cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s46t627/16
title: 16_Response-intensity relationship of the dark-adapted compound eyes of the wood tiger moth (Arctia plantaginis) determined by electroretinograms
DOI: 10.5061/dryad.s46t627/17
title: 17_DataRelatedToFig3_IndividualSpectralSensitivityCurves_ArctiaPlantaginis

description: 17 and 18: Two Excel files with data related to figure 3 and 5 in 'Henze MJ, Lind O, Mappes J, Rojas B, Kelber A (2018) An aposematic colour-polymorphic moth seen through the eyes of conspecifics and predators - sensitivity and colour discrimination in the wood tiger moth. Functional Ecology.'
DOI: 10.5061/dryad.s46t627/18
title: 18_DataRelatedToFig5_WavelengthsOfMaximalSensitivity_StandardCurves_ArctiaPlantaginis
DOI: 10.5061/dryad.s46t627/19
title: Spectral sensitivity, illumination spectra, background spectra and reflectance spectra of wood tiger moth wing areas used for visual modelling

description: One excel file related to Figures 4, 6 and 7 in 'Henze MJ, Lind O, Mappes J, Rojas B, Kelber A (2018) An aposematic colour-polymorphic moth seen through the eyes of conspecifics and predators - sensitivity and colour discrimination in the wood tiger moth. Functional Ecology.'
DOI: 10.5061/dryad.sb110/1
title: Accucirc Field Evaluation Data

description: This CSV file contains data on infant circumcisions performed and parent interview data. The first row contains variable names. See attached code book & forms for variable information.
DOI: 10.5061/dryad.sb110/2
title: AccuCirc Study Forms & Parent Questionnaire

description: This PDF file contains the parent questionnaire and study forms used in the collection of the data.
DOI: 10.5061/dryad.sb110/3
title: Accucirc Code Book

description: Code book for AccuCirc data
DOI: 10.5061/dryad.t1715/1
title: Herbivory on Phytolacca americana from Michigan to Florida in field
DOI: 10.6084/m9.figshare.12980864
title: UnAmbiguouslyMapped_ds.buccal_trim2-centrifuge-out.tsv

description: work documented here: https://hackmd.io/@astrobiomike/centrifuge-db-build
DOI: 10.6084/m9.figshare.12980864.v1
title: UnAmbiguouslyMapped_ds.buccal_trim2-centrifuge-out.tsv

description: work documented here: https://hackmd.io/@astrobiomike/centrifuge-db-build
DOI: 10.5061/dryad.0g1f2/1
title: Marchini and Rolian - Longshanks Growth Raw Data

description: Raw data for mechanisms of comparative limb elongation in wildtype and artificially selected mice. Contains three sheets (Gompertz growth data, histomorphometric data, BrDU assay data)
DOI: 10.5061/dryad.13n52/1
title: Online-Only Supplementary Materials

description: The online-only supplement of the manuscript
DOI: 10.5061/dryad.13n52/2
title: Human Alu Files

description: Files related to the Human Alu dataset used in the manuscript
DOI: 10.5061/dryad.13n52/3
title: Tree Simulation Files

description: Tree simulation files used to test the properties of the dual-birth model as well as to study the inference of trees generated by the model
DOI: 10.5061/dryad.13n52/4
title: README

description: README file describing the contents of the supplementary materials
DOI: 10.5061/dryad.15r51.1
title: Data from: Profound reversible seasonal changes of individual skull size in a mammal
DOI: 10.5061/dryad.15r51.1/1.1
title: Skull measurements from X-ray images in common shrews

description: Measurements in absolute values (mm) of braincase height, skull length, braincase width and tooth row and corrected by tooth row (cor) from individual (id) shrews captured/recaptured at different times (date) along their lifespan.
DOI: 10.5061/dryad.15r51.2
title: Data from: Profound reversible seasonal changes of individual skull size in a mammal
DOI: 10.5061/dryad.15r51.2/1.2
title: Skull measurements from X-ray images in common shrews

