cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v1q13/14
title: Time series data and melanistic morph analysis

description: This compressed directory contains four files relevant for the color (green vs. melanistic) morph time series analysis. The raw data is in 'Tcris_master_27.csv'. The associated R script 'bigMelanisticAnalysis.R' contains the code used to fit the Bayesian models for this data set and includes descriptions of relevant variables in the main data file. The JAGS models referenced in the R script are 'hiermod-refugio' and 'mod-hv'.
DOI: 10.5061/dryad.v1q13/15
title: Time series data and ARMA analyses

description: This compressed directory contains the data, models and scripts used for the ARMA model fits of the time series data for Timema cristiane (raw data = Tcris_master_26.csv, note the 2017 data are added to this in the R script), Geospiza fortis (fortis.csv), Geospiza scandens (scandens.csv), Panaxia dominula (data_medionigra.csv), and Biston betuleria (mothdat.csv). Except for the Timema data, these data were obtained from published studies (as described and documented in the paper), but are also included here for completeness. The main R script for fitting the ARMA models is 'predictingEvoAnalyses.R'. It relies on functions defined in 'predictingEvoFuncs.R', which are sourced at the beginning of the  'predictingEvoAnalyses.R' script. The individual JAGS models for the different ARMA models are defined in the 'dp-arma*model' text files, where * denotes the AR and MA lags.
DOI: 10.5061/dryad.v1q13/16
title: R workspace for mel-stripe selection experiment

description: This R workspace contains the results from fhaEcolSmel.R.
DOI: 10.5061/dryad.v1q13/17
title: Scripts and data for the linkage map

description: This compressed directory contains a series of perl sciprts and data files that we used to generate the linakge map for Timema cristinae. The specific steps we took, including some annotation/documentation of the scripts we used are in the README file. the offspringGenotype*txt data are included in a separate file.
DOI: 10.5061/dryad.v1q13/18
title: Genotype data for mapping families

description: This compressed directory contains the genotype data for the three mapping families (A, B, and C). These are required for the mapping scripts we also uploaded.
DOI: 10.5061/dryad.v1q13/9
title: Genotype estiamtes for FHA in 2013

description: Matrix of genotype estimates (mean of the posterior with genetoypes coded as 0, 1 or 2, but the mean being non-integer valued) for FHA in 2013. Rows denote SNPs and columns denote individuals. See scripts in melstripeSelectionFHA.tar.gz for details.
DOI: 10.5061/dryad.v5374/10
title: NG-6445_ED1110902_lib23171_1587_5

description: Sequence corresponding to 1D315
DOI: 10.5061/dryad.v5374/2
title: NG-6445_1a311001_lib23155_1575_6

description: Sequence corresponding to 1D0
DOI: 10.5061/dryad.v5374/3
title: NG-6445_1b311001_lib23156_1575_4

description: Sequence corresponding to 2D0
DOI: 10.5061/dryad.v5374/4
title: NG-6445_1c311101_lib23157_1575_4

description: Sequence corresponding to 3D0
DOI: 10.5061/dryad.v5374/5
title: NG-6445_1d311001_lib23158_1575_6

description: Sequence corresponding to 4D0
DOI: 10.5061/dryad.v5374/6
title: NG-6445_1e311001_lib23159_1553_6

description: Sequence corresponding to 5D0
DOI: 10.5061/dryad.v5374/7
title: NG-6445_1f311001_lib23160_1553_6

description: Sequence corresponding to 6M0
DOI: 10.5061/dryad.v5374/8
title: NG-6445_1g311001_lib23161_1553_6

description: Sequence corresponding to 7D0
DOI: 10.5061/dryad.v5374/9
title: NG-6445_1h311001_lib23162_1553_6

description: Sequence corresponding to 8D0
DOI: 10.17632/6wfnj5x4h9.1
title: Data for: Effect of Biochar on Fate and Transport of Manure-Borne Estrogens in Sandy Soil

description: Supplementary documents
DOI: 10.17632/ghhzw8ssv6.1
title: Data for: Time-resolved photoacoustic calorimetry of organometallic ligand substitution in alkane solvents: molybdenum-alkane sigma complex controls ultrafast ligand addition to molybdenum pentacarbonyl

