cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m5d8f45/2
title: peromyscus trap entry

description: Trap-entry times for Peromyscus leucopus collected over one 4-night trapping session during spring 2017, and two 4-night trapping sessions during fall 2017. Mice were trapped in plots invaded by buckthorn (Rhamnus cathartica) and plots with buckthorn removed.
DOI: 10.5061/dryad.rg5s170/1
title: supplemental files

description: This compressed file contains all trees and data used in the manuscript. It includes scripts used to perform all primary analyses. It includes a readme.txt file that provides a short description of all files included.
DOI: 10.5061/dryad.rp5ht80/1
title: RawData_for_Bairos-Novak_et_al

description: The raw data in an Excel spreadsheet used in the R analysis. See the 'metadata' tab of the spreadsheet for more information.
DOI: 10.5061/dryad.rp5ht80/2
title: R_Script_for_Bairos-Novak_et_al

description: The R programming language script used for loading, analyzing, and plotting the data. See the comments throughout the script for more information (lines preceeded by '#').
DOI: 10.5061/dryad.rt679ng/1
title: Data list for JAGS model: SJ transects

description: List (R data structure) of data required to parameterize the Bayesian model detailed in Appendix A2 with the San Juans elevational transects. Includes species occurrences, trap-level covariates, site-level covariates, and other objects in Appendix A2. Loading the file in R with `SJ.ls
DOI: 10.5061/dryad.rt679ng/2
title: Data list for JAGS model: Front Range transects, shared species

description: List (R data structure) of data required to predict occurrences and richness along the two Front Range transects with only species detected in both the Front Range and the San Juan range, using a model parameterized with the San Juan range. Loading the file in R with `FR.shared.ls
DOI: 10.5061/dryad.sc673ds/1
title: Marine environmental DNA biomonitoring reveals seasonal patterns in biodiversity and identifies ecosystem responses to anomalous climatic events

description: Unique DNA sequences obtained from IMOS zooplankton samples, using eight different metabarcoding assays, taken from Rottnest Island Western Australian on 55 occasions over five years.
DOI: 10.5061/dryad.t76fk80.2
title: Data from: Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences
DOI: 10.5061/dryad.t76fk80.2/10.2
title: Supplementary file - settings files for demographic inferences
DOI: 10.5061/dryad.t76fk80.2/11.2
title: si_files_SA.tar

description: SLiM simulations
DOI: 10.5061/dryad.t76fk80.2/12.2
title: figures_DAFi_RScripts
DOI: 10.5061/dryad.t76fk80.2/15.2
title: 1000G_genot-table

description: Contains as a compressed file the genotype table with annotation for 1000G data. Please see the README file for further description and information on how to make the figures. Author: Fanny Pouyet
DOI: 10.5061/dryad.t76fk80.2/18.2
title: Main README

description: This dryad page provides the data and the source code for the figures in " Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences " by Pouyet F,* Aeschbacher S*, Thiery A and Excoffier L. 
* first co-authors 

It contains as compressed files: 
-- 1 -- Genotype tables and annotations from 1000G and SGDP data 1000G_genot-table.zip SGDP_genotypetable-annotation.zip with README files that describe the data and how to use them.   
-- 2 -- the R scripts to perform the figures of INDA figures_INDA_Rscripts.zip  
-- 3 -- the confidence intervals of the estimates as well as the source code to estimate them confidenceIntervals.zip  
-- 4 -- the scripts (R and python) to make the SFS figures as well as estimate confidence intervals and compute the SFS figures_data_SFS_Rscripts.zip  
-- 5 -- the setting parameters for FastSimCoal demographic inferences Supplementary file - settings files for demographi ...  
-- 6 -- the scripts for SLiM simulations and analyses (bash and R code) + a table with parameters used in the SLiM simulations (.csv) + the scripts and raw data that I used to make the figures (.txt and .R) si_files_SA.tar.gz 

Extra READMEs describe the files and how to launch them to compute the statistics or to make the figures.
DOI: 10.5061/dryad.t76fk80.2/6.2
title: SGDP_genotypetable-annotation

description: It contains as compressed files:
 
 - Genotype tables and annotations from SGDP see the file README_columns genotypeTables
 