description: Measurements in absolute values (mm) of braincase height, skull length, braincase width and tooth row and corrected by tooth row (cor) from individual (id) shrews captured/recaptured at different times (date) along their lifespan.
DOI: 10.5061/dryad.15r51.2/2.2
title: Skull measurements for measurement error

description: Repeated skull measurements from X-ray images on 10 individuals used to calculate the technical measurement error
DOI: 10.5061/dryad.1f24f/1
title: Supplementary_Data

description: Raw Data
DOI: 10.5061/dryad.2fk71/1
title: Data.xlsx, complete collection of the analized data
DOI: 10.5061/dryad.2fk71/2
title: Data.zip, Part 1 of 31, archive of RT-DC raw data
DOI: 10.5061/dryad.4g87s/1
title: Leopard Diet

description: File containing the raw data used to determine the diet of leopard in Srepok Wildlife Sanctuary, Cambodia. Only confirmed leopard scats were used for the analysis and are shown here.
DOI: 10.5061/dryad.4g87s/2
title: Individual Leopard Genotype

description: File containing the genotype data from each individual leopard
DOI: 10.5061/dryad.4g87s/3
title: Line Transects

description: File containing the data collected for banteng, wild pig, and muntjac in 2014
DOI: 10.5061/dryad.4g87s/4
title: Camera Trap

description: Dates camera trap stations were set, checked, and collected
DOI: 10.5061/dryad.4g87s/5
title: Ungulates Density

description: File containing the density, estimated using Distance 6.2, of banteng, wild pig, and muntjac in the inner core zone (450 km2) of Srepok Wildlife Sanctuary during 2014
DOI: 10.5061/dryad.4g87s/6
title: Ungulates Detection Functions

description: File containing the Detection Functions produced in Distance 6.2 for banteng (A), wild pig (B), and muntjac (C) for line-transect data collected during 2014 in the Eastern Plains Landscape, Cambodia
DOI: 10.5061/dryad.4g87s/7
title: README

description: File describing the datasets accompanying the above publication
DOI: 10.5061/dryad.5770gm7/1
title: Data_and_code

description: To run the extinction models, first download the Stochastic Coextinction Model code from the Supplementary Information of Vieira and Almeida-Neto (2015) (see references). The script netcascade (April 2014).R is required for the analyses in this paper.

The supplementary information contains three scripts:
1. Main.R – This script runs simulations on the 8 networks to calculate PE, SE and VE for each species in each network.
2. IterativeNodeDeletion.R – A wrapper around netcascade (April 2014).R that calls netcascade() repeatedly to iteratively remove species from the network.
3. IterNodeDelMultiSim.R – A wrapper around IterativeNodeDeletion.R that runs IterativeNodeDeletion() multiple times to account for the stochasticity in the netcascade() algorithm.

And four datasets:
1. data/rvalues.csv – The expert-assigned dependency categories for each plant species in each network used to determine R values
2. data/webs – Folder containing the 8 interaction matrices 
3. data/phylogeny - contains (1) a set of 1000 phylogenies for the 13 Caribbean hummingbird species that were analysed (Caribbean_Phylogenies_.nex), (2) the maximum clade credibility (MCC) phylogeny (Caribbean_MCC_Phylogeny.nex)
4. data/traits - species-level data for body mass and bill length

If you use the extinction modelling code please cite the following two papers: 
1. Dalsgaard et al. (in press) Trait evolution, resource specialisation and vulnerability to plant extinctions among Antillean hummingbirds. Proceedings of the Royal Society B.
2. Vieira, M.C. and Almeida‐Neto, M., 2015. A simple stochastic model for complex coextinctions in mutualistic networks: robustness decreases with connectance. Ecology Letters, 18(2), pp.144-152. doi: 10.1111/ele.12394

If you use the data please cite:
Dalsgaard et al. (in press) Trait evolution, resource specialisation and vulnerability to plant extinctions among Antillean hummingbirds. Proceedings of the Royal Society B.

