cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kj424/1
title: Probabilistic selection task data_ Exp1A_Fig2a_Fig3a

description: Data corresponds to experiment 1A and Figure 2A/3A.
DOI: 10.5061/dryad.kj424/2
title: Probabilistic selection task data_ Exp1B_Fig2b_Fig3b_Schutte_etal

description: Data corresponds to Experiment 1B and Figure 2B/3B.
DOI: 10.5061/dryad.kj424/3
title: Reaction time data_ Exp2_Fig5_Schutte_etal

description: Data corresponds to Experiment 2 and Figure 5
DOI: 10.5061/dryad.kj424/4
title: Probabilistic selection task data_Exp3_Fig6_Fig7

description: Data corresponds to experiment 3 and Figure 6 and 7.
DOI: 10.5061/dryad.rb334/1
title: OphiuroidHC_TableS1

description: S1. Table of information on samples, exons and genes.
DOI: 10.5061/dryad.rb334/2
title: OphiuroidHC_Table S2

description: S2. Calibrations and fossil evidence used to date the molecular phylogeny.
DOI: 10.5061/dryad.rb334/3
title: OphiuroidHC_576taxa_trees

description: Nexus format RAxML tree with bootstrap values, and PLRS version.
DOI: 10.5061/dryad.rn0bp/1
title: Measurements of pair bond strength in birds

description: Collated from published sources found using Web of Science, Google Scholar and the Alexander Library of Ornithology (Bodleian Libraries, University of Oxford, UK), and from contacting researchers involved in long-term, detailed behavioural studies of the species in question. Parental cooperation scores were calculated by Remeš et al. (2015, PNAS). Data were collated in Excel.
DOI: 10.5061/dryad.rn0bp/2
title: Kenny_ESM_PhylogeneticTrees

description: 100 phylogenetic trees downloaded from http://birdtree.org. The birdtree.org website accompanies the following study: Jetz W, Thomas GH, Joy JB, Hartmann K, Mooers AO (2012) The global diversity of birds in space and time. Nature 491: 444-448. http://dx.doi.org/10.1038/nature11631, and the Jetz et al. article in Nature should be cited in the primary reference list of any publication that uses data culled from birdtree.org
DOI: 10.5061/dryad.05jb0/1
title: Franco et al_ eco-physiological &SDM

description: Growth (g FW day-1) of L. ochroleuca sporophytes, according to experimental temperatures (12, 15, 18, 20, 22, 24 º C) and nutrients availability (+, -), at 9, 18, 27 and 36 days in relation to day 0.
DOI: 10.5061/dryad.29722/1
title: Supplemental Material

description: Additional results from simulations supporting this manuscript
DOI: 10.5061/dryad.29722/2
title: Simulation-RScripts

description: R scripts used to perform all simulations in this study
DOI: 10.5061/dryad.29722/3
title: Simulation-Results

description: Results from all simulations in this study
DOI: 10.5061/dryad.30mv0/3
title: FC Dataset: steady-state DTT stress response

description: Raw FCS files and MATLAB analysis code. Flow cytometry analysis toolkit used in this code is available at https://github.com/springerlab
DOI: 10.5061/dryad.30mv0/4
title: FC Dataset: YFP/mCherry dual reporter noise assay

description: Raw FCS files and MATLAB analysis code. Flow cytometry analysis toolkit used in this code is available at https://github.com/springerlab
DOI: 10.5061/dryad.30mv0/5
title: FC Dataset: kinetic GAL pathway induction

description: Raw FCS files and MATLAB analysis code. Flow cytometry analysis toolkit used in this code is available at https://github.com/springerlab
DOI: 10.5061/dryad.3jm3s/1
title: Pini et al_JEcol_2016_0491_R1_Dryad archived data

description: This file contains % pollen and LOI data, P forms concentrations used for elaborations presented in the paper.
DOI: 10.5061/dryad.55dh5/1
title: Locality level data Pintar and Resetarits 2017 J Anim Ecol