 README files describe the files and how to launch them.
DOI: 10.5061/dryad.t76fk80.2/8.2
title: confidence Intervals

description: Files with 95% CI
DOI: 10.5061/dryad.v7k3140/15
title: p300 ChIP-seq peaks using uni- and multi-reads

description: ChIP-seq peaks detected following the standard ChIP-seq data processing pipeline of ENCODE (The ENCODE Project Consortium, 2012) using both uni-reads and multi-reads aligned by Permseq (Zeng et al., 2015) for p300.
DOI: 10.5061/dryad.v7k3140/16
title: p65 ChIP-seq peaks using uni- and multi-reads

description: ChIP-seq peaks detected following the standard ChIP-seq data processing pipeline of ENCODE (The ENCODE Project Consortium, 2012) using both uni-reads and multi-reads aligned by Permseq (Zeng et al., 2015) for P65.
DOI: 10.5061/dryad.v7k3140/17
title: PolII ChIP-seq peaks using uni- and multi-reads

description: ChIP-seq peaks detected following the standard ChIP-seq data processing pipeline of ENCODE (The ENCODE Project Consortium, 2012) using both uni-reads and multi-reads aligned by Permseq (Zeng et al., 2015) for PolII.
DOI: 10.5061/dryad.v7k3140/18
title: H3K4me1 ChIP-seq peaks using uni- and multi-reads

description: ChIP-seq peaks detected following the standard ChIP-seq data processing pipeline of ENCODE (The ENCODE Project Consortium, 2012) using both uni-reads and multi-reads aligned by Permseq (Zeng et al., 2015) for H3K4me1.
DOI: 10.5061/dryad.v7k3140/19
title: CTCF ChIP-seq peaks using uni- and multi-reads

description: ChIP-seq peaks detected following the standard ChIP-seq data processing pipeline of ENCODE (The ENCODE Project Consortium, 2012) using both uni-reads and multi-reads aligned by Permseq (Zeng et al., 2015) for CTCF.
DOI: 10.5061/dryad.v7k3140/20
title: H3K4me3 ChIP-seq peaks using uni- and multi-reads

description: ChIP-seq peaks detected following the standard ChIP-seq data processing pipeline of ENCODE (The ENCODE Project Consortium, 2012) using both uni-reads and multi-reads aligned by Permseq (Zeng et al., 2015) for H3K4me3.
DOI: 10.5061/dryad.v7k3140/21
title: H3K27ac ChIP-seq peaks using uni- and multi-reads

description: ChIP-seq peaks detected following the standard ChIP-seq data processing pipeline of ENCODE (The ENCODE Project Consortium, 2012) using both uni-reads and multi-reads aligned by Permseq (Zeng et al., 2015) for H3K27ac.
DOI: 10.5061/dryad.v7k3140/22
title: H3K27me3 ChIP-seq peaks using uni- and multi-reads

description: ChIP-seq peaks detected following the standard ChIP-seq data processing pipeline of ENCODE (The ENCODE Project Consortium, 2012) using both uni-reads and multi-reads aligned by Permseq (Zeng et al., 2015) for H3K27me3.
DOI: 10.5061/dryad.v7k3140/23
title: H3K36me3 ChIP-seq peaks using uni- and multi-reads

description: ChIP-seq peaks detected following the standard ChIP-seq data processing pipeline of ENCODE (The ENCODE Project Consortium, 2012) using both uni-reads and multi-reads aligned by Permseq (Zeng et al., 2015) for H3K36me3.
DOI: 10.17632/f274ywygj6.1
title: Data for: The elemental and isotopic inventory of lithium in hot and dry rhyolites

description: Li concentrations and isotope composition in glass and mineral phases in a rhyolite
DOI: 10.17632/g65nd97vjm.1
title: Data for: Liquid Assisted Grain Growth in Solution Processed Cu(In,Ga)(S,Se)2

description: Raw and .csv for XRD scans Excel spreadsheets for grain size distributions and histograms Time/temp dependent grain sizes for kinetic fitting (.csv)
DOI: 10.17632/mcpg4krt2z.1
title: Data for: Trions and biexcitons in ZnO/ZnMgO, CdSe/ZnS and CdSe/CdS core/shell nanowires
DOI: 10.17632/t9j2kzw3bg.1
title: Data for: Solidification path and microstructure evolution of a Mg-3Al-14La alloy: implications for the Mg-rich corner of the Mg-Al-La phase diagram