References:
Vieira, M.C. and Almeida‐Neto, M., 2015. A simple stochastic model for complex coextinctions in mutualistic networks: robustness decreases with connectance. Ecology Letters, 18(2), pp.144-152. doi: 10.1111/ele.12394
DOI: 10.5061/dryad.6d29p1h/1
title: R code for three-dimensional response surfaces

description: Sample R code for producing response surfaces representing the extent of forest cover along gradients of feedback strength and recovery time for a given rate of high-severity fire
DOI: 10.5061/dryad.6fb64/1
title: Zip file with 15 xml files used as input for 15 Beast analyses of ND2 data

description: Beast xml input files: ND2 alignments with models from Partition Finder for 15 species/species complex
DOI: 10.5061/dryad.6fb64/2
title: Zip file with 4 tree files used as input for CODEML branch- and branch-and-site models

description: Input trees for CODEML branch- and branch-and-site models for testing for signatures of parallel selection in mitolineages of different species co-occurring in four climate categories: regions that are least temperate, most temperate, least arid and most arid.
DOI: 10.5061/dryad.6fb64/3
title: Zip with 2 files: whole mitogenome alignment in nexus format and phylogenetic tree

description: Two files: (1) whole mitogenome alignment in nexus format  used for MrBayes phylogenetic analysis (rooted with lyrebird and partitioned as per PartitionFinder results), and (2) the 50% majority rule tree resulting from MrBayes analysis.
DOI: 10.5061/dryad.6fb64/4
title: Nexus alignment of 3796 codons for 13 mitochondrial coding genes

description: Coding gene alignment (11,388 nucleotides, 41 individuals) used for selection analyses, in nexus format
DOI: 10.5061/dryad.6vc12/1
title: RSucc & LoadLightening dataset 2018 GuindreParker&Rubenstein
DOI: 10.5061/dryad.7gt44/1
title: F-Benedectin-Benedectin-Index to Benedecting Document

description: Index to fiches obtained from FDA.
DOI: 10.5061/dryad.7q7k1/1
title: Arkansas 2016 and California 2014-15 R object

description: R object for Arkansas 2016 and California 2014-2015 Seasons in "tidy" format. That is, each variable is a column and each row corresponds to a single observation. This can be used directly with the R scripts in the github repo: https://github.com/bulksoil/LifeCycleManuscript
DOI: 10.5061/dryad.85n4k/1
title: heterozygosity-fitness

description: the file contains Standardized multilocus heterozygosity calculated at 37 putatively neutral markers as well as at 6 MHC-linked markers and fitness data of 147 male Alpine ibex of Gran Paradiso National Park (Italy). 
Please note that fitness data were only available for a subset of the genotyped individuals. 
The heterozygosity-fitness correlations were therefore based only on 147 out of the 247 individuals in file "genotypes_PNGP". 
The full dataset was however used for the calculations of diversity measures and also for the Standardized multilocus heterozygosity that was calculated for each individual as the ratio of its heterozygosity to the mean heterozygosity in the population of the loci at which the individual was genotyped (Coltman et al., 1999).
DOI: 10.5061/dryad.85n4k/2
title: genotypes_PNGP

description: The file contains microsatellite genotype data. 6 MHC-linked and 37 putatively neutral markers.
DOI: 10.5061/dryad.864rv/1
title: Labrador Atlantic Salmon Sequenced Microsatellite Data

description: Genepop file of sequenced microsatellite genotype data for 35 salmon populations in Labrador Canada.
DOI: 10.5061/dryad.9j0ks22/3
title: LynxData
DOI: 10.5061/dryad.9j0ks22/4
title: DeerMortalityData

description: This table contains the mortality data of 65 collared deer used to build the cox proportional hazard model in Gehr et al. 2018 (Behavioral Ecology). The column nr_days refers to the number of days a deer was monitored whereas entry_day and exit_day refer to the day the animal entered or left the study relative to the starting date of the study (30 November 2011). Fate refers to the fate of the animal (1 indicates died of non-lynx related causes, 0 indicates either alive at the end of monitoring or killed by lynx). Mort_cause refers to the cause of mortality. The code for mortalities: 2=disease/starvation, 3=road kill, 6=lynx kill, 7=dog kill, 10=hunting, 11=unknown. Human_risk refers to the mean human disturbance index value for all locations for each deer (composite of house density and distance to the closes road). Mean alti refers to the mean altitude of all locations for each deer. Mean_pr refers to the mean predation risk value (based on a lynx resource selection function) of all locations of each deer. Human_risk, mean_alti and mean_pr need to be scaled (mean=0 and SD=1) for the survival model.
DOI: 10.5061/dryad.9j0ks22/5
title: PredRisk_RandomLynxData