description: Locality level (sets of two patches) data file from Pintar, Matthew R., and William J. Resetarits, Jr. 2017. Context dependent colonization dynamics: regional reward contagion drives local compression in aquatic beetles. Journal of Animal Ecology. See the README for patch level data, which covers the entire dataset.
DOI: 10.5061/dryad.55dh5/2
title: Patch level data Pintar and Resetarits 2017 J Anim Ecol

description: Patch level (individual patches) data from Pintar, Matthew R., and William J. Resetarits, Jr. 2017. Context dependent colonization dynamics: regional reward contagion drives local compression in aquatic beetles. Journal of Animal Ecology. README file covers the entire dataset.
DOI: 10.5061/dryad.69gt3/3
title: ClimDBRainFall

description: Daily precipitation estimates for Konza Prairie LTER site as recorded by the ClimDB database.
DOI: 10.5061/dryad.69gt3/4
title: KFH011

description: Burn history for Konza Prairie watersheds.
DOI: 10.5061/dryad.69gt3/5
title: Processing Script

description: R script for processing flower data into the final datasheet that contains the stalk weight, stalk height, and burn history for all transect/watershed/year combinations in this study.
DOI: 10.5061/dryad.69gt3/6
title: Metadata

description: Metadata file that includes column descriptions and associated data sources for all data in the final analysis file as processed by the Processing R script.
DOI: 10.5061/dryad.6r5j8/1
title: Barents Sea fish abundances

description: Abundance counts of 41 fish species at 158 stations in the Barents Sea.  This is a subset of a larger data set that spans more stations and years.
DOI: 10.5061/dryad.6r5j8/2
title: Experimental data

description: Three samples of size n=10 each, one from a control and two from two treatments.  Each sample unit consists of abundances of 45 marine species.
DOI: 10.5061/dryad.7t23j/1
title: Raw data of mosquito life history traits measurements

description: Laboratory data form experimental infections of Anopheles coluzzii mosquitoes with Plasmodium falciparum malaria parasites
DOI: 10.5061/dryad.85c0s/10
title: Nexus_files

description: Nexus files of 12 gene alignments
DOI: 10.5061/dryad.85c0s/9
title: Supplementary_figure_legends

description: supplementary figure legends
DOI: 10.5061/dryad.874p9/1
title: misspecification in individual life history models

description: The files in this folder allow to replicate the results of the analyses presented in "Wolf in Sheep’s Clothing: Model Misspecification Undermines Tests of The Neutral Theory for Life Histories".

The statistical software R (R Core Team, 2016) is needed, along with a few libraries. Please, make sure to change the path to your working directory. The version of R used at the time of the original analysis was R version 3.2.3 (2015-12-10) "Wooden Christmas-Tree".

All figures from the main manuscript can be replicated using the data file "20161204_summary_stat.txt" and scripts "03_Tile_plots_main.txt" & "04_Tile_plots_suppl.txt".

Functions for simulating data are in the script "LRS_simul.txt".

These scripts were last checked on 2017-02-22. Please, send me an email (authierm at gmail dot com) if you have any remarks or questions.

References
R Core Team (2016). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
DOI: 10.5061/dryad.8j41r/1
title: Reticulated Python Diet and Sarcocystis infection

description: Lengths, locations, diet and presence of Sarcocystis infection in reticulated pythons captured between June 2009 and May 2010
DOI: 10.5061/dryad.f65s7/1
title: H. molleri Guadarrama

description: Genetic dataset in Genepop format including 547 tadpole samples of Hyla molleri, from 20 populations located across Sierra de Guadarrama (Central Spain), genotyped at 18 microsatellite loci.
DOI: 10.5061/dryad.f69mg/1
title: two tables of the two histograms

description: two tables of frequencies for the histograms of the paper
DOI: 10.5061/dryad.gf83v/10
title: toad range overlap analysis
DOI: 10.5061/dryad.gf83v/12
title: toaddataedit
DOI: 10.5061/dryad.gf83v/8
title: silene citation info
DOI: 10.5061/dryad.gf83v/9
title: silene_ultrametric_tree
DOI: 10.5061/dryad.n7c42/1
title: Data_for_GLMM

