cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m35k6/77
title: ModelSel_RBNU_2012_Occupancy

description: AIC model selection table and associated coefficients for red-breasted nuthatch 2012 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.mf42f/38
title: Fertilization
DOI: 10.5061/dryad.mf42f/39
title: Weed_Insect_Fungi
DOI: 10.5061/dryad.mf42f/40
title: Irrigation
DOI: 10.5061/dryad.n0d03/1
title: Dispersal rate data

description: Data supporting Figure 1a: dispersal rate function of population density and cooperation level
DOI: 10.5061/dryad.n0d03/2
title: Dispersal phenotype data

description: Data supporting Figure 1b: dispersal phenotype function of population density and cooperation level
DOI: 10.5061/dryad.n0d03/3
title: Colonization from single cell data

description: Data supporting Figure 2a: colonization from a single cell function of population density and cooperation level
DOI: 10.5061/dryad.n0d03/4
title: Colonization from a group data

description: Data supporting Figure 2b: colonization from a group function of population density and cooperation level
DOI: 10.5061/dryad.n5v84/1
title: Field data Gryseels et al. Rodent urban-rural genetic contrast

description: Explanations for datafile "Field data Gryseels et al. Differentiation of M.natalensis in synanthropy.xls"This datafile contains trapping and location information of small mammals captured as described in the manuscript "Genetic distinction between contiguous urban and rural multimammate mice in Tanzania despite gene flow"ID: Unique ID code of each captured animalProject: the samples used in the manuscript originate from 2 different projects (see details in manuscript)Locality: Unique code of the locality (which consists of a set of 100 traps placed in a grid for 1 night) where the animal is capturedTown: town, village or community where the animal is capturedDate: the date the animal was capturedSpecies: morphological identification of the animal (in case of Mastomys natalensis: confirmed by cytochrome b DNA sequence data)Latitude and longitude: the exact GPS location the animal was captured inside its trap
DOI: 10.5061/dryad.n5v84/2
title: Parameter settings for STRUCTURE clustering analyses

description: Parameter settings for STRUCTURE clustering analyses used in the manuscript
DOI: 10.5061/dryad.n5v84/3
title: Microsatellite data

description: Explanations for datafile "Microsatellite data.xls"This datafile contains microsatellite genotype information of Mastomys natalensis.General comment: "-9" describes a missing datapointColumn headings:ID --&gt; unique code of a captured and genotyped animal. For field information, see file "Field data Gryseels et al. Rodent urban-rural genetic contrast.txt"Info for STRUCTURE: Sample location information --&gt; A number code depicting the location (at the village level) the genotyped animal was captured. This information is used in the clustering algorithm in the software STRUCTURE.Info for STRUCTURE: Putative population origin --&gt; A number code depicting the location the genotyped animal was captured. This information is used in the clustering algorithm in the software STRUCTURE.Remaining columns --&gt; microsatellite repeat numbers at 15 different loci (column headers = names of the loci)
DOI: 10.5061/dryad.n5v84/4
title: IMa2 input file

description: The exact input file as used in IMa2 analyses in the manuscript.
DOI: 10.5061/dryad.p0r3v/1
title: Cheng et al PRSB Oyster Density Dataset 1

description: Oyster density data from Village North, Rat Rock, and Weber Point. Columns are variables and rows are replicate data points. Date = date of survey in month/day/year format. Site = one of the above described sites. Recorders = initials of surveyors. Mini-quadrat = quadrat number within the larger quadrat. Height = tidal height where Low = 0.0 m, Mid = 0.05 m, High = 0.10 m above mean lower low water. Distance = position of the quadrat in meters along the transect. Alive = number of live Olympia oysters. Ostrea.25m = number of live oysters per 0.25 meters squared. Notes = notes for each replicate.
DOI: 10.5061/dryad.p0r3v/2
title: Cheng et al PRSB Oyster Density Dataset 2

