fig. A12) signigficant old and unique forest stands; (Fig. A13) areas of primary priority for special elements; highest habitat suitability and population densities for (Fig. A14) American moose, (Fig. A15) American marten, and (Fig. A16) Northern Goshawk; (Fig. A17) 47 core areas selected by priority sites for representation, special elements, and focal species; (Fig. A18) cost-surface for American marten; and (Fig. A19) least-cost paths for American marten.
DOI: 10.6084/m9.figshare.3512198
title: Appendix B. A coarse-filter representivity-assessment framework.

description: A coarse-filter representivity-assessment framework.
DOI: 10.6084/m9.figshare.3512198.v1
title: Appendix B. A coarse-filter representivity-assessment framework.

description: A coarse-filter representivity-assessment framework.
DOI: 10.6084/m9.figshare.3512195
title: Appendix C. A table showing classes for assessing site potential for representation.

description: A table showing classes for assessing site potential for representation.
DOI: 10.6084/m9.figshare.3512192
title: Appendix D. A table showing coverages for assessing site potential for special elements.

description: A table showing coverages for assessing site potential for special elements.
DOI: 10.6084/m9.figshare.3512189
title: Appendix E. A table showing habitat suitability index (HSI) equations.

description: A table showing habitat suitability index (HSI) equations.
DOI: 10.6084/m9.figshare.3512186
title: Appendix F. A table showing habitat component composition and associated forest cover attributes for moose HSI.

description: A table showing habitat component composition and associated forest cover attributes for moose HSI.
DOI: 10.6084/m9.figshare.3512183
title: Appendix G. A figure showing the derivation of suitability index (SI) for each habitat component.

description: A figure showing the derivation of suitability index (SI) for each habitat component.
DOI: 10.6084/m9.figshare.3512183.v1
title: Appendix G. A figure showing the derivation of suitability index (SI) for each habitat component.

description: A figure showing the derivation of suitability index (SI) for each habitat component.
DOI: 10.6084/m9.figshare.3512180
title: Appendix H. A table showing chi-square values from regression analysis to determine the ability of habitat values and road density to predict moose pellet presence on transects.

description: A table showing chi-square values from regression analysis to determine the ability of habitat values and road density to predict moose pellet presence on transects.
DOI: 10.6084/m9.figshare.3512177
title: Appendix I. A flow chart indicating overlay process and data layers for cost–distance analysis.

description: A flow chart indicating overlay process and data layers for cost–distance analysis.
DOI: 10.6084/m9.figshare.3512177.v1
title: Appendix I. A flow chart indicating overlay process and data layers for cost–distance analysis.

description: A flow chart indicating overlay process and data layers for cost–distance analysis.
DOI: 10.6084/m9.figshare.3512174
title: Index Files

description: Index Files
DOI: 10.6084/m9.figshare.3512174.v1
title: Index Files

description: Index Files
DOI: 10.6084/m9.figshare.3512171
title: Appendix A. Descriptions of each weather variable, information on the weather stations and the methods used to derive estimates of weather conditions at Kettle Tarn (KT) and Lost Lake (LL), and a complete list of the weather models in the candidate set.

description: Descriptions of each weather variable, information on the weather stations and the methods used to derive estimates of weather conditions at Kettle Tarn (KT) and Lost Lake (LL), and a complete list of the weather models in the candidate set.
DOI: 10.6084/m9.figshare.3512171.v1
title: Appendix A. Descriptions of each weather variable, information on the weather stations and the methods used to derive estimates of weather conditions at Kettle Tarn (KT) and Lost Lake (LL), and a complete list of the weather models in the candidate set.

description: Descriptions of each weather variable, information on the weather stations and the methods used to derive estimates of weather conditions at Kettle Tarn (KT) and Lost Lake (LL), and a complete list of the weather models in the candidate set.
DOI: 10.6084/m9.figshare.3512168
title: Appendix A. A priori models considered to explain variation in duck nest survival in the Missouri Coteau region of North Dakota, USA.

