cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d7d7b2t/4
title: % Mosaic Cropland & Native Vegetation 1km-radius Window

description: Original data for this GIS raster was obtained from the ESA CCI Land Cover Layer 300m 2015 (www.esa-landcover-cci.org). We first reclassified the original data layer, denoting mosaic cropland and native vegetation habitat as present (1) or absent (0). We then used FRAGSTATS (McGarigal, Cushman, Neel, & Ene, 2012) to calculate the percent of the landscape occupied by mosaic habitat within a 1km-radius moving window. We re-sampled the source data from its native 300m resolution to 250m. Coordinate system: Asia South Albers Equal Area Conic.
DOI: 10.5061/dryad.d7d7b2t/5
title: Protected Area Correlation Length 8km-radius Window

description: Data for this GIS raster layer was obtained from the IUCN & UNEP-WCMC 2017 World Database on Protected Areas (http://www.protectedplanet.net/). We first reclassified the original data layer, denoting protected status as present (1) or absent (0). We then used FRAGSTATS (McGarigal, Cushman, Neel, & Ene, 2012) to calculate the correlation length or area-weighted mean of gyration within an 8km-radius moving window. Here correlation length measures the average distance an animal could travel within protected areas within an 8km-radius window. Data are at 250m resolution; units are in meters. Coordinate system: Asia South Albers Equal Area Conic.
DOI: 10.5061/dryad.d7d7b2t/6
title: Mean Annual Precipitation Focal Mean 32km-radius Window

description: Data for this GIS raster layer was obtained from the WorldClim Global Climate Data Portal (http://worldclim.org/version2). We then used neighborhood statistics in ArcGIS to calculate the focal mean of MAP within a 32km-radius moving window. We re-sampled the source data from its native 30-arcsec resolution (~1km) to 250m. Units are in millimeters of precipitation. Coordinate system: Asia South Albers Equal Area Conic.
DOI: 10.5061/dryad.d7d7b2t/7
title: Mainland Clouded Leopard Habitat Suitability Model - 4 Thresholds

description: The zip file contains four GIS raster layers representing a range of thresholds of the mainland clouded leopard habitat suitability model. Layers include 50th, 75th, 90th, and 97.5th percentiles of the multi-scale GLMM. Suitable habitat is classified as 1; all habitat below a specified threshold is classified as 0. Raster resolution: 250m; coordinate system: Asia South Albers Equal Area Conic.
DOI: 10.5061/dryad.g11gs40/1
title: All data and R codes

description: Instructions - 

“Scaling coef (Fig2-4)”
This main file is called “Final analysis.R” and will produce figure 2 to 4 and all tables in the supplementary materials. Open it with statistical software R. Within the script file: (1) check that all packages are installed in the computer (otherwise install before running the script), and (2) set the directory where the script (.R) file is in the computer. After having done that, everything else should work by running the file in R. The script will read all data, all functions (in the script “Functions.R”), calculate and save the tables (in folder “Tables”), and plot and save the images (in folder “Figures”).


“Size trajectories (Fig1)”
This file will create figure 1. It will read the raw data, calculate running means for each treatment, and plot the figures. Points represent each replicate culture, and lines represent each running mean.  

All files were created using R version 3.5.1 (2018-07-02) and were designed to run in Mac computers.
DOI: 10.5061/dryad.gj34813/1
title: insectivorousBat_Capture_BBS_Sumatra_Indonesia_2011_2012

description: Species occurrence data by harp trap and mist net in coffee plantations and forests Bukit Barisan Selatan Landscape from 2011 to 2012.
DOI: 10.5061/dryad.gj34813/2
title: vegetationMeasuresat_BatTrapPoints_BBS_Sumatra_Indoneisa_2011_2012

description: Presence-absence data of vegetation strata at all trap points of harp trap and mist nets at 9 study sites in Bukit Barisan Selatan Landscape, Sumatra, Indonesia, from 2011 to 2012.
DOI: 10.5061/dryad.hh3tc85/1
title: Samples and metadata
DOI: 10.5061/dryad.n5qb383/23
title: Torrey Pines Beach Binned Sand Elevations