description: This is the video of the in-situ synchrotron observation of alloy Mg-3Al-14La as it is melted and is re-solidified.
DOI: 10.5061/dryad.2h0k50s/24
title: Measurements of Specimens of Poecilia butleri
DOI: 10.5061/dryad.2h0k50s/25
title: Measurements of Specimens of Poecilia chica
DOI: 10.5061/dryad.2h0k50s/26
title: Measurements of Specimens of Poecilia gilli
DOI: 10.5061/dryad.2h0k50s/27
title: Measurements of Specimens of Poecilia hondurensis
DOI: 10.5061/dryad.2h0k50s/28
title: Measurements of Specimens of Poecilia latipinna
DOI: 10.5061/dryad.2h0k50s/29
title: Measurements of Specimens of Poecilia latipunctata
DOI: 10.5061/dryad.2h0k50s/30
title: Measurements of Specimens of Poecilia limantouri
DOI: 10.5061/dryad.2h0k50s/31
title: Measurements of Specimens of Poecilia mexicana
DOI: 10.5061/dryad.2h0k50s/32
title: Measurements of Specimens of Poecilia orri
DOI: 10.5061/dryad.2kc5rh0/1
title: Genepop_2016samples_allages

description: Genotypes at 95 selected loci for all samples collected in 2016 from southern Newfoundland (Yoy - Smolt).
DOI: 10.5061/dryad.2kc5rh0/2
title: FieldAges_1516

description: All individuals (age Yoy to 2+) sampled from southern Newfoundland, by age.
DOI: 10.5061/dryad.44v7p60/1
title: Mammal_roads_SAFEproject_2016

description: File contains: Information on the small mammals caught, location, distance from the edge, morphometric information.
DOI: 10.5061/dryad.47j2q8b/1
title: Data

description: collected 2017/2018 at the German Primate Center.
DOI: 10.5061/dryad.4h16331/2
title: offspring development

description: measurements of lesser black backed gull offspring body mass used to calculate body condition index
DOI: 10.5061/dryad.4h98fq7/1
title: ToE_analysis_results

description: Results from the time of emergence (ToE) analysis for 77 migratory bird species by week (see Fig. 6).  The field Class identifies the three classes of species considered in the analysis.  The fields with U and L identify the upper and lower limits of the 95% confidence bands for each metric.
DOI: 10.5061/dryad.5vn554c/1
title: Data S1 - Beetle species

description: Dung beetles caught in baited pitfall traps at each study site
during 2014-15 field survey. The most common species (Onthophagus taurus, Onthophagus nuchicornis, Aphodius pseudolividus) were chosen to use in laboratory experiments.
DOI: 10.5061/dryad.5vn554c/2
title: Data_S2 Soil Properties

description: Soil Properties. Results of soil chemical/physical properties from soil sampling at each study site during 2014-15 field survey.
DOI: 10.5061/dryad.5vn554c/3
title: Data_S3 Grassland Cover

description: Percept grazeable grassland cover around each sampling location with spatial location (county-level) at each study site during 2014-15 field survey.
DOI: 10.5061/dryad.60k13v2/1
title: Mesopygeum_6seqs_Sep18 (nuclear + chloroplast)

description: Mesopygeum nuclear and chloroplast datasets, 77 samples
DOI: 10.5061/dryad.60k13v2/2
title: Mesopygeum  chloroplast datasets, 77 samples

description: Mesopygeum  chloroplast datasets, 77 samples
DOI: 10.5061/dryad.60k13v2/3
title: Mesopygeum nuclear datasets, 77 samples

description: Mesopygeum  nuclear datasets, 77 samples
DOI: 10.5061/dryad.6v1r5n8.1
title: Data from: Molecular characterization of aldehydes and ketones in particle phase of mainstream and sidestream cigarette smoke
DOI: 10.5061/dryad.6v1r5n8.2
title: Data from: Molecular characterization of aldehydes and ketones in particle phase of mainstream and sidestream cigarette smoke
DOI: 10.5061/dryad.6v1r5n8.2/1.2
title: Raw data of GCMS, Orbitrap MS and FT-ICR MS

