cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3564024
title: Appendix A. Conversion of wet to dry biomass.

description: Conversion of wet to dry biomass.
DOI: 10.6084/m9.figshare.3564024.v1
title: Appendix A. Conversion of wet to dry biomass.

description: Conversion of wet to dry biomass.
DOI: 10.6084/m9.figshare.3564021
title: Appendix B. Extrapolation procedure for missing roots.

description: Extrapolation procedure for missing roots.
DOI: 10.6084/m9.figshare.3564021.v1
title: Appendix B. Extrapolation procedure for missing roots.

description: Extrapolation procedure for missing roots.
DOI: 10.6084/m9.figshare.3564018
title: Appendix C. Individual statistics for excavated trees.

description: Individual statistics for excavated trees.
DOI: 10.6084/m9.figshare.3564018.v1
title: Appendix C. Individual statistics for excavated trees.

description: Individual statistics for excavated trees.
DOI: 10.6084/m9.figshare.3564015
title: Appendix A. (A) Details for assessing the persistence of a population with an integrodifference model and a discussion of the effect of the harvesting function on population persistence, (B) details for assessing population persistence with separable dispersal kernels, (C and D) derived expressions for the critical harvesting rate and rate of environmental shift for Gaussian and sinuosoidal dispersal kernels, (E) derived approximate expressions for these critical rates, (F) parameterized...

description: (A) Details for assessing the persistence of a population with an integrodifference model and a discussion of the effect of the harvesting function on population persistence, (B) details for assessing population persistence with separable dispersal kernels, (C and D) derived expressions for the critical harvesting rate and rate of environmental shift for Gaussian and sinuosoidal dispersal kernels, (E) derived approximate expressions for these critical rates, (F) parameterized model for black rockfish (Sebastes melanops) in the California Current and demonstrated results for parameters, and (G) details on differences between small and large MPA simulations.
DOI: 10.6084/m9.figshare.3564015.v1
title: Appendix A. (A) Details for assessing the persistence of a population with an integrodifference model and a discussion of the effect of the harvesting function on population persistence, (B) details for assessing population persistence with separable dispersal kernels, (C and D) derived expressions for the critical harvesting rate and rate of environmental shift for Gaussian and sinuosoidal dispersal kernels, (E) derived approximate expressions for these critical rates, (F) parameterized...

description: (A) Details for assessing the persistence of a population with an integrodifference model and a discussion of the effect of the harvesting function on population persistence, (B) details for assessing population persistence with separable dispersal kernels, (C and D) derived expressions for the critical harvesting rate and rate of environmental shift for Gaussian and sinuosoidal dispersal kernels, (E) derived approximate expressions for these critical rates, (F) parameterized model for black rockfish (Sebastes melanops) in the California Current and demonstrated results for parameters, and (G) details on differences between small and large MPA simulations.
DOI: 10.6084/m9.figshare.3564012
title: Supplement 1. R scripts for conducting simulations found in the main text.

description: File List Functions.R (MD5: 4fe49e7590478dfb53231744e2fa8a28) Make.R (MD5: e3dbbd50c161bed0d877cfdeb338cba0) Parameters_nothresh.R (MD5: b38910d5219abf8d64ec8950a36e513a) Parameters_thresh.R (MD5: b2a0edfb60c02b275e4038c78ddb446d) Parameters.R (MD5: 7c5045eb74add3658885d25ff37c6883) Sim_noThresh.R (MD5: 1459224f81fe6a1b4136bb6b0d2c3061) Sim_thresh.R (MD5: 7874a5e8d18461613bed28b89833328f) Description These files replicate the simulations described in the main text in the “Management strategies” section.
DOI: 10.6084/m9.figshare.3564012.v1
title: Supplement 1. R scripts for conducting simulations found in the main text.

description: File List Functions.R (MD5: 4fe49e7590478dfb53231744e2fa8a28) Make.R (MD5: e3dbbd50c161bed0d877cfdeb338cba0) Parameters_nothresh.R (MD5: b38910d5219abf8d64ec8950a36e513a) Parameters_thresh.R (MD5: b2a0edfb60c02b275e4038c78ddb446d) Parameters.R (MD5: 7c5045eb74add3658885d25ff37c6883) Sim_noThresh.R (MD5: 1459224f81fe6a1b4136bb6b0d2c3061) Sim_thresh.R (MD5: 7874a5e8d18461613bed28b89833328f) Description These files replicate the simulations described in the main text in the “Management strategies” section.
DOI: 10.6084/m9.figshare.3564009
title: Supplement 1. Data and Stan code specifying the statistical model used to analyse prevalences of a phytoplasma disease in grapevines (bois noir) in the Baden region (SW-Germany) in a Bayesian framework.

