cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t7cd6.1
title: Data from: Historical and anthropogenic factors affecting the population genetic structure of Ontario’s inland lake populations of walleye (Sander vitreus)
DOI: 10.5061/dryad.t7cd6.2
title: Data from: Historical and anthropogenic factors affecting the population genetic structure of Ontario’s inland lake populations of walleye (Sander vitreus)
DOI: 10.5061/dryad.t7cd6.2/1.2
title: cena_walleye_usats

description: Contains microsatellite data in GenePop format with 3 digit alleles. The allele sizes are binned from raw data generated by Chris Cena.
DOI: 10.5061/dryad.v33f0/1
title: Waters_et_al_2015_Genepop

description: This is the Genepop file for "Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding." The file contains 413 individuals genotyped at 9410 RAD loci. The name of each sample also includes the origin (unmarked is wild or natural origin; hatchery is hatchery origin) and sex (M or F) of the fish.
DOI: 10.5061/dryad.v33f0/2
title: Sequence_SNP_information

description: This file contains the baseline sequence and polymorphism information for the 9410 RAD loci analyzed in this study.
DOI: 10.5061/dryad.vn536/1
title: SampleDetails_Genotypes_MEC15-500

description: This file contais three sheets. The first sheet contains information on parasite individuals used in this study (site, river and basin of origin, GPS coordinates of the sampling site, the genetic cluster to which the individuals were assigned and the probability to belong to their genetic clusters). The second sheet contains information about the sampling sites covered in this study. The third sheet contains individual multilocus genotypes at the 16 microsatellite markers used in this study.
DOI: 10.5061/dryad.14853/1
title: simulated data sets

description: Genetic data (*G) and environmental data (*E) infiles that were analyzed in this manuscript. These data sets were simulated in R according to the Wright-Fisher model with selection. Genetic data files with the 'sub' prefix include subsets of individuals and thus have lower sample sizes than the other files (2N = 50 or 100 instead of 200).
DOI: 10.5061/dryad.14853/2
title: data sets simulated with quantiNEMO

description: Genetic data (geno*) and environmental data (env*) infiles that were analyzed in this manuscript. These data sets were simulated using quantiNEMO.
DOI: 10.5061/dryad.14853/3
title: perl script to run quantiNEMO simulations

description: This is a wrapper script that I wrote to run quantiNEMO to generate the simulated data files that were analyzed in the paper.
DOI: 10.5061/dryad.14853/4
title: source code and binaries for spatpg software

description: This compressed directory contains the source C++ code for the software described in the paper. A compiled binary for Linux is also included. An up-to-date version of this software can be downloaded from SourceForge (http://sourceforge.net/projects/spatpg/).
DOI: 10.5061/dryad.14853/5
title: wrapper perl scripts for simulations

description: This compressed directory contains a set of perl scripts that were used to run the R Wright-Fisher simulations and generate the data sets analyzed in this paper.
DOI: 10.5061/dryad.17209/1
title: Farnsworth et al 2015 Data meta_all version 11 August 2015 DRYAD VERSION

description: Please see README file for description of data headers.
DOI: 10.5061/dryad.20cs5/1
title: Electrode array

description: Schematic (*.sch) and board files (*.brd; EAGLE Layout Editor 6.5, CadSoft) of the flexible printed circuit (FPC) and the interface board.
DOI: 10.5061/dryad.2b09s/1
title: List of extracted biopotential pain features

description: Reference: Steffen Walter, Philipp Werner, Sascha Gruss, Harald C. Traue, Ayoub Al-Hamadi, et al.: The BioVid Heat Pain Database: Data for the Advancement and Systematic Validation of an Automated Pain Recognition System. In Proceedings of IEEE International Conference on Cybernetics, 2013. Pain stimulation data:Extracted features of biomedical signals (SCL, ECG, EMG at trapezius, corrugator and zygomaticus muscle); 85 subjects; features extracted of time windows of 5.5 seconds; used to classify pain intensities; 5 classes (pain intensity 0 to pain intensity 4), 20 samples per class per subject.
DOI: 10.5061/dryad.31733/1
title: A571_Run4-TAG-10

description: Dioscorea abyssinica A571 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
DOI: 10.5061/dryad.31733/3
title: A571_Run7-TAG-9

description: Dioscorea abyssinica A571 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
DOI: 10.5061/dryad.31733/4
title: A571_RunHi-TAG-9