description: Summary of individual level variables and scrounging propensity across all replicates, data used in GLMM models
DOI: 10.5061/dryad.n7c42/2
title: Network_PA2012

description: Social network matrix for PA2012 replicate
DOI: 10.5061/dryad.n7c42/3
title: Network_CP2012

description: Social network matrix for CP2012 replicate
DOI: 10.5061/dryad.n7c42/4
title: Network_GW2012

description: Social network matrix for GW2012 replicate
DOI: 10.5061/dryad.pk8dv/1
title: Data record A_tomographic images.zip

description: OPT generated tomographic image stacks (*.bmp) throughout the volume of the splenic, duodenal and gastric lobes of ob/ob and control Mus Musculus pancreas  for the insulin and the anatomy channel. The individual image files are annotated to indicate phenotype, age (weeks), ID, pancreatic lobe, channel (insulin or anatomy) and sequential stack number using the following format: “XXXX_XXw_IDX_XL_XXXXXX_XXXX.bmp”.  (Note, when unzipped the data file will be 218 GB.)
DOI: 10.5061/dryad.pk8dv/2
title: Data record B_Isosurfaced 3D volumes.zip

description: Imaris (*.ims) files with segmented islet volumes (here defined as a continuous body of insulin positive cells) based on the signal from insulin specific antibodies and pancreatic lobular volumes based on the signal from endogenous tissue autofluorescence. These files contain both the anatomy and insulin channels and are annotated to indicate phenotype, age (weeks), ID and pancreatic lobe using the following format: “XXXX_XXw_IDX_XL.ims”.
DOI: 10.5061/dryad.qc10g/1
title: StutzBolnickData

description: Data to recreate results, including genotype scores and parasite infection and geographic locations.
DOI: 10.5061/dryad.qc10g/2
title: Alleles

description: FASTA file with inferred true MHC IIb alleles (removing sequencing error via Stepwise Threshold Clustering)
DOI: 10.5061/dryad.qc10g/3
title: MHC_master
DOI: 10.5061/dryad.qn4br/1
title: Fastq_files

description: Raw sequencing data of the nine sequenced individuals of Robinia pseudoacacia
DOI: 10.5061/dryad.qn4br/2
title: FastqcReports

description: reports about the quality of sequencing of each of the nine sequenced individuals of Robinia pseudoacacia
DOI: 10.5061/dryad.rb334/10
title: OphiuroidHC_FigS5

description: S5. 185 taxa all-sites amino acid RAxML tree with BS support.
DOI: 10.5061/dryad.rb334/11
title: OphiuroidHC_FigS6

description: S6. 185 taxa ASTRAL species tree, with local posterior probability support.
DOI: 10.5061/dryad.rb334/12
title: OphiuroidHC_DRYAD_readme_file

description: Word document with information on constituents of this Dryad package
DOI: 10.5061/dryad.rb334/4
title: OphiuroidHC_185taxa_RAxMLtrees
DOI: 10.5061/dryad.rb334/5
title: OphiuroidHC_185taxa_BEASTtrees
DOI: 10.5061/dryad.rb334/6
title: OphiuroidHC_576taxa_1484exon

description: Nexus format 416 gene, 1484 exon, 272,952 site, 576 taxa data-matrix.
DOI: 10.5061/dryad.rb334/7
title: OphiuroidHC_S7_revised_classification

description: Supplementary material S7, Revised classification of the recent Ophiuroidea.
DOI: 10.5061/dryad.rb334/8
title: OphiuroidHC_FigS3

description: S3. 576 taxa all-sites RAxML phylogeny with bootstrap (BS) support.
DOI: 10.5061/dryad.rb334/9
title: OphiuroidHC_FigS4

description: S4. 185 taxa all-sites nucleotide RAxML with BS support.
DOI: 10.5061/dryad.t5r56/1
title: Data_Injury_Prevention

description: demographics, perceptions regarding injury prevention and preventive measures
DOI: 10.5061/dryad.1bp06/1
title: Raw pollen and charcoal counts from surface samples