description: File List boisnoir.txt (MD5: 9c9e10c191527b1ef0232bad81d3fbed) Bois noir data (including grapes and environment) RStan_boisnoir.R (MD5: 10f54ea6eb0212643975b03f2c0a0f38) Stan code Description The first supplement (boisnoir.txt) contains the dataset used in the paper. Edaphic data was provided by “Regierungspräsidium Freiburg, Landesamt für Geologie, Rohstoffe und Bergbau (Hrsg.) (2012): Geologische Grundflächen. – Geologische Karte 1 : 50 000, Geodaten der Integrierten geowissenschaftlichen Landesaufnahme (GeoLa). http://www.lgrbbw.de; [26.01.2012]”. The second supplement (RStan_boisnoir.R) contains the model specification.
DOI: 10.6084/m9.figshare.3564009.v1
title: Supplement 1. Data and Stan code specifying the statistical model used to analyse prevalences of a phytoplasma disease in grapevines (bois noir) in the Baden region (SW-Germany) in a Bayesian framework.

description: File List boisnoir.txt (MD5: 9c9e10c191527b1ef0232bad81d3fbed) Bois noir data (including grapes and environment) RStan_boisnoir.R (MD5: 10f54ea6eb0212643975b03f2c0a0f38) Stan code Description The first supplement (boisnoir.txt) contains the dataset used in the paper. Edaphic data was provided by “Regierungspräsidium Freiburg, Landesamt für Geologie, Rohstoffe und Bergbau (Hrsg.) (2012): Geologische Grundflächen. – Geologische Karte 1 : 50 000, Geodaten der Integrierten geowissenschaftlichen Landesaufnahme (GeoLa). http://www.lgrbbw.de; [26.01.2012]”. The second supplement (RStan_boisnoir.R) contains the model specification.
DOI: 10.6084/m9.figshare.3564006
title: Supplement 1. Raw species data (sightings) collected by drifting baited stereo-videography in the Perth Canyon CMR.

description: File List UWA_PerthCanyon2013_DriftingPelagicCameras.txt (MD5: 6039727105e93ec73e53bd00c8748493) Description The data file contains 84 time-stamped, geo-referenced records (not including header row) of the pelagic wildlife (oceanic sharks and fishes) observed within and around the Commonwealth marine national park located at the head of the Perth submarine canyon in southwestern Australia. Sightings derive from a series of dedicated surveys undertaken in March, April and May 2013 using a novel system of drifting baited pelagic video cameras. Data fields include:<br> - Latitude (decimal degrees)<br> - Longitude (decimal degrees)<br> - Date (day/month/year)<br> - Time_UTC: Deployment time (GMT/UTC) of the video cameras. <br> - Sighting_UTC: Time of sighting (first arrival of species within field of view – GMT/UTC).<br> - Family/Genus/Species: Taxonomic identity.<br> - Full_name: Scientific name for the species.<br> - CAAB_code: Unique 8-digit identifier from coding system for aquatic organisms in the Australian region maintained by CSIRO Division of Marine and Atmospheric Research, Australia (http://www.marine.csiro.au/caab/). The data are supplied in ASCII text (tab delimited) format. No compression schemes were used and -9999 values denote records where no data are available.
DOI: 10.6084/m9.figshare.3564006.v1
title: Supplement 1. Raw species data (sightings) collected by drifting baited stereo-videography in the Perth Canyon CMR.

description: File List UWA_PerthCanyon2013_DriftingPelagicCameras.txt (MD5: 6039727105e93ec73e53bd00c8748493) Description The data file contains 84 time-stamped, geo-referenced records (not including header row) of the pelagic wildlife (oceanic sharks and fishes) observed within and around the Commonwealth marine national park located at the head of the Perth submarine canyon in southwestern Australia. Sightings derive from a series of dedicated surveys undertaken in March, April and May 2013 using a novel system of drifting baited pelagic video cameras. Data fields include:<br> - Latitude (decimal degrees)<br> - Longitude (decimal degrees)<br> - Date (day/month/year)<br> - Time_UTC: Deployment time (GMT/UTC) of the video cameras. <br> - Sighting_UTC: Time of sighting (first arrival of species within field of view – GMT/UTC).<br> - Family/Genus/Species: Taxonomic identity.<br> - Full_name: Scientific name for the species.<br> - CAAB_code: Unique 8-digit identifier from coding system for aquatic organisms in the Australian region maintained by CSIRO Division of Marine and Atmospheric Research, Australia (http://www.marine.csiro.au/caab/). The data are supplied in ASCII text (tab delimited) format. No compression schemes were used and -9999 values denote records where no data are available.
DOI: 10.6084/m9.figshare.3564003
title: Supplement 1. R-scripts for estimating the extra sums of squares in the main text.