description: Dioscorea abyssinica A571 sample - Whole genome sequencing (HiSeq) - .bam file containing reads after mapping on the chloroplast genome
DOI: 10.5061/dryad.31733/5
title: CR659_Run10-TAG-70

description: Dioscorea rotundata CR659 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
DOI: 10.5061/dryad.37hc1/1
title: scriptsAndCode

description: All the scripts and code used. Outside things like ABC toolbox or R of course.
DOI: 10.5061/dryad.37hc1/2
title: allExpBin.gz

description: gzip Binary format abc simulation data for the growth model.
DOI: 10.5061/dryad.392t9/6
title: Input file for structure analysis

description: Structure input file based on 19 nuclear SSR markers, -9 is used for missing data.
DOI: 10.5061/dryad.41sn4/1
title: Bird radar data_Lund_J Anim Ecol paper_for Dryad

description: Flight data from individual radar-tracked nocturnal passerines (songbirds) migrating over southern Sweden.
DOI: 10.5061/dryad.41sn4/2
title: Moth radar data_UK_J Anim Ecol paper_for Dryad

description: Flight data for individual radar-tracked nocturnal noctuid moths Autographa gamma migrating over southern UK
DOI: 10.5061/dryad.4n86v/1
title: JAPPL2015-0045_SOCHI

description: File geodatabase of inputs, including project area, planning units, conservation targets (including vector and raster) created in ArcGIS v10.1, for Marxan analysis on offset mitigation in the San Juan area of Colorado, USA.
DOI: 10.5061/dryad.608d7/1
title: Tidal Creek Gambusia: Life Histories and Environmental Data

description: Life-history data for all three species of Gambusia and all six Bahamian islands, as well as environmental variables (Gambusia density, piscivore density, #competitors, salinity, pH, and dissolved oxygen) that characterize the 42 sample sites.
DOI: 10.5061/dryad.617vp/1
title: Tedeschi et al_RSPB-2015-2320_NEW dataset for DRYAD

description: Raw Cq data for all gene expression analysis performed
DOI: 10.5061/dryad.6j2q7/1
title: shrub effects under climate change

description: The data set comprises plant-plant interactions; namely the effect of Sarcopoterium spinosum shrubs on survival and biomass of annual plant communities (quantified as RII-values) under three dimensions of increasing aridity: spatial, temporal, experimental. It originated from a large climate change experiment in Israel that was conducted for nine years of varying rainfall (temporal) in three different sites along a natural rainfall gradient (spatial) and included dry and wet manipulations of ambient rainfall (experimental).
DOI: 10.5061/dryad.7231d.2/1.2
title: Supp. Fig. 7 analysis ii

description: Analysis (ii). Plots are created from a 20 million generation BEAST analysis performed both with data and with an empty alignment. Plots compare the posterior distribution from an empty alighment (red line) with the posterior distribution when data was included (green line), and for calibrated nodes, with the theoretical prior (blue line). A-D, plots non-calibrated nodes: compares the posterior distribution from an empty alignment with the posterior distribution with data, and shows that the data is influencing the results. E-K, plots calibrated nodes: compares the posterior distribution from an empty alignment, the posterior distribution with data, and the theoretical prior placed on the node. For plots E-J, the expected prior (blue line) matches the observed prior (red line). For plot K, the expected prior does not match the observed prior: this is likely because the youngest soft bound on the root node calibration, which was left intentionally broad in order to not bias the results and to contain the true age of Araneomorphae divergence, overlaps with the oldest soft bound on other node calibrations, which pushes the observed root prior back in time. However, we do not feel this is a problem because the observed prior is still broad, still contains the true age of Araneomorphae divergence, and is still reasonable.
DOI: 10.5061/dryad.7231d.2/2.2
title: Supp. Fig. 8 analysis v

description: Analysis (v). Plots are created from a 20 million generation BEAST analysis performed both with data and with an empty alignment. Plots compare the posterior distribution from an empty alighment (red line) with the posterior distribution when data was included (green line), and for calibrated nodes, with the theoretical prior (blue line). A-E, plots non-calibrated nodes: compares the posterior distribution from an empty alignment with the posterior distribution with data, and shows that the data is influencing the results. F-K, plots calibrated nodes: compares the posterior distribution from an empty alignment, the posterior distribution with data, and the theoretical prior placed on the node. For plots F-J, the expected prior (blue line) matches the observed prior (red line). For plot K, the expected prior does not match the observed prior: this is likely because the youngest soft bound on the root node calibration, which was left intentionally broad in order to not bias the results and to contain the true age of Araneomorphae divergence, overlaps with the oldest soft bound on other node calibrations, which pushes the observed root prior back in time. However, we do not feel this is a problem because the observed prior is still broad, still contains the true age of Araneomorphae divergence, and is still reasonable.
DOI: 10.5061/dryad.7231d.2/3.2
title: analysis_i_CORRECTED_link_tip_dates