description: Tables and plots photoacoustic calorimetry signal amplitudes and lifetimes, observed rate constants as a function of ligand concentrations for substitution with molybdenum hexacarbonyl in alkane solvents. Solvent include pentane, hexane, heptane, octane, decane and dodecane. Plots of PAC amplitudes as a function of solvent expansivity to determine reaction enthalpies and reaction volumes. Ligands include acetonitrile, triethylphosphine oxide, triethylphosphine, tetrahydrofuran, tetrahydrothiophene, pyridine, triethylphoshite, triethylphosphate, and 1-bromobutane.
DOI: 10.5061/dryad.2g2p0/1
title: Lonnell_Hylander_Envdata_JBiogeography2018

description: Environmental data and a species-by-site matrix. The excel-file also has meta-data in separate sheets.
DOI: 10.5061/dryad.4402t80/1
title: Experimental Data Set

description: Experimental data assessing whether breeding pairs can discriminate between different, commonly encountered species of territorial intruders (intruder). We were particularly interested in testing whether pairs responded more quickly (time) to the presence of species that pose a higher level of threat to their offspring or territory, as well as assessing their subsequent rate of aggression (responses) towards the different levels of threat.
DOI: 10.5061/dryad.4402t80/2
title: Obervational Data Set

description: Observational data of the behaviors (aggression and chases) of breeding pairs in their natural habitat to assess sex differences in their ability to adjust aggressive responses toward intruders. This also allowed us to compare the responses of breeding pairs with naturally occurring solitary parents (i.e. individuals who are looking after the brood on their own) to determine whether the latter can compensate for the loss of their mate, with regard to the quantity (aggression_no, chase_no and aggression) and quality (aggression_initiation, chase_initiation and chase_distance) of the care they provide.
DOI: 10.5061/dryad.4g048/2
title: Cleaned Assembly

description: The file contains the filtered de novo assembly (TPM &gt; 1) produced from the unmapped reads using Trinity. There are 45,142 contigs present.
DOI: 10.5061/dryad.4g048/3
title: Blast2GO Annotation file

description: This file contains the entire database created using Blast2GO to annotate all the contigs from the filtered unmapped reads assembly (Trinity_TPM1.fasta).
DOI: 10.5061/dryad.4g048/4
title: Blast2Go Annotations (Text format)

description: This file contains a summary of the annotation using Blast2GO in text format for all the contigs from the filtered unmapped reads assembly (Trinity_TPM1.fasta).
DOI: 10.5061/dryad.4g048/5
title: Expression Matrix

description: This spreadsheet contains the raw expression level (counts) in each of the 10 libraries analyzed for differential expression.  The first row lists the names of the 10 RNA-seq libraries (see 'Note' in README). Raw counts were produced using RSEM v1.3.0.
DOI: 10.5061/dryad.4gh8b/10
title: ESM3: Taxon ages for full phylogenetic dataset

description: Numerical; per stage or substage
DOI: 10.5061/dryad.4gh8b/2
title: ESM2 Full Phylogenetic dataset

description: Nexus file with most parsimonious trees included
DOI: 10.5061/dryad.4gh8b/4
title: ESM4 Pruned Phylogenetic dataset

description: Nexus file with most parsimonious trees included
DOI: 10.5061/dryad.4gh8b/6
title: ESM6 Numerical time bins

description: Numerical ages, two binning methods (wide and per stage/substage)
DOI: 10.5061/dryad.4gh8b/7
title: ESM7 Ecomorphological data

description: Ready-to-use text file
DOI: 10.5061/dryad.4gr1303/1
title: Graft_Data

description: Gene expression in graft tissue
DOI: 10.5061/dryad.4gr1303/2
title: Pearlsac_Data

description: Gene expression in pearl sac
DOI: 10.5061/dryad.4gr1303/3
title: Pearls_Data

description: Pearl phenotypic data
DOI: 10.5061/dryad.4pd33/1
title: Mediterranean gap analysis in environmental space

description: This .zip folder contains the data and an R script to reproduce the gap analysis documented in Mannocci et al. 2018.
DOI: 10.5061/dryad.53qg6/1
title: Data files