description: Oyster density data from Bullhead Flat. Site = Bullhead Flat (all data from this file is from this site). Date = date of survey in month/day/year format. Year = year in full year format. Quadrat = quadrat number. OstreaLive = number of live oysters within the quadrat. OstreaDead = number of dead oysters within the quadrat.
DOI: 10.5061/dryad.p0r3v/3
title: Cheng et al PRSB Oyster Size Frequency Data

description: Oyster size frequency data from field quadrat surveys at Bullhead Flat. Date = date in month/day/year format. Site = Bullhead Flat for all rows. Recorders = initials of surveyors. Quadrat = quadrat number. Oyster.Length = oyster length in mm.
DOI: 10.5061/dryad.p0r3v/4
title: Cheng et al PRSB Oyster Recruitment Data

description: Oyster recruitment data from Bullhead Flat. Ceramic tiles were deployed on racks in the intertidal zone. Timeframe = frequency of sampling (Quarterly or Monthly). Date.In = date of tile outplant in month/day/year format. Date.Out = date of tile recovery in month/day/year format. Approximate.season = season that tile was deployed during. Year = year in full year format. Site = site that tiles were deployed at (China Camp = Bullhead Flat). Site Code = code for site (all values = CC). Frame = the frame number that the tile was attached to. Tile = letter for each tile per frame. oyster.count = number of oyster recruits per tile. count.m2 = number of oysters recruits extrapolated to a meter squared. days.in.field = the number of days that a tile was deployed for. count.m2.day = count.m2 column divided by the days.in.field column.
DOI: 10.5061/dryad.p3057/1
title: Plant species niche characteristics and trait data from the experiment
DOI: 10.5061/dryad.qr068/1
title: Naniwadekar_Datta_TCS_Hornbill_Data

description: Contains details (date, trail identity and length, time, hornbill species identity, perpendicular distance of the sighting, flock size of the bird) of all the hornbill sightings during distance sampling for hornbill density estimation in Namdapha Tiger Reserve. The details of the total number of replicate walks and effort across each trail can also be found here. The details regarding total sampling effort can be found here https://tropicalconservationscience.mongabay.com/content/v6/TCS-2013-Vol6(6)_734-748_Naniwadekar-and-Datta.pdf.
DOI: 10.5061/dryad.r3s16/1
title: Insect feeding trial data

description: File containing data from the feeding trials. The column 'plant' is the identifier and can be used in conjunction with 'treatments' file for analysis.
DOI: 10.5061/dryad.r3s16/2
title: Leaf CN

description: Carbon and nitrogen data from sugarcane leaves. The 'plant' column is the identifier to be used in conjunction with the 'treatments' file for analysis.
DOI: 10.5061/dryad.r3s16/3
title: Root silicon

description: Data from silicon analysis of sugarcane roots. The 'plant' column is the identifier to be used in conjunction with the 'treatments' file for analysis.
DOI: 10.5061/dryad.r3s16/4
title: Sugarcane photosynthesis

description: Photosynthesis data from each measuring 'event' throughout the experiment. The 'plant' column is the identifier to be used in conjunction with the 'treatments' file for analysis.
DOI: 10.5061/dryad.r3s16/5
title: Root CN

description: Carbon and nitrogen data from sugarcane roots. The 'plant' column is the identifier to be used in conjunction with the 'treatments' file for analysis.
DOI: 10.5061/dryad.r3s16/6
title: treatments

description: Identifier file to allow allocation of 'plant' to treatment combinations for analysis.
DOI: 10.5061/dryad.r3s16/7
title: Leaf silicon

description: Data from silicon analysis of sugarcane leaves. The 'plant' column is the identifier to be used in conjunction with the 'treatments' file for analysis.
DOI: 10.5061/dryad.r3s16/8
title: Root total non structural carbs

description: Data from the total non-structural carbohydrate analysis of sugarcane roots. The 'plant' column is the identifier and should be used in combination with the 'treatments' file for analysis.
DOI: 10.5061/dryad.r3s16/9
title: biomass