description: Raw pollen / spore counts for each of 50 surface samples, organized with rows as sites and columns as taxa (n = 55). Macroscopic charcoal concentration (#/cm3) was based on charcoal counts from sediment subsamples (distinct from pollen subsamples); charcoal data are in columns BL-BN. See "ReadMe" file for more information.
DOI: 10.5061/dryad.1bp06/2
title: readMe

description: A description of the entire data archive.
DOI: 10.5061/dryad.1bp06/3
title: CP13_SS_analysis

description: Matlab script to create Figure 2 in Morris et al. The script calls upon the data in the file TAS_SS_16_11_11.csv. To run, change the file path to lead to the location of this data file, under the "Load data" heading in the script.
DOI: 10.5061/dryad.1bp06/4
title: CP13_SS_discrimAnalysis

description: R script that performs Discriminant Analysis on the surface sample dataset and produced Figure 3 in Morris et al. The script calls upon the data in the file TAS_SS_16_11_11.csv, and CP13_10A_pollen_16_11_10.csv. To run, change the file path to lead to the location of this data file, under the "Load data" heading in the script. To run this script, set the working directory to the directory that contains both of these files, under the "Clear and set work space" heading in the script.
DOI: 10.5061/dryad.1bp06/5
title: CP13_10A_pollen_16_11_10

description: Pollen data from core CP13_10A, used in Morris et al. Note, only several samples from this dataset are used in this paper, for application of the discriminant analysis function.
DOI: 10.5061/dryad.215sn/1
title: Franugla_Microsat_Dat

description: Mikrosatellite data: alleles (fragment sizes in bp) of 7 loci from 576 individuals of 30 populations (as described in Materials & Methods, Table 1 and Supplementary Material).
DOI: 10.5061/dryad.215sn/2
title: Franugla_cpDNA_Dat

description: cpDNA data: nucleotide sequences at 8 differentiating loci in two chloroplast regions observed in 236 individuals from 30 populations (as described in Methods & Materials, Table 1, Fig. 6 and Supplementary Material).
DOI: 10.5061/dryad.25qg7/1
title: Langin et al 2017 Heredity - empirical data

description: This file contains genetic and spatial data associated with 544 Island Scrub-Jays that were sampled as part of this study.
DOI: 10.5061/dryad.25qg7/2
title: Langin et al 2017 Heredity - simulation data

description: This file contains the results of 180 simulations conducted as part of this study.
DOI: 10.5061/dryad.2p5rb/2
title: copy7.cl

description: Common Lisp program for simulating information diffusion in flocks of wild birds
DOI: 10.5061/dryad.3v9h5/1
title: Dataset

description: AIDS cases and deaths among men who have sex with men (MSM) in San Francisco
DOI: 10.5061/dryad.576hg/1
title: Microsatellite_genotype_data

description: This data file contains all the microsatellite genotype data. Samples are coded by their ID, nest number and locality. File contains three sheets. The first sheet contains worker genotypes used in Structure and PCoA analyses. The second sheet contains male and female (worker) genotypes from locality Tvärminne Road. The second sheet contains male, female (young queens) and female worker genotypes from locality Halsholmen. Diploid males are indicated. All other males are haploid, but their genotypes are coded as diploid (e.g. allele 198 in a male is coded 198/198).
DOI: 10.5061/dryad.576hg/2
title: Mitochondrial_sequences

description: This data file contains all the mitochondrial sequences used in the study Beresford et al. in a fasta format.
DOI: 10.5061/dryad.58nm4/1
title: Raw_Data_Morphology_Learning_Trials

description: An excel spreadsheet containing data for the morphology of lizards from hot and cold incubation, and the times taken to complete the learning task in a total of 16 trials.
DOI: 10.5061/dryad.5b1cc/1
title: Isotopic data of eared seals and mussels

description: Stable isotope values (δ13C and δ15N) of modern blue mussel (Mytilus edulis) shells, and stable isotope values (δ13C and δ15N) and condylobasal length of ancient and modern South American sea lion (Otaria flavescens) and fur seal (Arctocephalus australis) skulls. δ13C and δ15N: values not corrected for isotopic baseline shifts; δ13Ccor and δ15Ncor: values corrected for isotopic baseline shifts.
DOI: 10.5061/dryad.8t59p/1
title: Ogoma et al 2017_A low tech emanator against outdoor mosquito vectors_data