description: Binned sand elevations at Torrey Pines Beach. Raw sand level observations are binned to coordinates aligned with the wave estimates (MOP lines). MOP lines are separated 100m alongshore, and oriented from the 10m depth contour to the backbeach, to approximately follow the curving coastline. Bins centered on MOP lines with 5m cross-shore resolution are filled with median values, suppressing the effect of outliers. All surveys are binned, including surveys with transects not originally aligned to MOP lines and with alongshore spacing less than 100m. The observations are usually smooth over the 50m maximum distance of alongshore projection and 2.5m cross-shore projection. However, raw data should be used to define features with shorter scales (i.e., scarps, reef, canyon). Binned alongshore resolution can be adjusted in the repository code (separate download: analysis_code within analysis folder) by using different binning transects, while cross-shore resolution can be adjusted by redefining the "cres" variable. Be cautious with data at depths greater than 8m below MSL, as ocean temperature stratification can contaminate jet ski soundings.
DOI: 10.5061/dryad.n5qb383/24
title: Torrey Pines Beach Mapped Sand Elevations

description: Mapped sand elevations at Torrey Pines Beach. Elevation maps are created on the same grid as the binned observations, but are smoothed and fill in small data gaps. For each survey, bins containing less than 3 data points are considered unsampled and are discarded. Map boundaries are defined as grid points that are regularly sampled during unnourished quarterly full surveys (must be populated at least 25\% of the time as the most frequently full surveyed grid point, during times without nourishment). Grid points with an unnourished average depth greater than 8m are not mapped because speed of sound errors due to stratification may contaminate jet ski sonar measurements. When the estimated interpolation (or extrapolation) error is large (NMSE&gt;0.2), the map bin elevation is considered missing and filled with the value -99999.
DOI: 10.5061/dryad.n5qb383/25
title: Torrey Pines Beach Sand Level Survey Information

description: Information on sand level surveys conducted at Torrey Pines Beach. Complete lists of all survey filenames, dates, depth zones surveyed, alongshore regions surveyed, south and north-most surveyed MOP line indices with good coverage, regions influenced by nourishment, and vehicles and transects driven are included in this file.
DOI: 10.5061/dryad.n5qb383/28
title: Cardiff and Solana Beaches Binned Sand Elevations

description: Binned sand elevations at Cardiff and Solana Beaches. Raw sand level observations are binned to coordinates aligned with the wave estimates (MOP lines). MOP lines are separated 100m alongshore, and oriented from the 10m depth contour to the backbeach, to approximately follow the curving coastline. Bins centered on MOP lines with 5m cross-shore resolution are filled with median values, suppressing the effect of outliers. All surveys are binned, including surveys with transects not originally aligned to MOP lines and with alongshore spacing less than 100m. The observations are usually smooth over the 50m maximum distance of alongshore projection and 2.5m cross-shore projection. However, raw data should be used to define features with shorter scales (i.e., scarps, reef). Binned alongshore resolution can be adjusted in the repository code (separate download: analysis_code within analysis folder) by using different binning transects, while cross-shore resolution can be adjusted by redefining the "cres" variable. Be cautious with data at depths greater than 8m below MSL, as ocean temperature stratification can contaminate jet ski soundings.
DOI: 10.5061/dryad.n5qb383/29
title: Cardiff and Solana Beaches Mapped Sand Elevations

description: Mapped sand elevations at Cardiff and Solana Beaches. Elevation maps are created on the same grid as the binned observations, but are smoothed and fill in small data gaps. For each survey, bins containing less than 3 data points are considered unsampled and are discarded. Map boundaries are defined as grid points that are regularly sampled during unnourished quarterly full surveys (must be populated at least 25\% of the time as the most frequently full surveyed grid point, during times without nourishment). Grid points with an unnourished average depth greater than 8m are not mapped because speed of sound errors due to stratification may contaminate jet ski sonar measurements. When the estimated interpolation (or extrapolation) error is large (NMSE&gt;0.2), the map bin elevation is considered missing and filled with the value -99999.
DOI: 10.5061/dryad.qf36gd4/5
title: Source, results, and summary of results from genome-wide tests of allele frequency shifts

description: See Readme
DOI: 10.5061/dryad.sj70r00/1
title: Database_cultivated_fruits_explotation

description: Data on the consumption of cultivated fruit species by three brown howler groups inhabiting three small (&lt;10 ha) Atlantic forest fragments in southern Brazil.
DOI: 10.5061/dryad.sj70r00/2
title: Database_cultivated_fruits_phenology

description: Data on the phenology of cultivated fruit species exploited by three brown howler groups inhabiting three small (&lt;10 ha) Atlantic forest fragments in southern Brazil.
DOI: 10.17632/4rpgk38td8.1
title: Data for: Fully Automated and Comprehensive Left-Ventricular Contractility Analysis in Long-term Survivors of Breast Cancer Patients after Chemotherapy

description: Example full dataset of DENSE MRI data
DOI: 10.17632/ptr5stphj5.1
title: Data for: Suppression of fruit softening and extension of shelf life of pear by putrescine application
DOI: 10.17632/ytfs6hwt8t.1
title: Data for: An Early Tonian rifting event affecting the São Francisco-Congo paleocontinent recorded by the Lower Macaúbas Group, Araçuaí Orogen, SE Brazil.