description: This table contains the predations risk values (based on a lynx resource selection function) of the 41569 random locations drawn within lynx home ranges used in Gehr et al. 2018 (Behavioral Ecology). Predation risk was calculated for midnight. For information on the raw data or for R-code used to calculate the predation risk please contact the data owner.
DOI: 10.5061/dryad.9j0ks22/6
title: PredRisk_LynxData

description: This table contains the predations risk values (based on a lynx resource selection function) of the 5487 lynx locations that occurred during the night (sun angle &lt;=0) used in Gehr et al. 2018 (Behavioral Ecology). For information on the raw data or for R-code used to calculate the predation risk please contact the data owner.
DOI: 10.5061/dryad.9j0ks22/7
title: PredRisk_KillData

description: This table contains the predations risk values (based on a lynx resource selection function) of the 199 lynx killed roe deer used in Gehr et al. 2018 (Behavioral Ecology). As time of kill was unknown the predation risk values were calculated for midnight. For information on the raw data or for R-code used to calculate the predation risk please contact the data owner.
DOI: 10.5061/dryad.dp0fc/1
title: Perez-Rodriguez et al. 2018. Ecography. DATASET

description: Excel file with data of parasite prevalence per sampling site, plus the climatic and habitat structure metrics associated to each sampling site.
DOI: 10.5061/dryad.f0h35.1/1.1
title: Ocurrence of consumer-resource interactions from the persistence matrix

description: The matrix's columns represent resources, and rows represent consumers. The number indicates the persistence of the interactions, from less to more persistent (0 to 10). Total number of sample replicates was 10.
DOI: 10.5061/dryad.f0h35.2
title: Data from: High temporal variability in the occurrence of consumer–resource interactions in ecological networks
DOI: 10.5061/dryad.f0h35.2/1.2
title: Persistence of consumer-resources interactions from the persistence matrix

description: The columns represent consumers and rows represent resources. Each cell represents the persistence of each trophic interaction.
DOI: 10.5061/dryad.h2j0n/1
title: Protea_Trait_Data

description: Trait data for all individuals used in this study.
DOI: 10.5061/dryad.h2j0n/2
title: ProteaPhylogenies

description: Phylogenetic trees used in this study, including species trees from ASTRAL-II, SVDquartets, and RAxML, as well as 100 bootstrap trees from ASTRAL-II. Trees may also be found in the repository Data from: Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.; Mitchell N, Lewis PO, Lemmon EM, Lemmon AR, Holsinger KE; Date Published: January 20, 2017; https://doi.org/10.5061/dryad.vj32s
DOI: 10.5061/dryad.jh3kk/7
title: Data files for chloroplast haplotype analysis
DOI: 10.5061/dryad.k2611/1
title: Data for age related difference in each index

description: Data for age, body height weight, TUG time, and STS parameters.
DOI: 10.5061/dryad.k2611/2
title: Data for test-retest reliability

description: Data for test-retest reliability in young participants.
DOI: 10.5061/dryad.k2611/3
title: Data for agreement

description: Data for agreement between Wii balance board and laboratory graded force plate.
DOI: 10.5061/dryad.n925d21/1
title: JEB-2017-00575_main_data
DOI: 10.5061/dryad.n925d21/2
title: JEB-2017-00575_suppmat_data
DOI: 10.5061/dryad.p412r16/2
title: SI2

description: Appendix SI2 Number of DNA sequences ascribed to each plant taxonomic group for hoverflies caught at four grasslands in west Wales between June 1 and July 15 2014 (for location codes, see SI1).  Each sample has a site code, followed by E (early) or L (late), and the species name and sex.
DOI: 10.5061/dryad.q00k37c/1
title: The genotypes from 55,266 SNP scored in 1,210 cattle