description: The Raw data of GCMS, Orbitrap MS and FT-ICR MS
DOI: 10.5061/dryad.6v1r5n8.2/2.2
title: FT-ICR MS and Orbitrap MS data in Excel format
DOI: 10.5061/dryad.72db024/1
title: Data from Figure 2

description: PBMC cultured with or without digoxin, stimulated with BRSV or pokeweed mitogen.  Data correspond to Figure 2 in manuscript.
DOI: 10.5061/dryad.72db024/2
title: Data from Figure 1

description: Digoxin concentrations in serum.  Data correspond to Figure 1 in manuscript.
DOI: 10.5061/dryad.72db024/3
title: Data from Figure 3 - clinical scores

description: Calves were scored daily based on clinical signs (fever, cough, respiratory rate, etc.). Data correspond to Figure 3A in the manuscript.
DOI: 10.5061/dryad.72db024/4
title: Data from Figure 4

description: NS2 copy numbers in the lungs of calves on day 10.  Corresponds to Figure 4 in the manuscript.
DOI: 10.5061/dryad.766m402/1
title: data_check_TED_structure_groups

description: Raw AFLP scoring data
DOI: 10.5061/dryad.7h46hg2/1
title: Dataset_S1

description: Read alignments and deep-sequence phylogenies for individuals in the same potential transmission network in the population-based sample from Rakai, Uganda. The data can be used to reconstruct potential transmission networks; see the vignette at https://olli0601.github.io/Phyloscanner.R.utilities/index.html
DOI: 10.5061/dryad.7h46hg2/2
title: Dataset_S2

description: Individual-level meta-data on sequenced individuals. Gender and sequence sampling date (randomised to +- a few weeks) are publicly available. The data are useful to interpret reconstructed transmission networks; please see the vignettes at https://olli0601.github.io/Phyloscanner.R.utilities/index.html
DOI: 10.5061/dryad.7h46hg2/3
title: Dataset_S3

description: Epidemiologic evidence on the direction of transmission. The data can be used to validate phylogenetic inferences into the direction of transmission; please see the vignettes at https://olli0601.github.io/Phyloscanner.R.utilities/index.html
DOI: 10.5061/dryad.7h46hg2/4
title: Demo_Rakai

description: Preprocessed pairwise phylogenetic relationships. The data are provided for convenience to bypass computer-intensive calculations, and can be used to plot and assess phylogenetically reconstructed transmission networks; please see the vignettes at https://olli0601.github.io/Phyloscanner.R.utilities/index.html
DOI: 10.5061/dryad.8m40rb0/1
title: Data from: Tracking the temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages, Lamiaceae) across continents: leveraging Anchored Hybrid Enrichment and targeted sequence data

description: This folder includes the data and scripts to reproduce the analysis in this paper. The README file inside describes the files.
DOI: 10.5061/dryad.99k4n5s/2
title: Data fro variance-mean experiment

description: This includes data on population dynamics of host and parasite described in the variance-mean treatment in the manuscript.
DOI: 10.5061/dryad.99k4n5s/3
title: Post epidemic infection essay

description: This essay tested for selection in infection susceptibility of Daphnia hosts after the mean-variance treatment.
DOI: 10.5061/dryad.b4f2m1t/1
title: Dryad Exp 1 Zhou et al

description: Results of Experiment 1, examining the effects of playback of noise of different amplitudes on the response to aerial alarm calls. The noise overlapped the frequency of the alarm calls (6–10 kHz; alarm call peak frequency mean 9.1 kHz). Noise amplitudes ranged from 52–61 dB at 10 m, while alarm calls were broadcast at 52 dB at 10 m. Each location received a unique set of every type of playback. Playbacks included alarm calls mixed with noise, and control playbacks of noise alone or alarm calls alone. The amplitude of ambient noise was measured after each playback.
DOI: 10.5061/dryad.b4f2m1t/2
title: Dryad Exp 2 Zhou et al