description: BEAST file for analysis (i)
DOI: 10.5061/dryad.7231d.2/4.2
title: analysis_ii_

description: BEAST file for analysis (ii)
DOI: 10.5061/dryad.7231d.2/5.2
title: analysis_iii_

description: BEAST file for analysis (iii)
DOI: 10.5061/dryad.7231d.2/6.2
title: analysis_iv_

description: BEAST file for analysis (iv)
DOI: 10.5061/dryad.7231d.2/7.2
title: analysis_v_CORRECTED_link_tip_dates

description: BEAST file for analysis (v)
DOI: 10.5061/dryad.7231d.2/8.2
title: LAGRANGE 7 area

description: File for LAGRANGE 7 area range reconstruction
DOI: 10.5061/dryad.7231d.2/9.2
title: LAGRANGE 2 area

description: File for LAGRANGE 2 area range reconstruction
DOI: 10.5061/dryad.7pk05/1
title: Individual histories
DOI: 10.5061/dryad.82gq2/1
title: Foliar defence/nutrient, soil abiotic, and vegetation community data from subarctic tundra heath fertilization experiment

description: Contains data from a fertilization experiment in subarctic heath vegetation from near Abisko, Sweden. Data are soil abiotic properties, vegetation pinpoint hits, and plant foliar defence compounds/foliar nutrients. All units and coding is contained within the file. For further information, please see the published manuscript.
DOI: 10.5061/dryad.8hq3s/1
title: Raw abundance data - Pollinators

description: The raw abundance data for insects visiting flowers used in the publication.
DOI: 10.5061/dryad.b1500/1
title: Supplementary data archive for the Delhomme et al., 2015 manuscript.

description: This archive contains supplementary data for the Delhomme et al, 2015 manuscript. It contains two directories annotation and fasta. The annotation directory contains the metadata resulting from several analysis conducted on the transcriptome assembly. The fasta directory contains the transcriptome assembly and several different subsets of it.The description of the methods used to generate:1) the different fasta sets that can be found in the fasta directory2) the metadata summarized in the annotation tsv filecan be found in the manuscript method section.
DOI: 10.5061/dryad.dd3ph.2
title: Data from: Breaking and remaking a seed and seed predator interaction in the introduced range of Scotch Broom (Cytisus scoparius) in New Zealand
DOI: 10.5061/dryad.dd3ph.2/1.2
title: Seed weight and seedling survival

description: Variables:  id: unique identifier of individual seed/seedling, letter indicates the country of origin and the number is the unique seed number. 300 cases. A = Australia, B = England, C = Corsica, CH = Chile, F = France, NZ = New Zealand, S = Switzerland, U = USA. weight: seed weight in mg. country: identifier of country of origin of seeds, 8 cases. AUS = Australia, CHILE  = Chile, CORS = Corsica, ENG = England, FRA = France, NZ = New Zealand, SW = Switzerland, USA = USA. range: identifier of native or exotic status of seed origin, two cases. Native = native range, Exotic = exotic/non-native range. block: identifier of experimental block, 4 blocks. days: day number with day = 1 indicating germination of the seed and entry of the seedling into the experiment. Each date that the seedling was observed as alive added an additional number of days to this number. This column was derived from the date column where observation dates are recorded. days_post_leaf: the number of days since first true leaf was observed. height: seedling height in cm. date: date of germination of seed and entry of seedling into the experiment. censor: indicates if seedling was observed alive (0) or dead (1) at each observation date.
DOI: 10.5061/dryad.dd3ph.2/2.2
title: seed size and beetle size North Island

description: Variables: site: 5 sites on the North Island of New Zealand. Poutu, Masterton, Frost flat, Mangahao River, Palmerston North. plant: unique plant identifier within each site. seed_size_mg: mean weight of uninfested broom seeds in mg within each plant log_seed_size: natural log of seed_size_mg. beetle_sex: sex of beetles, M=male, F=female.  elytra_area: mean area of the beetle elytra in mm2. Cases: each row represents mean measurements on multiple beetles of the same sex (m/f) and mean seed size (mg) of uninfested seeds per plant in each of 5 sites.
DOI: 10.5061/dryad.dd3ph.2/3.2
title: seed size and beetle size means all sites