description: File List Extra.R (MD5: 2cff0832c7a9ea846e577676da9cd2dc) Description The code included in Extra.R allows estimating the extra sums of squares described as Equations 6 through 10.
DOI: 10.6084/m9.figshare.3564003.v1
title: Supplement 1. R-scripts for estimating the extra sums of squares in the main text.

description: File List Extra.R (MD5: 2cff0832c7a9ea846e577676da9cd2dc) Description The code included in Extra.R allows estimating the extra sums of squares described as Equations 6 through 10.
DOI: 10.6084/m9.figshare.3564000
title: Supplement 1. Experimental data and metadata, pairwise phylogenetic distances, and algal species descriptions.

description: File List metadata.csv (MD5: 2511c0d61b2b0dcf5ad32ff0e241cb1d) experimental_data.csv (MD5: 46d4e769aa936ebeb42ce326ed685d62) Pairwise_PDs.csv (MD5: 6a1d85a375afc2ce09a7d9a75e763aa7) Species_details.csv (MD5: 16b40b08d40f42d86c789fc1260abfd2) Description The Metadata file describes the contents of the other supplemental materials. The first column, “Tab”, identifies in which supplemental file a variable appears. For each variable (listed under the column entitled “Header”), the units, a short description, a full description, and notes are listed. The Experimental Data file is organized by experimental bottle (column 1), followed by descriptions of that bottle's treatment, focal species, invader species, and inoculation density (columns 2–5). Day of experiment (DOE) is listed in column 6, which together with bottle (column 1) uniquely identifies rows. Columns 7–46 contain data collected from counts of algal focal species density performed on a hemacytometer, chlorophyll <i>a</i> fluorescence intensity measurements, information on whether a species successfully invaded a resident community for the invasion treatments, final day of exponential growth of the focal species, sensitivity calculations, and data from counts of steady-state density of each species in the multi-species mesocosms. Column 47 is reserved for notes about the quality of the data. Dots indicate that a variable has no applicable entry for that particular bottle and DOE combination. Full descriptions of the variables (column headers) in the Experimental Data are available in the Metadata file. The Pairwise Phylogenetic Distances file describes the phylogenetic distance (column 3) between every two species combination used in this experiment, where the species are listed in columns 1 and 2. A description of how the phylogenetic tree and distances were calculated is described in the main text Methods under "Calculating phylogenetic distance". The Species Details file describes algal cultures' (identified in column 1) original supplier and code (column 2), the NCBI Sequence Read Archive accession number (column 3), and data regarding cell biovolume for each culture (columns 4–7).
DOI: 10.6084/m9.figshare.3564000.v1
title: Supplement 1. Experimental data and metadata, pairwise phylogenetic distances, and algal species descriptions.

description: File List metadata.csv (MD5: 2511c0d61b2b0dcf5ad32ff0e241cb1d) experimental_data.csv (MD5: 46d4e769aa936ebeb42ce326ed685d62) Pairwise_PDs.csv (MD5: 6a1d85a375afc2ce09a7d9a75e763aa7) Species_details.csv (MD5: 16b40b08d40f42d86c789fc1260abfd2) Description The Metadata file describes the contents of the other supplemental materials. The first column, “Tab”, identifies in which supplemental file a variable appears. For each variable (listed under the column entitled “Header”), the units, a short description, a full description, and notes are listed. The Experimental Data file is organized by experimental bottle (column 1), followed by descriptions of that bottle's treatment, focal species, invader species, and inoculation density (columns 2–5). Day of experiment (DOE) is listed in column 6, which together with bottle (column 1) uniquely identifies rows. Columns 7–46 contain data collected from counts of algal focal species density performed on a hemacytometer, chlorophyll <i>a</i> fluorescence intensity measurements, information on whether a species successfully invaded a resident community for the invasion treatments, final day of exponential growth of the focal species, sensitivity calculations, and data from counts of steady-state density of each species in the multi-species mesocosms. Column 47 is reserved for notes about the quality of the data. Dots indicate that a variable has no applicable entry for that particular bottle and DOE combination. Full descriptions of the variables (column headers) in the Experimental Data are available in the Metadata file. The Pairwise Phylogenetic Distances file describes the phylogenetic distance (column 3) between every two species combination used in this experiment, where the species are listed in columns 1 and 2. A description of how the phylogenetic tree and distances were calculated is described in the main text Methods under "Calculating phylogenetic distance". The Species Details file describes algal cultures' (identified in column 1) original supplier and code (column 2), the NCBI Sequence Read Archive accession number (column 3), and data regarding cell biovolume for each culture (columns 4–7).
DOI: 10.6084/m9.figshare.3563997
title: Supplement 1. R code for conducting the statistical analysis described in the main text.

