cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3555510.v1
title: Appendix D. Detailed Wilcoxon’s matched pairs test results testing for the improvement of species distribution models with the addition of herbivore and/or plant variables.

description: Detailed Wilcoxon’s matched pairs test results testing for the improvement of species distribution models with the addition of herbivore and/or plant variables.
DOI: 10.6084/m9.figshare.3555507
title: Appendix E. Spearman rank correlation between species prevalence and the combined importance of vertical or horizontal biotic interactions.

description: Spearman rank correlation between species prevalence and the combined importance of vertical or horizontal biotic interactions.
DOI: 10.6084/m9.figshare.3555507.v1
title: Appendix E. Spearman rank correlation between species prevalence and the combined importance of vertical or horizontal biotic interactions.

description: Spearman rank correlation between species prevalence and the combined importance of vertical or horizontal biotic interactions.
DOI: 10.6084/m9.figshare.3555504
title: Appendix F. Variable importance for generalized linear models (GLM), generalized additive models (GAM), and boosted regression tree models (BRT) based on species cover data.

description: Variable importance for generalized linear models (GLM), generalized additive models (GAM), and boosted regression tree models (BRT) based on species cover data.
DOI: 10.6084/m9.figshare.3555504.v1
title: Appendix F. Variable importance for generalized linear models (GLM), generalized additive models (GAM), and boosted regression tree models (BRT) based on species cover data.

description: Variable importance for generalized linear models (GLM), generalized additive models (GAM), and boosted regression tree models (BRT) based on species cover data.
DOI: 10.6084/m9.figshare.3555501
title: Appendix A. Map of the study area in Finland with the studied drainage basins.

description: Map of the study area in Finland with the studied drainage basins.
DOI: 10.6084/m9.figshare.3555501.v1
title: Appendix A. Map of the study area in Finland with the studied drainage basins.

description: Map of the study area in Finland with the studied drainage basins.
DOI: 10.6084/m9.figshare.3555498
title: Appendix B. Means and ranges for the main environmental variables of lakes for each drainage system.

description: Means and ranges for the main environmental variables of lakes for each drainage system.
DOI: 10.6084/m9.figshare.3555498.v1
title: Appendix B. Means and ranges for the main environmental variables of lakes for each drainage system.

description: Means and ranges for the main environmental variables of lakes for each drainage system.
DOI: 10.6084/m9.figshare.3555495
title: Appendix C. Modeling results for phytoplankton when only the cladocerans (seven species) were used as zooplankton grazers for phytoplankton.

description: Modeling results for phytoplankton when only the cladocerans (seven species) were used as zooplankton grazers for phytoplankton.
DOI: 10.6084/m9.figshare.3555495.v1
title: Appendix C. Modeling results for phytoplankton when only the cladocerans (seven species) were used as zooplankton grazers for phytoplankton.

description: Modeling results for phytoplankton when only the cladocerans (seven species) were used as zooplankton grazers for phytoplankton.
DOI: 10.6084/m9.figshare.3555492
title: Appendix D. The intercorrelations between all physicochemical and geographical variables.

description: The intercorrelations between all physicochemical and geographical variables.
DOI: 10.6084/m9.figshare.3555492.v1
title: Appendix D. The intercorrelations between all physicochemical and geographical variables.

description: The intercorrelations between all physicochemical and geographical variables.
DOI: 10.6084/m9.figshare.3555489
title: Appendix E. Response shapes (partial dependency plots) for the phytoplankton Staurastrum sp. based on GBM models.

description: Response shapes (partial dependency plots) for the phytoplankton Staurastrum sp. based on GBM models.
DOI: 10.6084/m9.figshare.3555489.v1
title: Appendix E. Response shapes (partial dependency plots) for the phytoplankton Staurastrum sp. based on GBM models.

description: Response shapes (partial dependency plots) for the phytoplankton Staurastrum sp. based on GBM models.
DOI: 10.6084/m9.figshare.3555486
title: Appendix F. Response shapes (partial dependency plots) for the zooplankton Daphnia galeata based on GBM models.