description: A priori models considered to explain variation in duck nest survival in the Missouri Coteau region of North Dakota, USA.
DOI: 10.6084/m9.figshare.3512168.v1
title: Appendix A. A priori models considered to explain variation in duck nest survival in the Missouri Coteau region of North Dakota, USA.

description: A priori models considered to explain variation in duck nest survival in the Missouri Coteau region of North Dakota, USA.
DOI: 10.6084/m9.figshare.3512165
title: Supplement 1. MATLAB source code for the generation of a null model via matrix permutation methods and the test of the difference between pairs of correlation matrices.

description: File List Downloadable MATLAB files<br> permcorr.m<br> permcorr.txt<br> permdiff.m<br> permdiff.txt Description This supplement contains the MATLAB code files for testing the difference between pairs of correlation matrices via the generation of a null model with matrix permutation methods. <br> The MATLAB function permdiff.m calculates a sum of squared differences between elements of two input matrices and the probability that this difference is significantly different than zero. It invokes the function permcorr.m to randomly permute the input matrices and generate a null model. The files are provided in both a compiled MATLAB code format (i.e., *.m) and a text format.
DOI: 10.6084/m9.figshare.3512165.v1
title: Supplement 1. MATLAB source code for the generation of a null model via matrix permutation methods and the test of the difference between pairs of correlation matrices.

description: File List Downloadable MATLAB files<br> permcorr.m<br> permcorr.txt<br> permdiff.m<br> permdiff.txt Description This supplement contains the MATLAB code files for testing the difference between pairs of correlation matrices via the generation of a null model with matrix permutation methods. <br> The MATLAB function permdiff.m calculates a sum of squared differences between elements of two input matrices and the probability that this difference is significantly different than zero. It invokes the function permcorr.m to randomly permute the input matrices and generate a null model. The files are provided in both a compiled MATLAB code format (i.e., *.m) and a text format.
DOI: 10.6084/m9.figshare.3512162
title: Appendix A. A photograph of alien dominated shrublands at Mission Trails Park in coastal San Diego County, California.

description: A photograph of alien dominated shrublands at Mission Trails Park in coastal San Diego County, California.
DOI: 10.6084/m9.figshare.3512162.v1
title: Appendix A. A photograph of alien dominated shrublands at Mission Trails Park in coastal San Diego County, California.

description: A photograph of alien dominated shrublands at Mission Trails Park in coastal San Diego County, California.
DOI: 10.6084/m9.figshare.3512159
title: Appendix A. A table showing the averaged transition matrices for each site in burned and unburned heathland.

description: A table showing the averaged transition matrices for each site in burned and unburned heathland.
DOI: 10.6084/m9.figshare.3512159.v1
title: Appendix A. A table showing the averaged transition matrices for each site in burned and unburned heathland.

description: A table showing the averaged transition matrices for each site in burned and unburned heathland.
DOI: 10.6084/m9.figshare.3512156
title: Appendix B. A table showing the elasticity values of averaged population projection matrices of four sites in burned and four sites in unburned heathland.

description: A table showing the elasticity values of averaged population projection matrices of four sites in burned and four sites in unburned heathland.
DOI: 10.6084/m9.figshare.3512156.v1
title: Appendix B. A table showing the elasticity values of averaged population projection matrices of four sites in burned and four sites in unburned heathland.

description: A table showing the elasticity values of averaged population projection matrices of four sites in burned and four sites in unburned heathland.
DOI: 10.6084/m9.figshare.3512153
title: Appendix A. Photographs showing Jackrabbit Spring pool and representative native vegetation reaches, saltcedar reaches, and cleared reaches during and after removal of saltcedar.

description: Photographs showing Jackrabbit Spring pool and representative native vegetation reaches, saltcedar reaches, and cleared reaches during and after removal of saltcedar.