description: File List R_code.R (MD5: eb4a55faf02614a7f20f05f2f6117fc2) Description The code contains the function to estimate the relative contributions of selection, drift, dispersal limitation, and homogenizing dispersal to the community assembly of the heath vegetation, as well as the function to evaluated the importance of abiotic variables and spatial eigenvectors to the abundance of species through a Redundancy Analysis.
DOI: 10.6084/m9.figshare.3563997.v1
title: Supplement 1. R code for conducting the statistical analysis described in the main text.

description: File List R_code.R (MD5: eb4a55faf02614a7f20f05f2f6117fc2) Description The code contains the function to estimate the relative contributions of selection, drift, dispersal limitation, and homogenizing dispersal to the community assembly of the heath vegetation, as well as the function to evaluated the importance of abiotic variables and spatial eigenvectors to the abundance of species through a Redundancy Analysis.
DOI: 10.6084/m9.figshare.3563994
title: Supplement 1. R code and scripts for computing multilevel models with spatial autocorrelation for zooplankton spatial distribution data.

description: File List Zooplankton_Myvatn_Code.r (MD5: 77e338006e7b29cb5a5e4d08df920736) Description Zooplankton_Myvatn_Code.r contains R code to create multilevel models with spatial autocorrelation, analyze the significance of random effects, and compare the best multilevel model for zooplankton spatial distribution data. Comment lines specify the inputs to the function and the outputs from the function. The code may be called from an R program as an external function, or it may be placed in-line within a R program.
DOI: 10.6084/m9.figshare.3563994.v1
title: Supplement 1. R code and scripts for computing multilevel models with spatial autocorrelation for zooplankton spatial distribution data.

description: File List Zooplankton_Myvatn_Code.r (MD5: 77e338006e7b29cb5a5e4d08df920736) Description Zooplankton_Myvatn_Code.r contains R code to create multilevel models with spatial autocorrelation, analyze the significance of random effects, and compare the best multilevel model for zooplankton spatial distribution data. Comment lines specify the inputs to the function and the outputs from the function. The code may be called from an R program as an external function, or it may be placed in-line within a R program.
DOI: 10.6084/m9.figshare.3563991
title: Supplement 1. Data files used in the main text.

description: File List mcn.csv (MD5: c241373a3099e770c3ba80880e8d111f) pina.csv (MD5: b08c108632fdb725f36a66eeee6dc7a7) Description Individual tree list files for Monument Canyon, New Mexico (NAD83 / UTM zone 13N), and Pinaleño Mountains, Arizona (NAD83 / UTM zone 12N), derived from the technique given in Swetnam and Falk (2014, http://dx.doi.org/10.1016/j.foreco.2014.03.016).
DOI: 10.6084/m9.figshare.3563991.v1
title: Supplement 1. Data files used in the main text.

description: File List mcn.csv (MD5: c241373a3099e770c3ba80880e8d111f) pina.csv (MD5: b08c108632fdb725f36a66eeee6dc7a7) Description Individual tree list files for Monument Canyon, New Mexico (NAD83 / UTM zone 13N), and Pinaleño Mountains, Arizona (NAD83 / UTM zone 12N), derived from the technique given in Swetnam and Falk (2014, http://dx.doi.org/10.1016/j.foreco.2014.03.016).
DOI: 10.6084/m9.figshare.3563988
title: Supplement 1. R script for carrying out the permutation procedure described in the main text.

description: File List BetaFStat.r (md5: 1b9d503b3f162ea2b6f522ba989aaa4b) Description The R code provided in BetaFStat.R performs hypothesis tests on differences in alpha and beta components of species richness and Shannon diversity among habitat types using sample-based randomization.
DOI: 10.6084/m9.figshare.3563988.v1
title: Supplement 1. R script for carrying out the permutation procedure described in the main text.

description: File List BetaFStat.r (md5: 1b9d503b3f162ea2b6f522ba989aaa4b) Description The R code provided in BetaFStat.R performs hypothesis tests on differences in alpha and beta components of species richness and Shannon diversity among habitat types using sample-based randomization.
DOI: 10.6084/m9.figshare.3563985
title: Supplement 1. R code, extended statistical output, and additional graphics.