description: Response shapes (partial dependency plots) for the zooplankton Daphnia galeata based on GBM models.
DOI: 10.6084/m9.figshare.3555486.v1
title: Appendix F. Response shapes (partial dependency plots) for the zooplankton Daphnia galeata based on GBM models.

description: Response shapes (partial dependency plots) for the zooplankton Daphnia galeata based on GBM models.
DOI: 10.6084/m9.figshare.3555483
title: Appendix A. Details on the reefs of the Great Barrier Reef used in this study described by Black et al. (1990).

description: Details on the reefs of the Great Barrier Reef used in this study described by Black et al. (1990).
DOI: 10.6084/m9.figshare.3555483.v1
title: Appendix A. Details on the reefs of the Great Barrier Reef used in this study described by Black et al. (1990).

description: Details on the reefs of the Great Barrier Reef used in this study described by Black et al. (1990).
DOI: 10.6084/m9.figshare.3555480
title: Appendix B. Date and time of spawning, mean egg size, time to motility, and the collection location of 20 broadcast spawner species.

description: Date and time of spawning, mean egg size, time to motility, and the collection location of 20 broadcast spawner species.
DOI: 10.6084/m9.figshare.3555480.v1
title: Appendix B. Date and time of spawning, mean egg size, time to motility, and the collection location of 20 broadcast spawner species.

description: Date and time of spawning, mean egg size, time to motility, and the collection location of 20 broadcast spawner species.
DOI: 10.6084/m9.figshare.3555477
title: Supplement 1. Data and code for the survival and competence dynamics model and estimate of proportion of larvae retained.

description: File List Supplement_Model_code.txt (md5: 383aad018982f54b357e3b01e8d838d2) Description The code provided in Supplement_Model_code.txt is for Davies Reef, based on the estimates from Black et al. (1990). For the other reefs, the same code must be run with the appropriate flushing rate (as detailed below). For Davies Reef, the code for calibrating survival and competence parameters must be run separately for all species, before doing the regression between time to motility and proportion of larvae settling while retained. The code for each species is very similar. Here, we provide the data and code for <i>Acropora gemmifera</i>. Then, we provide the data for the other species and give instructions on how to change the <i>A. gemmifera</i> code to be run for each of the other species (as detailed below).
DOI: 10.6084/m9.figshare.3555477.v1
title: Supplement 1. Data and code for the survival and competence dynamics model and estimate of proportion of larvae retained.

description: File List Supplement_Model_code.txt (md5: 383aad018982f54b357e3b01e8d838d2) Description The code provided in Supplement_Model_code.txt is for Davies Reef, based on the estimates from Black et al. (1990). For the other reefs, the same code must be run with the appropriate flushing rate (as detailed below). For Davies Reef, the code for calibrating survival and competence parameters must be run separately for all species, before doing the regression between time to motility and proportion of larvae settling while retained. The code for each species is very similar. Here, we provide the data and code for <i>Acropora gemmifera</i>. Then, we provide the data for the other species and give instructions on how to change the <i>A. gemmifera</i> code to be run for each of the other species (as detailed below).
DOI: 10.6084/m9.figshare.3555474
title: Appendix A. Summary statistics for each species combination used in competition assays.

description: Summary statistics for each species combination used in competition assays.
DOI: 10.6084/m9.figshare.3555474.v1
title: Appendix A. Summary statistics for each species combination used in competition assays.

description: Summary statistics for each species combination used in competition assays.
DOI: 10.6084/m9.figshare.3555471
title: Appendix A. Details on the environmental variables used in the study.

description: Details on the environmental variables used in the study.
DOI: 10.6084/m9.figshare.3555471.v1
title: Appendix A. Details on the environmental variables used in the study.

description: Details on the environmental variables used in the study.
DOI: 10.6084/m9.figshare.3555468
title: Appendix B. Computational details of the null model showing that lakes within watersheds are more connected than across watersheds.

description: Computational details of the null model showing that lakes within watersheds are more connected than across watersheds.
DOI: 10.6084/m9.figshare.3555468.v1
title: Appendix B. Computational details of the null model showing that lakes within watersheds are more connected than across watersheds.