description: Samples_Supplementary File 1 U-Pb (LA-MC-ICP-MS)_Supplementary File 2 Lu-Hf (LA-ICP-MS)_Supplemntary File 3
DOI: 10.5061/dryad.360k8v0/4
title: Composition of bacterial community
DOI: 10.5061/dryad.4395r55/1
title: ipyrad Parameter files

description: File includes the ipyrad parameter specifications used to process the Illumina sequencing reads of Corbicula individuals for the 85, 90, and 95% similarity thresholds and across 75, 50, and 25% taxon coverages.
DOI: 10.5061/dryad.4395r55/2
title: RAxML matrices

description: File contains the data matrices used to construct the phylogenomic trees in RAxML. Files are labeled with their corresponding similarity threshold (85, 90, or 95%) and taxon coverage (25, 50, or 75%). We also include the matrices used to re-run (rr) analyses where individuals were dropped (id). See Results section for further details.
DOI: 10.5061/dryad.4395r55/3
title: MrBayes matrix

description: File contains the data matrix used to construct the Bayesian phylogenomic tree in MrBayes for the 90% similarity threshold with 75% of taxa included.
DOI: 10.5061/dryad.4395r55/4
title: mPTP Analysis

description: File contains the 90% similarity threshold with 75% taxon coverage .fasta alignment file and the maximum likelihood tree from RAxML used to construct the mPTP tree.
DOI: 10.5061/dryad.4395r55/5
title: BEAST input

description: 90% similarity threshold with 75% taxon coverage .nex data matrix used to estimate Corbicula lineage divergence times in BEAST.
DOI: 10.5061/dryad.4395r55/6
title: Structure matrices

description: File contains all Structure input files for analyses across 34 Corbicula individuals, each of the invasive Forms, and for C. sandai. Files were created using the 90% similarity threshold including 75% of individuals dataset.
DOI: 10.5061/dryad.4nb12g2.1
title: Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography
DOI: 10.5061/dryad.4nb12g2.1/1.1
title: ReadMe

description: General instructions and information concerning files included herein.
DOI: 10.5061/dryad.4nb12g2.1/2.1
title: 33 dpf microCT reconstruction of juvenile zebrafish

description: 33 dpf microCT reconstruction of juvenile zebrafish with nominal 1.43um voxel resolution. This is an 8-bit multi-page tiff series z-stack. We recommend opening with Fiji (Fiji Is Just ImageJ).
DOI: 10.5061/dryad.4nb12g2.1/3.1
title: 5 dpf (samples 1-5) microCT reconstructions of larval zebrafish

description: 5, 5 dpf microCT reconstructions of larvalzebrafish with nominal .743um voxel resolution. These are 8-bit multi-page tiff series z-stacks. We recommend opening with Fiji (Fiji Is Just ImageJ) using the bio-formats plugin.
DOI: 10.5061/dryad.4nb12g2.1/4.1
title: Zebrafish Brain Segmentation and Nuclear Detection (Virtual Reality)

description: Virtual Reality project of our cell detection pipeline, viewable for free in the scientific VR platform syGlass View available here: https://www.syglass.io/view
DOI: 10.5061/dryad.4nb12g2.1/5.1
title: Zebrafish Embryonic to Juvenile Development (Virtual Reality)

description: Virtual Reality project of a 2, 3, 4, 5 and 33 dpf zebrafish reconstructed with microCT, viewable for free in the scientific VR platform syGlass View available here: https://www.syglass.io/view
DOI: 10.5061/dryad.4nb12g2.1/6.1
title: Zebrafish Juvenile 1.43um voxel size (Virtual Reality)

description: Virtual Reality project of a 33 dpf juvenile zebrafish reconstructed with microCT, viewable for free in the scientific VR platform syGlass View available here: https://www.syglass.io/view
DOI: 10.5061/dryad.4nb12g2.1/7.1
title: Registration Pipeline

description: Files are provided for registering our manually segmented 5-dpf fish onto our other samples. Uses elastix/transformix, which can be found here: http://elastix.isi.uu.nl/
DOI: 10.5061/dryad.4nb12g2.1/8.1
title: Nuclear Detection Validation