description: The data was collected in Kilombero Valley Tanzania to evaluate efficacy of a low technology transfluthrin emanator against outdoor biting mosquito vectors of malaria, dengue and arboviruses.
DOI: 10.5061/dryad.8t59p/2
title: Ogoma et al 2017_A low tech emanator against outdoor mosquito vectors_Temp data

description: This data includes information on the effect of temperature on efficacy of transfluthrin treated emanators.
DOI: 10.5061/dryad.925mv/1
title: McGarvey_EtAl_RawData

description: These are raw data files (.csv) for the 15 freshwater fishes modeled in "On the use of climate covariates in aquatic species distribution models: are we at risk of throwing the baby out?" (McGarvey et al.). The files are formatted for MaxEnt ('species with data' format) and include MaxEnt batch files that can be used to re-run the models.
DOI: 10.5061/dryad.9gc00/1
title: DRYAD_Suring_coll_aa

description: For a detailed description of the data and data depositiion we refer to the Readme file. This file contains taxonomic names of applied species, library IDs used for transcriptome sequencing, NCBI bioproject codes per dataset including NCBI accession numbers. Also, we provide the number of specimens used for RNA extraction, the locations where these animials were sampled, in which life stage they were during sampling, and at what date they were sampled.
DOI: 10.5061/dryad.b4217/1
title: Data for Krüger et al. 2017 DOI: 10.1111/ecog.02590

description: The zip file contains eight folders, one with the environmental data used for modelling (Sea Surface Temperature SST, Chlorophyll CHLOR, Wind Speed WIND, Sea Ice Cover ICE, Bathymetry BATH) and their projections for each representative concentration pathways (RCPs) for 2050 and 2100. One folder with the distribution of fisheries types in .csv (geographic coordinate system, WGS84) and geotiff images for the species and fisheries distribution models (files with the name pred) and projections for each scenario. Also the scripts used for SDMs and GWPCA are presented in the file.
DOI: 10.5061/dryad.cn74h/1
title: Matrices and control files

description: Here we provide all the necessary files to run the analyses described in the paper. Files are organized by folders.

dating_analysis -&gt; control files necessary to run the dating analysis.

ddrad_data -&gt; Intermediate files from pyrad's steps 3 and 5, and matrices derived from the ddRAD method used for the phylogenetic and introgression analyses.

genome_skimming_matrices -&gt; matrices derived from genome skimming method used in the phylogenetic analyses.

JML_analysis -&gt; all the files used to run and visualize the JML analysis.
DOI: 10.5061/dryad.cn74h/2
title: read_subsets_1

description: Files with the subsets of reads used in the study

Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering).

cp indicates chloroplast reads
mt indicates mitochondrial reads
nr indicates nuclear ribosomal reads
DOI: 10.5061/dryad.cn74h/3
title: read_subsets_2

description: Files with the subsets of reads used in the study

Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering).

cp indicates chloroplast reads
mt indicates mitochondrial reads
nr indicates nuclear ribosomal reads
DOI: 10.5061/dryad.d6c07/1
title: Site and plot level data

description: The data file includes two sheets one which provides the site level data and one which provides the plot level data. The data provided includes, species richness, seed bank richness including the germinants from the seed bank of the invasive species African lovegrass, estimated kg per dry weight of key species, cover estimates for key species, detailed soil nutrient data and site and plot-level descriptions.
DOI: 10.5061/dryad.f65s7/2
title: E. calamita Guadarrama

description: Genetic dataset in Genepop format including 652 tadpole samples of Epidalea calamita, from 21 populations located across Sierra de Guadarrama (Central Spain), genotyped at 16 microsatellite loci.
DOI: 10.5061/dryad.f65s7/3
title: P. perezi Guadarrama