description: Computational details of the null model showing that lakes within watersheds are more connected than across watersheds.
DOI: 10.6084/m9.figshare.3555462
title: Appendix A. Details of selection of broodstock, electrofishing, genotyping, and conversion of preserved juvenile mass measurements into estimates of fresh mass.

description: Details of selection of broodstock, electrofishing, genotyping, and conversion of preserved juvenile mass measurements into estimates of fresh mass.
DOI: 10.6084/m9.figshare.3555462.v1
title: Appendix A. Details of selection of broodstock, electrofishing, genotyping, and conversion of preserved juvenile mass measurements into estimates of fresh mass.

description: Details of selection of broodstock, electrofishing, genotyping, and conversion of preserved juvenile mass measurements into estimates of fresh mass.
DOI: 10.6084/m9.figshare.3555459
title: Appendix B. Statistical analysis and model selection.

description: Statistical analysis and model selection.
DOI: 10.6084/m9.figshare.3555459.v1
title: Appendix B. Statistical analysis and model selection.

description: Statistical analysis and model selection.
DOI: 10.6084/m9.figshare.3555453
title: Appendix A. Graphs of performance metrics comparing open and closed occupancy models based on expected values data, and a table of model comparisons for three amphibian species.

description: Graphs of performance metrics comparing open and closed occupancy models based on expected values data, and a table of model comparisons for three amphibian species.
DOI: 10.6084/m9.figshare.3555453.v1
title: Appendix A. Graphs of performance metrics comparing open and closed occupancy models based on expected values data, and a table of model comparisons for three amphibian species.

description: Graphs of performance metrics comparing open and closed occupancy models based on expected values data, and a table of model comparisons for three amphibian species.
DOI: 10.6084/m9.figshare.3555450
title: Supplement 1. Data files for the amphibian example in the manuscript, C source code, executable, and associated files for simulating data under the open-model structure, for input to program PRESENCE.

description: File List genpres4_stag.c<b> – </b>C source code rngs.c, rngs.h<b> – </b>supplemental files for random number generation. genpres4_stag.exe – Executable of the program above. data_examples.zip – three amphibian data files used in the example readme.pdf – Explanation of files and their use Description genpres4_stag.c, along with rngs.c and rngs.h, generate simulated data under the open model described in the manuscript. Amphibian data used in the example are located in data_examples.zip. All files and their uses are explained in readme.pdf.
DOI: 10.6084/m9.figshare.3555450.v1
title: Supplement 1. Data files for the amphibian example in the manuscript, C source code, executable, and associated files for simulating data under the open-model structure, for input to program PRESENCE.

description: File List genpres4_stag.c<b> – </b>C source code rngs.c, rngs.h<b> – </b>supplemental files for random number generation. genpres4_stag.exe – Executable of the program above. data_examples.zip – three amphibian data files used in the example readme.pdf – Explanation of files and their use Description genpres4_stag.c, along with rngs.c and rngs.h, generate simulated data under the open model described in the manuscript. Amphibian data used in the example are located in data_examples.zip. All files and their uses are explained in readme.pdf.
DOI: 10.6084/m9.figshare.3555447
title: Appendix A. Additional analyses and species-specific detectability and occupancy estimates.

description: Additional analyses and species-specific detectability and occupancy estimates.
DOI: 10.6084/m9.figshare.3555447.v1
title: Appendix A. Additional analyses and species-specific detectability and occupancy estimates.

description: Additional analyses and species-specific detectability and occupancy estimates.
DOI: 10.6084/m9.figshare.3555444
title: Supplement 1. BUGS-language model specification of hierarchical community occupancy model.