description: Data for Experiment 2, examining the effect of noise of different frequencies, but constant amplitude (58 dB at 10 m), on the response to aerial alarm calls (52 dB at 10 m). Alarm calls have a mean peak frequency of c 9.1 kHz. Noise was of a frequency that either overlapped with the alarm calls (6–10 kHz) or did not overlap the alarm calls (2–6 kHz). The data also include the proportion of time the focal bird had its head up in the 10 s of noise immediately before the alarm call. Each location received a unique set of every playback type. Playbacks included alarm calls mixed with noise, and control playbacks of noise alone or alarm calls alone. The amplitude of ambient noise was recorded after each playback.
DOI: 10.5061/dryad.cj62621/10
title: R syntax

description: The file that are used by [prediction.R].
DOI: 10.5061/dryad.cj62621/11
title: R syntax to condcut prediction

description: R syntax to condcut prediction based on the posterior distribution of model parameter [mcmc_result.csv].
DOI: 10.5061/dryad.cj62621/3
title: Data file

description: This is the long format that each row is a participant.
DOI: 10.5061/dryad.cj62621/4
title: Data file

description: This is the format that each row is a participant for each round.
DOI: 10.5061/dryad.cj62621/5
title: Influenza surveillance data

description: The influenza proxy used in the analysis.
DOI: 10.5061/dryad.cj62621/6
title: Data file

description: This file contains information on the baseline titer distribution.
DOI: 10.5061/dryad.cj62621/7
title: Data file (MCMC result)

description: The mcmc result for the manuscript.
DOI: 10.5061/dryad.cj62621/8
title: R syntax to fit the digraph model

description: R syntax to fit the digraph model on the household data. This will create a data file [mcmc_result.csv] for further analysis. Noted that Supplementary Table 5 was also generated from this file.
DOI: 10.5061/dryad.cj62621/9
title: R syntax

description: The file that are used by [indirect_benefit_main.r].
DOI: 10.5061/dryad.hh37793/1
title: Figure1_b-c.tar

description: This .tar.gz file is a compressed folder that contains all of the unprocessed data of Figure 1b and Figure 1c
DOI: 10.5061/dryad.hh37793/2
title: Figure1_d.tar

description: This .tar.gz file is a compressed folder that contains all of the unprocessed data of Figure 1d
DOI: 10.5061/dryad.hh37793/3
title: Figure1_e.tar

description: This .tar.gz file is a compressed folder that contains all of the unprocessed data of Figure 1e
DOI: 10.5061/dryad.hh37793/4
title: Figure2_b.tar

description: This .tar.gz file is a compressed folder that contains all of the unprocessed data of Figure 2b
DOI: 10.5061/dryad.hk81qh1/1
title: Turbill.Stojanovski_data

description: Data from experiment testing for effects of manipulation of perceived predation risk on foraging effort and regulation of body temperature by house mice.
DOI: 10.5061/dryad.j6f4858/1
title: Observed nest occupancy, success and number of fledged young for osprey during 1973-2012

description: Nest occupancy, success and number of fledged young for osprey in Voyageurs National Park observed during 1973-2012 from aerial surveys. Predictors associated with each nest include descriptors for weather, ice-out dates, nest and foraging habitat, fish resources and various measures of potential intraguild predation and competition from bald eagles.
DOI: 10.5061/dryad.j6f4858/2
title: Heronry occupancy and number of nests of great blue herons observed during 1973-2012

description: Heronry occupancy and number of nests of great blue herons in Voyageurs National Park observed during 1973-2012 from aerial surveys. Predictors associated with each heronry include descriptors for nesting and foraging habitat, fish resources and various measures of potential intraguild predation and competition from bald eagles and osprey.
DOI: 10.5061/dryad.qq340d4/1
title: Le_Roux_et_al_2019_ECOGRAPHY_42(1-10)

description: See txt file
DOI: 10.5061/dryad.rt679ng/3
title: Data list for JAGS model: Front Range transects, all species

description: List (R data structure) of data required to predict occurrences and richness along the two Front Range transects with all species detected in the Front Range, using a model parameterized with the San Juan range. This requires generating species-specific responses from the parameterized genus-level or family-level distributions. Loading the file in R with `FR.all.ls
DOI: 10.5061/dryad.t76fk80.2/1.2
title: regions.YRIrecomb1p5