description: Genetic dataset in Genepop format including 516 tadpole samples of Pelophylax perezi, from 17 populations located across Sierra de Guadarrama (Central Spain), genotyped at 15 microsatellite loci.
DOI: 10.5061/dryad.ft66g/1
title: McIntyre_Strauss_2017_evolution_cytotypes

description: zipped file containing four csv data files and a metadata text file
DOI: 10.5061/dryad.j0p8c/1
title: Microarray_deposit to Dryad online
DOI: 10.5061/dryad.jq362/1
title: data_package_MensensEtAl2017_JournalOfEcology

description: This data package contains data from the publication: Mensens, C., De Laender, F., Janssen, C.R., Sabbe, K. & De Troch M. (2017) Different response-effect trait relationships underlie contrasting responses to two chemical stressors. Journal of Ecology. Details about the content of the package can be found in the Readme.txt file in the zip folder.
DOI: 10.5061/dryad.kf6r5/1
title: Chemistry Panels

description: All data from the chemistry panels is included, as well as animal age, sex and month of capture.
DOI: 10.5061/dryad.n511h/1
title: Data for texture, average colour and quantised colour for camouflage uniforms

description: .RData file contents: PatternNames - camouflage pattern identifier; SumMaxResponses - sum of maximum responses per pixels (across logical maps) for each Log-Gabor filter (described by spatial frequency and orientation); ColDistAvgColours - pairwise distances of average colours of patterns; ColDistQntColours - pairwise distances of quantised colours of patterns
DOI: 10.5061/dryad.n7c42/5
title: Network_BB2013

description: Social network matrix for BB2013 replicate
DOI: 10.5061/dryad.n7c42/6
title: Network_MP2013

description: Social network matrix for MP2013 replicate
DOI: 10.5061/dryad.pk8dv/4
title: Data record D_Visual reference images

description: Representative iso-surfaced reconstruction images of each sample for visual reference (*.jpg). These files are annotated to indicate phenotype, age (weeks), ID and lobe (XXXX_XXw_IDX_XL.jpg).
DOI: 10.5061/dryad.pk8dv/5
title: Data record C Volumetric and spatial statistics

description: Excel sheets (*.xls) providing information about individual the islet β-cell volumes, their corresponding 3D coordinates and related aspect ratio information, together with information on pancreatic lobular volumes. These files are annotated to indicate phenotype, age (weeks), ID, pancreatic lobe and channel (XXXX_XXw_IDX_XL_XXXXXX.xls)
DOI: 10.5061/dryad.qc561/1
title: R code for the stochastic dynamic model

description: R code for the stochastic dynamic optimization model, including example plots and the forward simulation.
DOI: 10.5061/dryad.qf20f/1
title: Coordinates&Distances

description: This file contains the estimated coordinates (latitude, longitude) for each individual return migration and the calculated distances to breeding colony.
DOI: 10.5061/dryad.rb334/13
title: OphiuroidHC_distribution_summary

description: Excel file of family latitude, longitude and depth distribution summary histogram values, with ggplot script, used to generate Figure 4.
DOI: 10.5061/dryad.rf4s0/1
title: Germano et al. Temp Trans Data For Publication 2017

description: Data on post-release movement and survival of desert tortoise as a function of personality scores
DOI: 10.5061/dryad.rm4j6
title: Dryad Item 10.5061/DRYAD.RM4J6
DOI: 10.5061/dryad.s211m/1
title: Tooth measurements

description: Measurements of some spatulate-, compressed cone-chisel-, pencil-shaped teeth from the Upper Jurassic of the Lusitanian Basin
DOI: 10.5061/dryad.s3s7p/1
title: Multistate input file and body condition data - Blomberg et al.

description: This text file contains the .inp file necessary to run our multi-state survival analysis in Program MARK, as well as body condition data for females as a comma separated file.
DOI: 10.5061/dryad.s612m/1
title: Strategic_Coop_ms_data

description: Data file used for all analyses within manuscript and ESM. Variables are annotated. Data overlaps with data used in two other studies (Burton-Chellew et al 2016, Conditional cooperation and confusion in public goods games, PNAS; and Burton-Chellew et al 2017, Social learning and the demise of costly cooperation in humans, PRSB).