description: Biomass data from sugarcane plants. The column 'plant' is the identifier and can be used in conjunction with 'treatments' file for analysis.
DOI: 10.5061/dryad.v8s83/1
title: nurse plant growth

description: lf/ht 1 are initial measurements lf/ h2 is at the time of planting lf/ht3 are at the end of year 2014 and lf/ht4 are at the end of the year 2015 (Second year.)
DOI: 10.5061/dryad.v8s83/2
title: diversityoutput numbers

description: ls means outputs for different diversity measurements of the ABG of all plants within a plot
DOI: 10.5061/dryad.v8s83/3
title: getting divserity lsmeans

description: r code to acquire LS means for diversity
DOI: 10.5061/dryad.087b9/1
title: Egg data for Dryad

description: Output from climwin analyses
DOI: 10.5061/dryad.1nr07/1
title: behavioural_data

description: Each participant’s data are saved in a separate file, e.g. ‘psychophysics_participant_[participant_numer].mat’. The file is a Matlab structure array containing five fields: button presses for the pre-experiment are saved in ‘pre_button’, those for the main experiment in ‘main_button’. Both are a matrix in which each column is a separate trial. Each row is a frame in the presentation of a stimulus. At a refresh rate of 120 Hz this means that 120 rows comprise a second of experimentation. For each frame, a value of 1 indicates a right button press, a value of -1 a left button press and a value of 0 that no button was pressed. ‘pre_gamma’ contains the gamma shape and scale parameter resulting from the pre-experiment. Dominance durations for the main experiment’s replay stimulus were sampled from this gamma distribution. ‘main_conditions’ is a vector containing the order in which conditions appeared through the trials. Lastly, ‘main_output’ summarises statistics computed from the experiment, each row is one of the five experimental runs. The columns are trial number, median dominance for the sphere turning left, median dominance for the sphere turning right, median dominance for all percepts, number of percept switches and total mixed percept durations, as well as gamma shape and scale parameters for each trial’s dominance durations.
DOI: 10.5061/dryad.1nr07/2
title: MRI_scans

description: There are 16 files in the repository, one scan for each participant in NIFTI format. The filename is equivalent to the participant number.
DOI: 10.5061/dryad.2c220/1
title: arachnothera.bam.tar.gz

description: Bam and index files of Arachnothera reads mapped to pseudo-reference genome
DOI: 10.5061/dryad.2c220/2
title: irena.bam.tar.gz

description: Bam and index files of Irena reads mapped to pseudo-reference genome
DOI: 10.5061/dryad.2c220/3
title: arach.uce.mar17.cs

description: Pseudo-reference genome for Arachnothera
DOI: 10.5061/dryad.3jm7h/4
title: Expt1MetschBST

description: Transmission data for Exp1. Hosts: Daphnia dentifera, Ceriodaphnia dubia. Parasite: Metschnikowia bicuspidata. Variables include transmission rate (Beta), parasite growth rate (sigdeath), host species and host clone.
DOI: 10.5061/dryad.3jm7h/5
title: Expt2PastBST

description: Transmission data for Exp2. Hosts: Daphnia dentifera, Ceriodaphnia dubia. Parasite: Pasteuria ramosa. Variables include transmission rate (beta), parasite growth rate (sigma/tau), overall transmission potential (bs/t), first host species (host 1) and second host clone (host 2).
DOI: 10.5061/dryad.3jm7h/6
title: Expt2MetschBST

description: Transmission data for Exp2. Hosts: Daphnia dentifera, Ceriodaphnia dubia. Parasite: Metschnikowia bicuspidata. Variables include transmission rate (beta), parasite growth rate (sigma/tau), overall transmission potential (bs/t), first host species (host 1) and second host clone (host 2).
DOI: 10.5061/dryad.3jm7h/7
title: MHMP_PhilTrans

description: Code for all of the analyses within this manuscript
DOI: 10.5061/dryad.610md/1
title: Theriot et al., diatom, 7 gene dataset, with all charsets defined