description: Validation of our nuclear detection pipeline is provided, scripts and user segmentations are provided herein.
DOI: 10.5061/dryad.6b604g8/2
title: DataFig 2

description: data files for Fig 2
DOI: 10.5061/dryad.6b604g8/3
title: DataFig 3

description: data files for Fig 3
DOI: 10.5061/dryad.6b604g8/4
title: DataFig4

description: data files for Fig 4
DOI: 10.5061/dryad.6b604g8/5
title: DataFig5

description: data files for Fig 5
DOI: 10.5061/dryad.6b604g8/6
title: DataFig6

description: data files for Fig 6
DOI: 10.5061/dryad.6vv10h0/1
title: Mosquito life history data: Egg counting reference curve
DOI: 10.5061/dryad.6vv10h0/2
title: Mosquito life history data: Egg production rate
DOI: 10.5061/dryad.8qb118r/1
title: BMI,grip strength, standing long jump, sit and reach, 50 m dash, and endurance run
DOI: 10.5061/dryad.cd56364/1
title: parins-fukuchi_data
DOI: 10.5061/dryad.d7d7b2t/8
title: Mainland Clouded Leopard Habitat Suitability Model - Continuous

description: This GIS raster layer is the projected multi-scale habitat suitability model for the mainland clouded leopard, based on beta coefficients of the GLMM and a mean of 79.47 camera trap nights averaged across all camera stations. Model projection units are number of clouded leopard observations predicted across multivariate niche space, given 79.47 active camera trap nights. Thus the specific output value is of little importance; the model output should rather be interpreted on a relative scale. Habitat &gt;4000m elevation was reclassified as non-suitable and assigned the lowest model output value. Resolution: 250m; coordinate system: Asia South Albers Equal Area Conic.
DOI: 10.5061/dryad.d7d7b2t/9
title: Top 28 High Quality Habitat Patches for the Mainland Clouded Leopard

description: This GIS raster layer contains the top 28 patches of high quality habitat for the mainland clouded leopard, based on the 90th percentile threshold of the habitat suitability model. We identified and ranked all habitat patches &gt;1000km2, based on descending habitat area. Table S8 in the Supplementary Information file associated with Macdonald et al. (2019) provides additional information for each habitat patch, including associated protected areas, mean correlation length within each patch, and percent of patch area designated as protected. Resolution: 500m; coordinate system: Asia South Albers Equal Area Conic.
DOI: 10.5061/dryad.k24b5k2/1
title: Blackbird genotypes

description: Excel file of genotype by scored alleles for each individual (n tot = 822). The last seven columns provide data for each microsatellite used with biallelic scores written in a format to be read by / transformed to most population genetics software packages. A value of 999 indicated a missing (i.e. NA) value. The column "pop_name_paper" provides information on the population the individual belongs as named in the paper.
DOI: 10.5061/dryad.mm05699/1
title: Microstructure Characteristics and Thickness Loss

description: Measured characteristics (mineralogy, crystal density, organic content and Mg/Ca ratio) for each studied microstructure. Thickness loss values for each microstructure after 100 days under the two pH treatments (ambient and reduced). Values given as mean ± 1sd.
DOI: 10.5061/dryad.mr47gq3/1
title: Sample location, phenotypic, climatic and Gwas data
DOI: 10.5061/dryad.mr47gq3/2
title: Allelic effect size
DOI: 10.5061/dryad.mr47gq3/3
title: Gwas diameter.txt
DOI: 10.5061/dryad.mr47gq3/4
title: Gwas Height.txt
DOI: 10.5061/dryad.n5qb383/30
title: Cardiff and Solana Beaches Sand Level Survey Information

description: Information on sand level surveys conducted at Cardiff and Solana Beaches. Complete lists of all survey filenames, dates, depth zones surveyed, alongshore regions surveyed, south and north-most surveyed MOP line indices with good coverage, regions influenced by nourishment, and vehicles and transects driven are included in this file.
DOI: 10.5061/dryad.n5qb383/31
title: Cardiff and Solana Beach Characteristics