description: See ReadMe for descriptions of files formatted for various population genetic analysis software.
DOI: 10.5061/dryad.5n8v4/1
title: Environmental and Effect size data

description: The data includes effect sizes of macroinvertebrate community responses to dam removals and the related geographic, environmental, spatial, temporal, sampling method, and taxonomic resolution information.
DOI: 10.5061/dryad.75373/1
title: WHELDballardetalPLOSMedicine.anonsav

description: SPSS data file of individual participant data
DOI: 10.5061/dryad.7db01/1
title: Filtered_Microsatellite_genotypes_CR_mtSTRs_HR_haplotypes

description: The Excel file ‘Filtered_Microsatellite_genotypes_CR_mtSTRs_HR_haplotypes.xlsx’ contains the CR haplotypes, the mtSTRs, the HR haplotypes and genotypes at 13 microsatellite loci of all individuals used in the analyses to detect genetic structure in Arlequin v3.5.2.3 (Excoffier & Lischer 2010, GenAlEX v6.5 (Peakall & Smouse 2006, 2012), STRUCTURE v2.3 (Pritchard et al. 2000) and Geneland (Guillot et al. 2005).
DOI: 10.5061/dryad.7db01/2
title: Unfiltered_microsatellite_genotypes_CR_mtSTRs_HR_haplotypes

description: The Excel file ‘Unfiltered_Microsatellite_genotypes_CR_mtSTRs_HR_haplotypes.xlsx’ contains the CR haplotypes, the mtSTRs, the HR haplotypes and genotypes at 13 microsatellite loci of all individuals used in the COLONY2 (Wang 2004, Jones & Wang 2010) analyses to remove putative relatives before the analysis of genetic structure
DOI: 10.5061/dryad.7db01/3
title: POWSIM_input_sample_size_frequencies

description: The Excel file ‘POWSIM_input_sample_size_frequencies.xlsx’ contains the input data used for the power analysis of the genetic markers conducted in POWSIM v4.1 (Ryman & Palm 2006). The file contains two tables, one table entitled ‘Cyprus’ which contains the sample sizes and the CR, HR haplotype and microsatellite allele frequencies pertaining to this study. The second table entitled ‘Roberts (2004)’ contains the sample sizes and approximate allele frequencies used in the global assessment of green turtle genetic structure (Roberts et al. 2004).
DOI: 10.5061/dryad.7db01/4
title: The "mainparams.txt" file contains the parameters for the STRUCTURE analysis

description: The file ‘mainparams’ contains the main parameter settings used for the STRUCTURE v2.3 (Pritchard et al. 2000) analysis of genetic structure with the data description for each parameter
DOI: 10.5061/dryad.97d83g0/8
title: post.hoc.simulation.R

description: used to perform post-hoc simulations and species delimitation with spedeSTEM.
DOI: 10.5061/dryad.9m771/1
title: 2008 to 2010 5 day MoveAve datasets

description: Full Data Sets aligned with 5-day Moving Average Weather Data
DOI: 10.5061/dryad.9m771/2
title: 2010 FINAL turf model build with Wisc Damon V3 SAS

description: SAS code of Logistic Regression for building Models
DOI: 10.5061/dryad.9m771/3
title: 2010 FINAL turf model build with Wisc Damon V3 ROC Analysis

description: Additional SAS code for model build with ROC curve display
DOI: 10.5061/dryad.9m771/4
title: Final Model Build Brief Description

description: A brief text summary of the model build approach
DOI: 10.5061/dryad.9m771/5
title: 2016 Data for Primary ANOVA SAS

description: Raw, multi-site validation data for Meta-analysis
DOI: 10.5061/dryad.dk1j0/10
title: HDI_1990_2015

description: HDI is a composite index of average achievement in key dimensions of human development (dimensionless indicator between 0 and 1). This index is based on method introduced 2010 and updated 2011. The subnational data for HDI were collected from multiple national-level datasets, and national-level HDI was collected from UNDP. Years with missing data were interpolated over time thin plate spines, assuming smooth trend over time. The dataset has a global extent at 5 arc-min resolution, and the annual data is available for each year over 1990-2015. HDI sub-national data covers 39 countries and 66% of global population in 2015.
DOI: 10.5061/dryad.dk1j0/11
title: pedigree_GDP_per_capita_PPP_1990_2015