description: This file contains the genotypes from 55,266 SNP markers scored in 1,210 cattle. Samples were genotyped with the Illumina BovineSNP50 BeadChip version 1 and version 2. Genotypes were called using GenomeStudio.
DOI: 10.5061/dryad.s59v1/1
title: Data_S1

description: Accession numbers, isolate name, host of origin, and data on the year and geographical location (country) of collection of the samples that led to the Rabies virus sequences utilized in the work. Values and reference work of all host expected heterozygosity data used in the work.
DOI: 10.5061/dryad.s59v1/2
title: Rabies_ALL_SPECIES_N.FULL.DATED

description: Alignment of the Rabies virus N gene sequences used in the study in nexus format.
DOI: 10.5061/dryad.s59v1/3
title: Rabies_ALL_SPECIES_G.FULL.DATED

description: Alignment of Rabies virus G gene sequences used in the work in nexus format
DOI: 10.5061/dryad.sp54s/1
title: Genotypes_adults

description: Genotypes of adult individuals.
DOI: 10.5061/dryad.sp54s/2
title: significant association index

description: List of significant association index
DOI: 10.5061/dryad.t1715/2
title: Lepidopteran herbivores collected from Phytolacca americana from Michigan to Florida
DOI: 10.5061/dryad.t1715/3
title: Palatability of Phytolacca americana from Michigan to Florida in lab
DOI: 10.17632/4p8yn2rrh8.1
title: Data for: A novel dynamic hypersphere based support vector data description and its application to batch process monitoring

description: Pensim data is the test data of semiconductor etch process in manuscript.; Machine Data is the test data of fed-batch penicillin fermentation process in manuscript.
DOI: 10.5061/dryad.15r51.1/2.1
title: Skull measurements for measurement error

description: Repeated skull measurements from X-ray images on 10 individuals used to calculate the technical measurement error
DOI: 10.5061/dryad.19nr2/3
title: Historical evolution of ACS literature

description: Genesis and evolution of the science of agent-based complex systems seen from the perspective of its citation network from 1990 to January 2016. The dynamic graph shows the temporal dynamics of the agent-based modeling (blue vertices) and individual-based modeling (red vertices) corpora. Vertices are positioned based on the ForceAtlas2 layout algorithm without vertex overlapping. The video uploaded here is a high-resolution version of the one provided alongside the manuscript.
DOI: 10.5061/dryad.19nr2/4
title: Bibliographic Dataset

description: Bibliographic dataset compiling all Scopus records relevant to Agent-based Complex Systems (ACS) science (i.e. the fields of agent-based and individual-based modelling). This dataset was post-processed and used to create a citation graph using the Diderot R package (https://cran.r-project.org/package=Diderot).
DOI: 10.5061/dryad.2fk71/10
title: Data.zip, Part 9 of 31
DOI: 10.5061/dryad.2fk71/3
title: Data.zip, Part 2 of 31
DOI: 10.5061/dryad.2fk71/4
title: Data.zip, Part 3 of 31
DOI: 10.5061/dryad.2fk71/5
title: Data.zip, Part 4 of 31
DOI: 10.5061/dryad.2fk71/6
title: Data.zip, Part 5 of 31
DOI: 10.5061/dryad.2fk71/7
title: Data.zip, Part 6 of 31
DOI: 10.5061/dryad.2fk71/8
title: Data.zip, Part 7 of 31
DOI: 10.5061/dryad.2fk71/9
title: Data.zip, Part 8 of 31
DOI: 10.5061/dryad.5dd92/1
title: Sequencing images. imaging field 1, part 1 of 3

description: Sequencing images. imaging field 1, part 1 of 3
DOI: 10.5061/dryad.5dd92/2
title: Sequencing images. imaging field 1, part 2 of 3

description: Sequencing images. imaging field 1, part 2of 3
DOI: 10.5061/dryad.5dd92/3
title: Sequencing images. imaging field 1, part 3 of 3