description: Regions from hg19 with recombination rate above 1.5cM/Mb (using YRI recombination map - see the publication). Mutations in these regions that are GC-conservative (A to T, T to A, G to C
and C to G) can be considered as neutral for demographic inferences.
DOI: 10.5061/dryad.t76fk80.2/14.2
title: 1000G.extraData_distanceHotspotPhastcons

description: Annotations of distance to hotspots and distance to conserved elements (phastcons) in centimorgans for 1000G data.
DOI: 10.5061/dryad.t76fk80.2/16.2
title: 1000G_Nb_DerAll_byPop

description: Files from which the SFS are computed. Author:  Fanny Pouyet
DOI: 10.5061/dryad.v3539d2.2
title: Data from: Innate ability of goats to sense and avoid ingestion of noxious insects while feeding
DOI: 10.17632/53b9fcc8ph.1
title: Data for: A Calculator for Easy Estimation of coverage with shRNA, CRISPR, and cDNA libraries

description: User guide for the MALTA software, that calculates the number of picks required to cover a library of known content and abundance.
DOI: 10.17632/76bnbbhyfx.1
title: Data for: Microclimate Tourism and Microclimate Tourism Security & Safety in China

description: Researches Data in China was searched from CNKI Database through filling 气候，社会风气，微气候，旅游安全，气候安全into those searching conditions of theme, title, keywords. Researches Data out of China was searched from CNKI Foreign Research Database (data sources was generated from Taylor & Francis Journal Database 1940-now) through filling Climate，Social Climate，Microclimate，Tourism Security&Safety，Climate Security & Safetry into those searching conditions of theme, title, keywords.
DOI: 10.17632/8rd3rj9t6p.1
title: Data for: Microclimate Tourism and Microclimate Tourism Security & Safety in China

description: Researches Data in China was searched from CNKI Database through filling 气候，社会风气，微气候，旅游安全，气候安全into those searching conditions of theme, title, keywords. Researches Data out of China was searched from CNKI Foreign Research Database (data sources was generated from Taylor & Francis Journal Database 1940-now) through filling Climate，Social Climate，Microclimate，Tourism Security&Safety，Climate Security & Safety into those searching conditions of theme, title, keywords.
DOI: 10.17632/9vtrjgz2kz.1
title: Data for: Inventory Control with Flexible Demand: Cyclic Case with Multiple Batch Supply and Demand Processes

description: Problem instances considered in Section 6 of the paper
DOI: 10.17632/bpfm2znwht.1
title: Exchange Rate Dynamics
DOI: 10.17632/c9h6ry4vx5.1
title: Data for: A Calculator for Easy Estimation of coverage with shRNA, CRISPR, and cDNA libraries

description: This is a video that instructs how to use the MALTA software to calculate library coverage.
DOI: 10.17632/mk73djpcss.1
title: Data for: Multistage integrated water security assessment in a typical region of Northwestern China
DOI: 10.17632/mmyc6dg9xk.1
title: Data for: Decline of a once common carnivore linked to satellite-detected forest disturbance: the case for supportive space-based monitoring

description: Data associated with article "Satellite-detected forest disturbance forecasts American marten population decline: the case for supportive space-based monitoring". File DataDescription.csv contains descriptions of files and fields within files. File MartenSCRJAGS.txt provides pseudocode in BUGS language used for fitting model in JAGS.
DOI: 10.17632/s4vy6nxr5n.1
title: Data for: A new numerical simulator considering the effect of enhanced liquid on relative permeability

description: raw expeimental data
DOI: 10.5061/dryad.2h0k50s/33
title: Measurements of Specimens of Poecilia petenensis
DOI: 10.5061/dryad.2h0k50s/34
title: Measurements of Specimens of Poecilia salvatoris
DOI: 10.5061/dryad.2h0k50s/35
title: Measurements of Specimens of Poecilia sphenops
DOI: 10.5061/dryad.2h0k50s/36
title: Measurements of Specimens of Poecilia sulphuraria
DOI: 10.5061/dryad.2h0k50s/37
title: Measurements of Specimens of Poecilia velifera
DOI: 10.5061/dryad.2h0k50s/38
title: Measurements of Specimens of Poecilia vivipara
DOI: 10.5061/dryad.30kk201/1
title: CDI-data