description: Nexus DNA sequence file of aligned sequences. 208 taxa (207 diatoms, 1 outgroup).  9349 bases. 7 genes.  In order: nuclearly-encoded SSU, chloroplast encoded atpB, psaA, psaB, psbA, psbC,rbcL. Ends trimmed for each gene so that at least 50% of individual sequences have a base.  Character set information included, identifying genes, inferred paired and unpaired sites for SSU, and codon positions.  Each protein encoding gene further trimmed so that each begins with a first codon position.
DOI: 10.5061/dryad.610md/2
title: Fig.S1.SaturationPlot.psaA3

description: Plot of transitions and transversions from F84 distances as calculated in DAMBE5, for diatom plus Bolidomonas psaA 3rd codon position.
DOI: 10.5061/dryad.610md/3
title: Fig.S2.7gene.full

description: Maximum likelihood tree with all terminals identified, from analysis of 7 genes (SSU, atpB, psaA, psaB, psbA, psbC, rbcL) for 207 diatoms and Bolidomonas pacifica (outgroup).
DOI: 10.5061/dryad.610md/4
title: Fig.S3.cplastonly

description: Maximum likelihood tree with all terminals identified, from analysis of 6 genes (atpB, psaA, psaB, psbA, psbC, rbcL) for 207 diatoms and Bolidomonas pacifica (outgroup).
DOI: 10.5061/dryad.610md/5
title: Fig.S4.ssuonly

description: Maximum likelihood tree with all terminals identified, from analysis of SSU for 207 diatoms and Bolidomonas pacifica (outgroup).
DOI: 10.5061/dryad.610md/6
title: Table.S1.Taxa.GenbankNumbers

description: Taxa, authorities, sources, and Genbank accession numbers for 7 gene dataset on diatoms submitted by Theriot et al.
DOI: 10.5061/dryad.610md/7
title: Table.S2.PrimerTable

description: Table of primers used for DNA sequencing for dataset submitted by Theriot et al. (7 genes, diatoms).
DOI: 10.5061/dryad.9kd74/1
title: Raw pattern photos
DOI: 10.5061/dryad.d5h06/1
title: Aphid and plant performance

description: This datafile contains raw data that were used in the accompanied manuscript. One sheet contains the results for effects of temperature and plant composition on aphid performance growing on Plantago lanceolata. The other sheets contain the results for effects of temperature, plant composition and aphid infestation on plant performance.
DOI: 10.5061/dryad.f2j00/4
title: ContigsMacra12

description: Taraxacum officinale microspecies Macranthoides accession 12 genomic sequences of repetitive DNA assembled following the procedure by Novak et al. 2010.
DOI: 10.5061/dryad.f2j00/5
title: ContigsMacra13

description: Taraxacum officinale microspecies Macranthoides accession 13 genomic sequences of repetitive DNA assembled following the procedure by Novak et al. 2010.
DOI: 10.5061/dryad.h1v0m/1
title: Dataset

description: Provides for each focal observation the duration and feeding behaviour recorded
DOI: 10.5061/dryad.hf756/1
title: Slope.com Script

description: A file containing the R scripts for comparing the different ontogenetic allometries described in the main manuscript.
DOI: 10.5061/dryad.hf756/2
title: Ontogenetic Allometry Data

description: Growth data for all the ontogenetic allometries described in the main manuscript
DOI: 10.5061/dryad.hf756/3
title: Data for Supp. Fig. 4

description: Data for Supplementary Figure 4.
DOI: 10.5061/dryad.hm55b/3
title: Data and results 2

description: Part 2. tar.gz compressed folder containing: initial tree data for running R pipeline (data/) and a results folder for every analysis run (results/). References for phylogenetic trees can be found in metadata.csv. For more details, see: https://github.com/DomBennett/Project-EDBMM
DOI: 10.5061/dryad.hm55b/4
title: Data and results 3