description: Variables:  site: 13 sites in North and South islands of New Zealand, two records per site as male and female beetles were treated separately. East Block (Lincoln, Canterbury), FF (Frost Flat, Waikato), Hanmer Pasture (Canterbury), Hanmer River (Hanmer Riverbed, Canterbury), Hanmer Forest (Canterbury), Jack’s Pass (Canterbury), Mangahao River (Manawatu - Wanganui), Masterton (Wellington), PN (Palmerston North, Manawatu – Wanganui), Poutu (Manawatu – Wanganui), Taitapu Alt (Canterbury), Waimakariri Forest (Canterbury), Wimakariri River Bed (Canterbury). 14 sites mentioned in main text but one of these had no beetles (Waiouru, Manawatu – Wanganui). seed_size_mg: mean of seed size from multiple plants per site. log_seed_size: natural log of seed_size_mg. elytra_area: mean of elytra area for beetles on multiple plants per site, mm2. beetle_sex: sex of beetles. Cases: each row represents the mean of one sex of beetles from multiple plants per site. One male and one female beetle per plant were measured. Two seeds (each containing a beetle) were measured per plant.
DOI: 10.5061/dryad.dd3ph.2/4.2
title: beetle size and beetle fecundity 2007 & 2008

description: Variables: elytra_area: elytra area of individual beetles in mm2. log_elytra_area: natural log of elytra_area. eggs_laid: number of eggs laid by individual beetles. log_eggs: natural log of eggs_laid. year: year of measurement, 2007 or 2008. Cases: each row represents data from one female beetle whose fecundity and size were recorded in the lab.
DOI: 10.5061/dryad.dn08t/1
title: ASTRAL_speciesTree_fromMrBayesGeneTrees_OxalisHybSeq

description: ASTRAL species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with Bayesian inference). Oxalis corniculata was used as outgroup.
DOI: 10.5061/dryad.dn08t/2
title: ASTRAL_speciesTree_fromRAxMLGeneTrees_OxalisHybSeq

description: ASTRAL species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with maximum likelihood). Oxalis corniculata was used as outgroup.
DOI: 10.5061/dryad.dn08t/3
title: MP-EST_speciesTree_fromMrBayesGeneTrees_OxalisHybSeq

description: MP-EST species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with Bayesian inference). Oxalis corniculata was used as outgroup.
DOI: 10.5061/dryad.dn08t/4
title: MP-EST_speciesTree_fromRAxMLGeneTrees_OxalisHybSeq

description: MP-EST species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with maximum likelihood). Oxalis corniculata was used as outgroup.
DOI: 10.5061/dryad.dn08t/5
title: STAR_speciesTree_fromMrBayesGeneTrees_OxalisHybSeq

description: STAR species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with Bayesian inference). Oxalis corniculata was used as outgroup.
DOI: 10.5061/dryad.dn08t/6
title: STAR_bootstrappedSpeciesTree_fromRAxMLGeneTrees_OxalisHybSeq

description: Bootstrapped STAR species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with maximum likelihood). Oxalis corniculata was used as outgroup.
DOI: 10.5061/dryad.f52s2/1
title: Hagler Data Archive for MEE Paper

description: Raw data file for prey retention studies
DOI: 10.5061/dryad.fh2nt/1
title: Sampled values for all probability variables of the benefit-risk assessment

description: The sampled values are based on probabilistic modelling of data from published clinical trials and from individual case safety reports contained in VigiBase, the WHO international database of suspected adverse drug reactions. The first two columns are used to determine what scenario of the assessment that is considered: the first column indicates the type of distribution over the derived risk intervals for the serious adverse effects, and the second column indicates the proportion of the sampled risk values that is attributed to the background. Each of the following columns belongs to one of the probability variables for one of the three considered treatment alternatives. Variables are listed in the order obtained when traversing the decision tree in Figure 3 top to bottom, starting from the leftmost level. There are 10,000 rows for each scenario. Abbreviations: HDMP=high-dose methylprednisolone, LDMP=low-dose methylprednisolone, NT=no treatment.
DOI: 10.5061/dryad.fh2nt/2
title: Sampled values for all utility variables of the benefit-risk assessment