description: Sequencing images. imaging field 1, part 3 of 3
DOI: 10.5061/dryad.6k1s9d4/1
title: Alignments of phased Sanger data

description: Sample codes follow the main text. "a" and "b" refer to reconstructed alleles. Numbers preceded by the caret symbol refer to assignments to a priori groupings used by BPP.
DOI: 10.5061/dryad.6k1s9d4/2
title: Alignments of unphased Sanger data

description: Sample codes follow the main text. Numbers preceded by the caret symbol refer to assignments to a priori groupings used by BPP.
DOI: 10.5061/dryad.6k1s9d4/3
title: Floral morphometric data

description: Sample codes give the herbarium (Index Herbariorum codes), collector, and collector number. Floral number is sequential where multiple flowers were available on a specimen. For area codes, refer to text. All units are in centimeters except Floral length/width and Zygomorphy, which are unitless ratios.
DOI: 10.5061/dryad.6k1s9d4/4
title: Leaf landmark data

description: The landmark file is in TPS format. Sample codes give the herbarium (Index Herbariorum codes), collector, and collector number. For area codes in the classifier file, refer to text.
DOI: 10.5061/dryad.7q7k1/2
title: California 2016 R object.

description: R object containing the data for the California 2016 season in "tidy" format.
DOI: 10.5061/dryad.7q7k1/3
title: OTU Table Clustered at 97% for all samples

description: A gzipped tab separated file. The OTU identifiers are in the column 'OTUID'. This is a matrix where each row represents one OTU and each column represents one sample (corresponding to "SampleID" in the mapping file). The data can be unzipped in the UNIX/LINUX terminal using the command 'gunzip lc_study_otu_table.tsv.gz'
DOI: 10.5061/dryad.7q7k1/4
title: Sample Metadata

description: A tab separated file with information about the samples in the OTU table.
DOI: 10.5061/dryad.7q7k1/5
title: R object containing taxonomic information for each OTU

description: This is an R object (.rds file) containing the taxonomic information for all possible OTUs detected in this dataset. These are the GreenGenes 13_8 97% reference OTUs.
DOI: 10.5061/dryad.7q7k1/6
title: Organellar OTUs

description: R object (.rds file) containing all of the detected mitochondrial and plastid OTUs from the Greengenes 13_8 reference database.
DOI: 10.5061/dryad.82600/2
title: Original data for figures in the manuscript

description: The zip file includes the original data of Figures from Fig.1 to Fig 8, SFig.1 to SFig.7.
The files can be accessed by common softwares such as origin edit software, Jade 5.0 for XRD, NOVAWIN for N2 adsorption/desorption isotherms, PEAK 4.1 for XPS, EC-LAB and Landt programs for electrochemical data.
DOI: 10.5061/dryad.8310n/1
title: Taylor et al - Inhaler inhalation audio and flow data

description: The .mat file contains data in the form of a 287x4 cell matrix. Each row corresponds to a different inhaler inhalation recording. Column 1 contains the anonymized participant numbers, Column 2 contains the inspiratory flow range group to which each recording belongs to. Details of this labeling is given in the manuscript. Column 3 contains the inhalation flow signals and Column 4 contains the acoustic envelope signals from the inhalation audio recordings. Signals are low pass filtered below 4Hz. Moving average filter not applied to acoustic envelope signals until after flow estimation.
DOI: 10.5061/dryad.84827/1
title: Table S1

description: Excel spreadsheet of unique disulphides in a culled set of X-ray structures described by G. Wang and R. Dunbrack, Jr. (file pdbaanr).
DOI: 10.5061/dryad.84827/2
title: Table S2

description: Excel spreadsheet of labile disulphide bonds present in some molecules of a protein crystal but absent in others (same PDB, sheet 1), or present in some structures of a protein but absent in others (different PDB, sheet 2).
DOI: 10.5061/dryad.85n4k/3
title: heterozygosity-IKC

description: The file contains individual kerato conjunctivitis dataset.
DOI: 10.5061/dryad.d4q54/1
title: Data Analysis R script

description: R script containing data formatting, and models for analysis of experiment 1 and experiment 2 data