description: Part 3. tar.gz compressed folder containing: initial tree data for running R pipeline (data/) and a results folder for every analysis run (results/). References for phylogenetic trees can be found in metadata.csv. For more details, see: https://github.com/DomBennett/Project-EDBMM
DOI: 10.5061/dryad.hm55b/5
title: Data and results 4

description: Part 4. tar.gz compressed folder containing: initial tree data for running R pipeline (data/) and a results folder for every analysis run (results/). References for phylogenetic trees can be found in metadata.csv. For more details, see: https://github.com/DomBennett/Project-EDBMM
DOI: 10.5061/dryad.hm55b/6
title: Data and results 5

description: Part 5. tar.gz compressed folder containing: initial tree data for running R pipeline (data/) and a results folder for every analysis run (results/). References for phylogenetic trees can be found in metadata.csv. For more details, see: https://github.com/DomBennett/Project-EDBMM
DOI: 10.5061/dryad.jh6h1/1
title: raw data

description: Microfossil occurrence data from Neptune Sandbox Berlin
DOI: 10.5061/dryad.k3m40/1
title: cachedistance data dryad

description: Data were collected in the field and entered into SPSS. Column headings are: SquirrelID=individual squirrels, obsnum = observation number for each individual squirrel, site=which of 4 sites the data were collected from, cachedistance=distance of the cache, in metres, from the nearest tree, numsqpres=the number of other squirrels present at the time the focal squirrel made the cache, disturbances=the number of people that passed through the site during the observation period
DOI: 10.5061/dryad.k3m40/2
title: foragedistance data dryad

description: Data were collected in the field and entered into SPSS. Column headings are: SquirrelID=individual squirrels, obsnum = observation number for each individual squirrel, site=which of 4 sites the data were collected from, cachedistance=distance of the cache, in metres, from the nearest tree, numsqpres=the number of other squirrels present at the time the focal squirrel made the cache, disturbances=the number of people that passed through the site during the observation period
DOI: 10.5061/dryad.k3m40/3
title: human predation data dryad

description: Data were collected in the field and entered into SPSS. Data columns are as follows: location=site where squirrel was observed, Squirrel_ID=individual squirrel ID, V3=observation number for each squirrel, date=date of observation, time=time of day observation was taken, No_of_human=number of humans present when the squirrel was observed, No_of_dog=number of dogs present when the squirrel was observed, distancem=distance in metres between the squirrel and the nearest human and/or dog, escaped_or_not=whether or not the squirrel stopped it's current activity and ran, escaped=whether or not the squirrel stopped it's current activity and ran using 0 for no and 1 for yes
DOI: 10.5061/dryad.k3m40/4
title: artificial cache data

description: data were collected in the field and entered into an Excel file. Column definitions are within the file itself.
DOI: 10.5061/dryad.k5n8d/1
title: Species occurrences

description: Species occurrences coordinates; coordinate system: RGF93
DOI: 10.5061/dryad.k5n8d/2
title: Environmental variables

description: Raster files of environmental variables used for MaxEnt models and measures of ecological overlap: temperature, precipitation, percentage of meadow, density of hedgerows, TWI, winter NDVI, spring EVI; coordinate system: RGF93
DOI: 10.5061/dryad.k5n8d/3
title: Maxent suitability outputs

description: Maps of habitat suitability produced by MaxEnt for each species; coordinate system: RGF93
DOI: 10.5061/dryad.m35k6/78
title: ModelSel_RBNU_2013_Occupancy

description: AIC model selection table and associated coefficients for red-breasted nuthatch 2013 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/79
title: ModelSel_STJA_2012_Occupancy

description: AIC model selection table and associated coefficients for Steller’s jay 2012 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/80
title: ModelSel_STJA_2013_Occupancy

description: AIC model selection table and associated coefficients for Steller’s jay 2013 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/81
title: ModelSel_SWTH_2012_Occupancy

description: AIC model selection table and associated coefficients for Swainson’s thrush 2012 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/82
title: ModelSel_SWTH_2013_Occupancy

description: AIC model selection table and associated coefficients for Swainson’s thrush 2013 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.