description: This is the source data for GDP per capita (PPP), published as an indication of accuracy and precision. Reports the scale (national, sub-national) and type (reported, interpolated, extrapolated) of each year of data. Detail description is given in a linked article and metadata is provided as an attribute in the NetCDF file itself.
DOI: 10.5061/dryad.dk1j0/7
title: Administrative units

description: Represents the administrative units used for GDP per capita (PPP) and HDI data products. National administrative units have id 1-999, sub-national ones 1001-
DOI: 10.5061/dryad.dk1j0/8
title: GDP_per_capita_PPP_1990_2015

description: The GDP per capita (PPP) dataset represents average gross domestic production per capita in a given administrative area unit. GDP is given in 2011 international US dollars. Gap-filled sub-national data were used, supplemented by national data where necessary. Datagaps were filled by using national temporal pattern. Dataset has global extent at 5 arc-min resolution for the 26-year period of 1990-2015. Detail description is given in a linked article and metadata is provided as an attribute in the NetCDF file itself.
DOI: 10.5061/dryad.dk1j0/9
title: GDP_PPP_1990_2015_5arcmin

description: This global dataset represents the gross domestic production (GDP) of each grid cell. GDP is given in 2011 international US dollars. The data is derived from GDP per capita (PPP) which is multiplied by gridded population data HYDE 3.2 (the years of population data not available (1991-1999) were linearly interpolated at grid scale based on data from years 1990 and 2000). Dataset has global extent at 5 arc-min resolution for the 26-year period of 1990-2015. Detail description is given in a linked article and metadata is provided as an attribute in the NetCDF file itself.
DOI: 10.5061/dryad.g3vm8/1
title: 17-0611.R1 data files

description: data corresponding to: "Demography and selection shape transcriptomic divergence in field crickets". See readme for list and description of files.
DOI: 10.5061/dryad.j4r4j13/1
title: SI Appendix 2 - all data and refs
DOI: 10.5061/dryad.j4r4j13/2
title: Data processing script and terms

description: Script and files that were used to filter out trace, oo- and marine taxa from the original PBDB download.
DOI: 10.5061/dryad.j4sf2/1
title: fia.oak.plot.data

description: Forest Inventory Analysis forest plot data for naturally assembled forests; standard plots that have oak trees in them throughout the continental U.S. Data are from the US Forest Service.
DOI: 10.5061/dryad.j4sf2/2
title: US.oak.trait.means

description: Six leaf and stem functional traits for 49 U.S. oak species.
DOI: 10.5061/dryad.j4sf2/3
title: Oaks.of.the.Americas.dated.phylogeny

description: Dated phylogeny of the Oaks of the Americas from Hipp et al 2018. Dates are in millions of years. Phylogeny was pruned to 49 US tree species.
DOI: 10.5061/dryad.k214j/2
title: Gene Expression Analyses in R (limma and WGCNA)

description: Data files and R-scripts for gene expression analyses (limma and WGCNA)
DOI: 10.5061/dryad.v5374/11
title: NG-6445_Erick1300502_lib23163_1553_6

description: Sequence corresponding to 1D211
DOI: 10.5061/dryad.v5374/12
title: NG-6445_ED2110902_lib23172_1587_5

description: Sequence corresponding to 2D315
DOI: 10.5061/dryad.v5374/13
title: NG-6445_ED2300502_lib23164_1553_6

description: Sequence corresponding to 2D211
DOI: 10.5061/dryad.v5374/14
title: NG-6445_ED3110902_lib23173_1587_5

description: Sequence corresponding to 3D315
DOI: 10.5061/dryad.v5374/15
title: NG-6445_ED3300502_lib23165_1553_6

description: Sequence corresponding to 3D211
DOI: 10.5061/dryad.v5374/16
title: NG-6445_ED4110902_lib23174_1587_5

description: Sequence corresponding to 4D315
DOI: 10.5061/dryad.v5374/17
title: NG-6445_ED4300502_lib23166_1587_5