description: Characteristics of Cardiff and Solana Beaches. MOP DEFINITIONS: The beach site locations are defined using MOP lines. Backbeach locations of each line (spaced 100m apart in the alongshore) and the corresponding offshore locations in 10m depth are included, as well as the MOP site names, index number, and the angle of the line relative to true north. REGIONS: The monitoring schemes at each beach evolved over time with consistently surveyed regions spanning between 1.6 and 2.7km alongshore. Region outlines, and MOP site names and index numbers within each region are provided, as well as times with minimal nourishment influence. SECTIONS: Beaches were split into sections spanning 700-900m alongshore. Location outlines, MOP sites and index numbers, and times of minimal nourishment influence are provided for each section. Additionally, features (e.g. reef) are listed. The sections that are labeled as 1D, have a coherent seasonal cross-shore sand exchange signal along the profile, as identified with empirical orthogonal function analysis. During times of minimal nourishment influence, these 1D sections are recommended for testing 1-D cross-shore beach profile evolution models. Note that cobble may be present even in 1D sections, especially at Cardiff when subaerial sand levels are eroded. NOURISHMENT: Sand nourishment placement locations and start and end times are provided. The nourishment placement outline is defined as the bulge in the 2m contour (relative to MSL) location between the pre and post-nourishment surveys. HARD SUBSTRATE: Subaerial substrate is monitored by the ATV driver, however, offshore substrate is difficult to identify. Areas with underlying hard substrate erode to minimum levels significantly less than adjacent sandy areas. Specifically, these areas are defined as areas with mapped minimum surface greater than 30cm relative to the time- and alongshore-averaged mapped profile in the alongshore uniform sections. These locations agree qualitatively with limited available sidescan sonar which helped to identify the hard substrate as rocky reef. VOLUMES: For each survey, maps are used to estimate sand volumes relative to the minimum surface. The minimum value in each mapped grid point over the study period is used to calculate the minimum surface. The total volume is estimated over the survey area, while subaerial volume is calculated over an area which extends from the mean shoreline position (average location of the intersection of the profile with MSL) to the backbeach. Estimates are provided for each beach, region and section. Volume estimates are discarded if more than 10% of the mapped area has NMSE&gt;0.2. BEACH WIDTHS: Beach width is calculated along each MOP line as the positive slope intersection of the MSL contour with the mapped profile where NMSE&lt; 0.2. If more than one intersection is found, the most offshore MSL position is used, as long as no negative slope intersection is seaward of it. Alongshore-averaged beach widths are provided for each beach, region and section when less than 10% of MOP lines were missing estimates.
DOI: 10.5061/dryad.n5qb383/33
title: Imperial Beach Binned Sand Elevations

description: Binned sand elevations at Imperial Beach. Raw sand level observations are binned to coordinates aligned with the wave estimates (MOP lines). MOP lines are separated 100m alongshore, and oriented from the 10m depth contour to the backbeach, to approximately follow the curving coastline. Bins centered on MOP lines with 5m cross-shore resolution are filled with median values, suppressing the effect of outliers. The observations are usually smooth over the 50m maximum distance of alongshore projection and 2.5m cross-shore projection. However, raw data should be used to define features with shorter scales (i.e., scarps). Binned alongshore resolution can be adjusted in the repository code (separate download: analysis_code within analysis folder) by using different binning transects, while cross-shore resolution can be adjusted by redefining the "cres" variable. Be cautious with data at depths greater than 8m below MSL, as ocean temperature stratification can contaminate jet ski soundings.
DOI: 10.5061/dryad.n5qb383/34
title: Imperial Beach Mapped Sand Elevations

description: Mapped sand elevations at Imperial Beach. Elevation maps are created on the same grid as the binned observations, but are smoothed and fill in small data gaps. For each survey, bins containing less than 3 data points are considered unsampled and are discarded. Map boundaries are defined as grid points that are regularly sampled during unnourished quarterly full surveys (must be populated at least 25\% of the time as the most frequently full surveyed grid point, during times without nourishment). Grid points with an unnourished average depth greater than 8m are not mapped because speed of sound errors due to stratification may contaminate jet ski sonar measurements. When the estimated interpolation (or extrapolation) error is large (NMSE&gt;0.2), the map bin elevation is considered missing and filled with the value -99999.
DOI: 10.5061/dryad.n5qb383/35
title: Imperial Beach Sand Level Survey Information

description: Information on sand level surveys conducted at Imperial Beach. Complete lists of all survey filenames, dates, depth zones surveyed, alongshore regions surveyed, south and north-most surveyed MOP line indices with good coverage, regions influenced by nourishment, and vehicles and transects driven are included in this file.
DOI: 10.5061/dryad.n5qb383/37
title: Analysis

description: All code and files used in processing and figure creation are included in this folder. All data files created and used in processing are formatted in the Network Common Data Form (NetCDF) and can be read using MATLAB, Python, Fortran, C, C++, Java, and other languages. Code is written in MATLAB (R2018b). Although MATLAB is a proprietary language, the .m files can be read with a text viewer.