description: These data have been generated by probabilistic modelling driven by qualitative relations specified between the considered clinical outcomes of the benefit-risk assessment. The first two columns are used to determine what scenario of the assessment that is considered: the first column indicates the severity of the relapse as measured by the patient's starting EDSS value, and the second column indicates the so called minimum utility difference between lethal and non-lethal outcomes. Each of the following columns belongs to the utility variable corresponding to one of the considered clinical outcomes. Variables are listed in the order obtained when viewing all branches of the decision tree in Figure 3 top to bottom. There are 10,000 rows for each scenario.
DOI: 10.5061/dryad.fh2nt/3
title: Resulting samples for the expected utility of the three alternatives

description: The data displayed in this file are the resulting samples for the expected utility of the three considered treatment alternatives in all considered scenarios. They have been obtained by combining the data displayed in the two files 'Sampled values for all probability variables of the benefit-risk assessment' and 'Sampled values for all utility variables of the benefit-risk assessment', using the decision tree depicted in Figure 3 and the formulae given in Figure 1. The first four columns are used to determine what scenario of the assessment that is considered: the first column indicates the type of distribution over the derived risk intervals for the serious adverse effects; the second column indicates the proportion of the sampled risk values that is attributed to the background; the third column indicates the severity of the relapse as measured by the patient's starting EDSS value; and the fourth column indicates the so called minimum utility difference between lethal and non-lethal outcomes. The fifth, sixth, and seventh columns then show the computed expected utility values for high-dose methylprednisolone (HDMP), low-dose methylprednisolone (LDMP), and no treatment (NT), respectively. There are 10,000 rows for each scenario.
DOI: 10.5061/dryad.fh2nt/4
title: Resulting preference rates for the three alternatives

description: The data in this file has been computed directly from the raw data in the file 'Resulting samples for the expected utility of the three alternatives'. This file contains the same scenarios as that file, discernible from the the first four columns, but shows only a single value for each treatment alternative in each scenario. This value, the preference rate, is the fraction of all 10,000 sampling iterations for a given scenario in which the indicated alternative was the preferred one, i.e. had the highest expected utility. Preference rates for high-dose methylprednisolone (HDMP), low-dose methylprednisolone (LDMP), and no treatment (NT) are shown in columns 5-7, respectively. Figures 10 and 11 have been generated based on precisely this data.
DOI: 10.5061/dryad.g9049.1
title: Data from: No evidence for a trade-off between sperm length and male premating weaponry
DOI: 10.5061/dryad.g9049.2/1.2
title: Phylogenies of the Primates, Ungluates, Pheasants, Stalk-eyed flies and Onthophagine dung beetles

description: Phylogenies in NEXUS format of all species of Primates, Ungluates, Pheasants, Stalk-eyed flies and Onthophagine dung beetles used in this study. All phylogenies are based on published molecular phylogenies. Since no branch lengths were available for most phylogenies, all branch lengths are set to 1 for consistency.
DOI: 10.5061/dryad.g9049.2/2.2
title: References

description: References accompanying the data flies and phylogenies
DOI: 10.5061/dryad.j1305/3
title: Data from provisioning observations (body mass analysis)
DOI: 10.5061/dryad.m0420/1
title: Microsatellit genotypes RSPB
DOI: 10.5061/dryad.mt24h/10
title: No.5 TB patient's microbiome (Group B)

description: Group A means the microbiome from lesion-free lung lobe; Group B means the microbiome from lesion-forming lung lobe; Group H means the microbiome from healthy individuals.
DOI: 10.5061/dryad.mt24h/2
title: No.1 TB patient's microbiome (Group B)

description: Group A means the microbiome from lesion-free lung lobe; Group B means the microbiome from lesion-forming lung lobe; Group H means the microbiome from healthy individuals.
DOI: 10.5061/dryad.mt24h/3
title: No.2 TB patient's microbiome (Group A)

description: Group A means the microbiome from lesion-free lung lobe; Group B means the microbiome from lesion-forming lung lobe; Group H means the microbiome from healthy individuals.
DOI: 10.5061/dryad.mt24h/4
title: No.2 TB patient's microbiome (Group B)

description: Group A means the microbiome from lesion-free lung lobe; Group B means the microbiome from lesion-forming lung lobe; Group H means the microbiome from healthy individuals.
DOI: 10.5061/dryad.mt24h/5
title: No.3 TB patient's microbiome (Group A)

description: Group A means the microbiome from lesion-free lung lobe; Group B means the microbiome from lesion-forming lung lobe; Group H means the microbiome from healthy individuals.