description: File List Ants_and_Ecosystem_Functions.html (MD5: 4c3a02abbc6344156498e959dab14044) Description Commented and executed R code, statistical output, and additional and diagnostic graphics for all analyses in this publication. HTML file was generated within RStudio using the knitr function. The original R code and all raw data files called for these analyses also are available from the Harvard Forest Data Archive (http://harvardforest.fas.harvard.edu/data-archive/), dataset HF160-07.
DOI: 10.6084/m9.figshare.3563982
title: Supplement 1. JAGS code used to implement the tree survival and aboveground biomass models and assess their goodness of fits to the data.

description: File List JAGS_code.txt (MD5: 4501e2ba5ba8b38375752267e2b2ef64) Description JAGS code used to implement the tree survival and aboveground biomass models and assess their goodness of fits to the data.
DOI: 10.6084/m9.figshare.3563982.v1
title: Supplement 1. JAGS code used to implement the tree survival and aboveground biomass models and assess their goodness of fits to the data.

description: File List JAGS_code.txt (MD5: 4501e2ba5ba8b38375752267e2b2ef64) Description JAGS code used to implement the tree survival and aboveground biomass models and assess their goodness of fits to the data.
DOI: 10.6084/m9.figshare.3563979
title: Supplement 1. Data files and R-scripts for statistical analysis and integral projection modeling described in the main text.

description: File List Establishment.and.survival.csv (MD5: a2d7c17a4976be7762b43a815126fdbe) Reproduction 2006&2007.csv (MD5: 54ce76bd982cb1e15162c40ea7276aed) July 2007 census and biomass2 edited.csv (MD5: 38a41af122fb6b90dfb723b3b740a6e0) Tall Thistle 2006 Updated Dec 2010.csv (MD5: 5dd859826ace0e751cd51c10bc4d4c0f) Tall Thistle 2007 Updated Dec 2010.csv (MD5: 0de9c392b393e594a49c65a3f3118235) IPM statistics bolting.R (MD5: dc8c3868f1e24ad0446c0266a529c361) IPM Statistics growth.R (MD5: 21260c8b65c0606e110207c2060800d9) IPM statistics recruitment.R (MD5: 6914a0c0c892f76c0977c24a9a649eea) IPM statistics initial size.R (MD5: cff5c4ee3d3c58ff056d3e8aa390f7c1) IPM statistics seed production.R (MD5: 1de9453716f25b3d8f5ae4b276237050) IPM statistics survival.R (MD5: 4b93fdf09019f572f0e88715fba0482d) IPM.Parameters.csv (MD5: d3ab447e0c4ddc1ae12d89af3fb5d5d9) IPM model and bootstrap.R (MD5: 5e92d9d9072b67f4ca9e1e20538f99b9) Description For the statistical analysis the file “IPM statistics growth.R” needs to be executed first. The statistical results are saved in the file “IPM.Parameters.csv”, allowing the execution of the “IPM model and bootstrap.R”-file without running the statistics scripts first. Description of variables: <i>Establishment and Survival.csv</i> -- TABLE: Please see in attached file. -- <i>Reproduction 2006&2007</i> -- TABLE: Please see in attached file. -- <i>July 2007 census and biomass2 edited</i> -- TABLE: Please see in attached file. -- <br> <i>Tall thistle 2006 Updated Dec 2010</i> <i>Tall thistle 2007Updated Dec 2010 </i> -- TABLE: Please see in attached file. --
DOI: 10.6084/m9.figshare.3563976
title: Supplement 1. R script for analyzing the effects of environmental variables, linear features (roads, power lines, rivers) and linear feature combinations on moose step selection.

description: File List moose.r (MD5: eca62b33b44187ca6fe4c82269008b96) Description The R code includes the commands to run a basic ("mcb"), barrier ("mcr"), corridor ("mcor") and a combined ("mco") cox proportional hazard model testing for the effects of environmental variables, linear features (roads, power lines, rivers) and linear feature combinations on moose step selection. The code to calculate QIC values ("QIC.coxph", from Mathieu Basille), a customized predict function for cox proportional hazard models ("prcph2"), the code to reproduce model predictions, graphs and the code for seasonal models is also provided. The code should be run consecutively. The data file to be used with the R-script moose.r to analyze the effects of environmental variables, linear features (roads, power lines, rivers) and linear feature combinations on moose step selection may be obtained from the authors upon request. The data was derived from moose GPS relocation data collected in Central-Norway during 2006-2010. A description of the variables can be found in the R-script moose.r. Please ask the Norwegian Institute for Nature Research (NINA) for consent before using this data for publication. Contact Erling.Solberg@nina.no and Christer.Rolandsen@nina.no.<b></b>