description: Sequence corresponding to 4D211
DOI: 10.5061/dryad.v5374/18
title: NG-6445_ED5110902_lib23175_1587_5

description: Sequence corresponding to 5D315
DOI: 10.5061/dryad.v5374/19
title: NG-6445_ED5300502_lib23167_1587_5

description: Sequence corresponding to 5D211
DOI: 10.17632/df6gm9zs2r.1
title: Data for: The transition from a passive to an active continental margin in the Jiamusi Block: constraints from late Paleozoic sedimentary rocks

description: Table 1 Locations of samples and composition of investigated sandstones. Table 2 Major, REE and trace element analyses for sandstone samples from the Baoqing area. Table 3 U–Pb isotopic data for zircons from sandstone samples in the Baoqing area.
DOI: 10.17632/thxg683hfp.1
title: Data for: Do Private Donations Depress Electoral Turnout? An Empirical Investigation of Voter Participation

description: Replication data and code for article submission
DOI: 10.5061/dryad.14cf0/1
title: Data from: Combinations of plant water-stress and neonicotinoids can lead to secondary outbreaks of Banks grass mite (Oligonychus pratensis Banks)

description: These data are a collection of field and greenhouse studies conducted in northern Utah in 2013 and 2015. A series of Excel files were used to document the responses of spider mites and plant phenotypes to neonicotinoid pesticides and drought stresses.
DOI: 10.5061/dryad.14hp7/1
title: BeetleAndEnviroData.Stone.et.al.2017

description: This data set contains abundance, species richness, composition and environmental data sampled in 80 flight intercept trap locations. This data was used for data analyses and any species sampled in less that two trap locations have been excluded.
DOI: 10.5061/dryad.1k3p2ht/1
title: Cleaning_Analysis

description: The data sets available here are parts of the following article:


Quimbayo JP and Zapata FA
Cleaning interactions by gobies on a tropical eastern Pacific coral reef

Description: 

Matrix showed temporal variation of the cleaning activity of gobies cleaners at Gorgona Island, Tropical Eastern Pacific. Each column in this matrix had information on the species richness and abundance of clients observed during this study. Moreover, this matrix has information on the cleaning frequency, and the number of cleaning events observed to each trophic group. A cleaning event is defined as the observation of a cleaner removing ectoparasites, diseased tissue, and/or mucus from the body surface, gills or buccal cavity of the clients.

Data are provided in the form of comma separated values files (csv). 


All R codes for reproducing analyses are available from the authors on request. 

Any additional queries should be directed to the corresponding author 
Juan P. Quimbayo (quimbayo.j.p@gmail.com)

The release of this data does not exempt those who reuse the data from following 
community norms for scholarly communication, in particular from the citation of this 
paper and the original data authors as detailed above.
DOI: 10.5061/dryad.1k3p2ht/2
title: Clients_&_Cleaners

description: The data sets available here are parts of the following article:


Quimbayo JP and Zapata FA
Cleaning interactions by gobies on a tropical eastern Pacific coral reef

Description: 

Matrix showed the list of clients attended by gobies cleaners at Gorgona Island, Tropical Eastern Pacific. A cleaning event is defined as the observation of a cleaner removing ectoparasites, diseased tissue, and/or mucus from the body surface, gills or buccal cavity of the clients.

Data are provided in the form of comma separated values files (csv). 


All R codes for reproducing analyses are available from the authors on request. 

Any additional queries should be directed to the corresponding author 
Juan P. Quimbayo (quimbayo.j.p@gmail.com)