description: File List BUGS_code.txt (MD5: 5101dc4c7becb6442fbaed48ca40bc88)Description BUGS_code.text: Provided in this file is the BUGS-language code for specification of the hierarchical community occupancy model presented in the associated publication. The code expects several data variables to be available and these are specified as follows: n the number of species; nzeroes the number of “zero species” added during data augmentation; era the time period during which a site is surveyed (0 = historical; 1 = modern); elev the standardized elevation; elev2 the squared elevation; R1 a dummy variable representing one of the three regions; R2 a dummy variable representing one of the three regions; jday the standardized day of year; jday2 the squared day of year; X the multi-dimensional occurrence history array; J the number of sites; K a vector of the number of surveys per site (per era); zone_LS, zone_US, zone_TR, zone_CA, zone_HU, zone_XX dummy variables indicating whether a species belongs in a certain life zone grouping; H a vector indicating which paired sites belong in the historic time period; M a vector indicating which paired sites belong in the modern time period; L the number of paired sites per era.
DOI: 10.6084/m9.figshare.3555444.v1
title: Supplement 1. BUGS-language model specification of hierarchical community occupancy model.

description: File List BUGS_code.txt (MD5: 5101dc4c7becb6442fbaed48ca40bc88)Description BUGS_code.text: Provided in this file is the BUGS-language code for specification of the hierarchical community occupancy model presented in the associated publication. The code expects several data variables to be available and these are specified as follows: n the number of species; nzeroes the number of “zero species” added during data augmentation; era the time period during which a site is surveyed (0 = historical; 1 = modern); elev the standardized elevation; elev2 the squared elevation; R1 a dummy variable representing one of the three regions; R2 a dummy variable representing one of the three regions; jday the standardized day of year; jday2 the squared day of year; X the multi-dimensional occurrence history array; J the number of sites; K a vector of the number of surveys per site (per era); zone_LS, zone_US, zone_TR, zone_CA, zone_HU, zone_XX dummy variables indicating whether a species belongs in a certain life zone grouping; H a vector indicating which paired sites belong in the historic time period; M a vector indicating which paired sites belong in the modern time period; L the number of paired sites per era.
DOI: 10.6084/m9.figshare.3555441
title: Appendix A. Details of model formulation and assessment.

description: Details of model formulation and assessment.
DOI: 10.6084/m9.figshare.3555441.v1
title: Appendix A. Details of model formulation and assessment.

description: Details of model formulation and assessment.
DOI: 10.6084/m9.figshare.3555438
title: Appendix B. Details of final model, component-rate submodels, and model simulations.

description: Details of final model, component-rate submodels, and model simulations.
DOI: 10.6084/m9.figshare.3555438.v1
title: Appendix B. Details of final model, component-rate submodels, and model simulations.

description: Details of final model, component-rate submodels, and model simulations.
DOI: 10.6084/m9.figshare.3555432
title: Appendix A. Alpine marmot (Marmota marmota) life cycle.

description: Alpine marmot (Marmota marmota) life cycle.
DOI: 10.6084/m9.figshare.3555429
title: Appendix B. Complementary analyses using seasonal indices.

description: Complementary analyses using seasonal indices.
DOI: 10.6084/m9.figshare.3555426
title: Appendix C. Complementary analyses of lagged effects.

description: Complementary analyses of lagged effects.
DOI: 10.6084/m9.figshare.3555423
title: Appendix D. Additional information on burrow temperature and efficiency of snow insulation during winter.

description: Additional information on burrow temperature and efficiency of snow insulation during winter.
DOI: 10.6084/m9.figshare.3555420
title: Appendix A. Descriptive details including methods for assembling database, tables that summarize the kinds of studies examined, and figures that present results from truncated analyses and analyses with Hedges’ d.

description: Descriptive details including methods for assembling database, tables that summarize the kinds of studies examined, and figures that present results from truncated analyses and analyses with Hedges’ d.
DOI: 10.6084/m9.figshare.3555417
title: Appendix B. Descriptive information for all studies used in the meta-analysis, including citation, system, predator and prey species, and number of lines in the database.

description: Descriptive information for all studies used in the meta-analysis, including citation, system, predator and prey species, and number of lines in the database.
DOI: 10.6084/m9.figshare.3555414
title: Appendix C. Summary of number of articles and lines in database, classified by prey species, predator species, and refuge type.

description: Summary of number of articles and lines in database, classified by prey species, predator species, and refuge type.
DOI: 10.6084/m9.figshare.3555408
title: Appendix A. Search string and detailed description of data collection, construction of log response ratios, mixed model analysis, and tests of bias.