The release of this data does not exempt those who reuse the data from following 
community norms for scholarly communication, in particular from the citation of this 
paper and the original data authors as detailed above.
DOI: 10.5061/dryad.2bs5231/1
title: Supplemental Figure 1

description: Supplemental Figure 1. Scree and loadings plots for Principal components analysis of Procrustes-transformed landmark data of Leukoma staminea from Argyle Creek and Argyle Lagoon (PC1 v. PC2).
DOI: 10.5061/dryad.2bs5231/2
title: Supplemental Figure 2

description: Supplemental Figure 2. Principal components analysis of Procrustes-transformed landmark data of Leukoma staminea from Argyle Creek and Argyle Lagoon (A-D: PC2 v. PC3; E-H: PC3 v. PC4).
DOI: 10.5061/dryad.478kp63/1
title: Pine marten encounter histories for use in SCR analysis using oSCR package in R

description: Data collected in the field and processed in lab to obtain genotypes. id= pine marten id/genotype, occasion = visit (1-5), trapid = detector name, sex = f/m, session = region name, site = name of cluster in which detector was located
DOI: 10.5061/dryad.478kp63/2
title: Pine marten trap locations and operational data for use with oSCR package

description: Pine marten detector data relating to location of detectors and whether they were operational. X = British National Grid easting, Y = British National Grid northing, o1-o5 = whether detector was operational for each session, site = name of cluster which detector belongs to, region = LL (Central Scotland), BO (Borders) or HI (Highlands)
DOI: 10.5061/dryad.478kp63/3
title: Red squirrel detection histories and covariates for occupancy analysis in UNMARKED R package

description: Detection/non-detection data site and survey specific covariates for red squirrels. 0=name of cluster which detector belongs to, region = CS (Central Scotland), BO (Borders) and HI (Highlands), X = BNG easting, Y= BNG northing, species = red squirrel, visit1-5 = detection (1) /non detection (0), cover = % of 100m buffer which is forested, bl = % of cover which is broadleaved, gs = portion of feeders within 500m used by grey squirrels, tCov1-tCov5 = hair (feeder only used) or both (feeder and camera used)
DOI: 10.5061/dryad.4g048/1
title: Raw Assembly

description: This file contains the raw, de novo assembly produced from the unmapped reads using Trinity. There are 104,588 contigs present.
DOI: 10.5061/dryad.4g048/10
title: C2 Unmapped Reads
DOI: 10.5061/dryad.4g048/11
title: C3 Unmapped Reads
DOI: 10.5061/dryad.4g048/12
title: C4 Unmapped Reads
DOI: 10.5061/dryad.4g048/13
title: C9 Unmapped Reads
DOI: 10.5061/dryad.4g048/6
title: Sample Matrix for EdgeR

description: This spreadsheet contains only two columns. The first column is the group (control or pulsed) and the second the library ID (4,7,9,10,11,12,13,14,15,16). This file is only used by EdgeR to analyze differential expression.
DOI: 10.5061/dryad.4g048/7
title: Differential Expression Results

description: This spreadsheet contains the results from calculations of differential expression for each contig.  Only 39,714 contigs were assessed for differential expression.  The columns are: Contig_name; sampleA; sampleB; LogFC (fold change); logCPM (counts per million); P-value; FDR (false discovery rate).
DOI: 10.5061/dryad.4g048/9
title: C1 Unmapped Reads
DOI: 10.5061/dryad.4gh8b/11
title: ESM5 Taxon ages for pruned phylogenetic dataset

description: Numerical; per stage or substage
DOI: 10.5061/dryad.4gh8b/12
title: ESM 8 R script

description: –
DOI: 10.5061/dryad.4gh8b/9
title: ESM1 Supplementary information

description: Bauplan data, supplementary methods, supplementary figures, supplementary tables
DOI: 10.5061/dryad.72262/1
title: Appendix_S02_2018-01-08

description: Input data and analysis scripts for Appendix S2
DOI: 10.5061/dryad.72262/2
title: Appendix_S04_2018-01-08

description: Inputs data and analysis scripts for Appendix S4
DOI: 10.5061/dryad.72262/3
title: Appendix_S05a_2018-01-08

description: Input data and analysis scripts for part of Appendix S5
DOI: 10.5061/dryad.9m771/6
title: Primary ANOVA GLIMMIX

description: SAS code to obtain the primary ANOVA results for meta-analysis
DOI: 10.5061/dryad.9m771/7
title: 2016 Dollar Spot Model Meta-Analysis

description: SAS code for univariate meta-analysis approach to validate model as a fungicide spray advisor
DOI: 10.5061/dryad.9m771/8
title: 2016 Meta-Analysis Results

description: Met-analysis raw data and preliminary meta-analysis results