description: Search string and detailed description of data collection, construction of log response ratios, mixed model analysis, and tests of bias.
DOI: 10.6084/m9.figshare.3555405
title: Appendix B. A list of publications for the meta-analysis.

description: A list of publications for the meta-analysis.
DOI: 10.6084/m9.figshare.3555402
title: Appendix C. Detailed results for mixed model analysis and tests of bias.

description: Detailed results for mixed model analysis and tests of bias.
DOI: 10.6084/m9.figshare.3555396
title: Appendix D. A table of log response ratios partitioned by consumer attributes.

description: A table of log response ratios partitioned by consumer attributes.
DOI: 10.6084/m9.figshare.3555393
title: Appendix A. Proof that the C statistic of a d-sep test is a maximum likelihood estimate.

description: Proof that the C statistic of a d-sep test is a maximum likelihood estimate.
DOI: 10.6084/m9.figshare.3555390
title: Appendix B. Calculating the AIC statistic for d-sep tests.

description: Calculating the AIC statistic for d-sep tests.
DOI: 10.6084/m9.figshare.3555387
title: Supplement 1. Data set used in Appendix B.

description: File List simulated.data.txt (md5: 6a3ca4e3e66df36f5310cfec2d1c08ee) Description This test file, can be imported into R using the read.table() function; for instance myfile
DOI: 10.6084/m9.figshare.3555387.v1
title: Supplement 1. Data set used in Appendix B.

description: File List simulated.data.txt (md5: 6a3ca4e3e66df36f5310cfec2d1c08ee) Description This test file, can be imported into R using the read.table() function; for instance myfile
DOI: 10.6084/m9.figshare.3555384
title: Appendix A. Detailed description of the Metropolis-within-Gibbs MCMC sampler for a spatial mark-resight model augmented with telemetry location data and with individual identi cation rate of marks &lt; 100 %.

description: Detailed description of the Metropolis-within-Gibbs MCMC sampler for a spatial mark-resight model augmented with telemetry location data and with individual identi cation rate of marks &lt; 100 %.
DOI: 10.6084/m9.figshare.3555384.v1
title: Appendix A. Detailed description of the Metropolis-within-Gibbs MCMC sampler for a spatial mark-resight model augmented with telemetry location data and with individual identi cation rate of marks &lt; 100 %.

description: Detailed description of the Metropolis-within-Gibbs MCMC sampler for a spatial mark-resight model augmented with telemetry location data and with individual identi cation rate of marks &lt; 100 %.
DOI: 10.6084/m9.figshare.3555381
title: Supplement 1. R code and data to run spatial mark–resight model for raccoon camera trap and telemetry data.

description: File List Raccoon_data.R: R list object with following slots $n: matrix with unmarked photo-counts for each trap (rows) and sampling period (columns) $yknown: 3-dimensional array with individual photographic encounter histories (counts) of all tagged and radio-collared individuals (rows) at each camera (columns) and each sampling period (3rd dimension) $X: matrix with X and Y coordinates (columns) of each camera trap (rows), in UTM scaled to km $mi: vector with total number of photos of marked individuals that could be identified to individual level for each sampling period $mall: vector with total number of photos of marked individuals, identified and unidentified, for each sampling period $M: size of the augmented data set $Eff: 3-dimensional array with information on how many days each camera trap (column) was functional during each sampling period (3rd dimension), expanded to hold the same information for each individual in the augmented data set (row), for easier array multiplication in the MCMC algorithm $collar: vector of length M with “TRUE” for individuals with radio-collars and “FALSE” for individuals without collars, tagged or unmarked $locs: list of length sum(collar) with 2-dimensional matrices containing X and Y coordinates of radio telemetry locations for each of the collard individuals SSp.dbf, SSp.shp, SSp.shx: Shapefile with outline of South Core Banks (which comprises the state-space for the raccoon analysis) Rscript_Raccoons.R: R code to load data and run raccoon analysis MCMC_algorithm.txt: R code for MCMC algorithm for spatial mark-resight analysis of raccoon data Description Data files and code are set up to repeat the spatial mark–resight analysis of raccoon camera trapping and telemetry data from South Core Bank, NC, as presented in the Application example in the manuscript.