cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.nnvbyc
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Pseudacanthicus leopardus (Fowler, 1914)"
 ]
}

 The dataset includes 30 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033959-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12801940
title: 18S Amplicon sequence variants (ASVs) data of NEREA Augmented Observatory

description: Illumina paired-end V9-18S raw reads (FASTQ format, 2 X 150 PE) were pre-processed with cutadapt and vsearch to remove primer sequences, trim low quality bases and unify mixed orientation reads produced in the ligation-based library preparation; the procedure was implemented in a custom bash script. Processed reads were then used to generate amplicon sequence variants (ASVs) using the DADA2 R library; the pipeline was adapted from the one described on the program website (https://benjjneb.github.io/dada2/tutorial.html); no further quality filtering was implemented at this stage, except for discarding all reads with ambiguities (parameter maxN = 0 of function filterAndTrim). Filtered forward (F) and reverse (R) reads were used to train the error model and then denoised by applying the trained error model to generate ASVs. Finally, F and R reads were merged and checked for chimeras; allowing no mismatches in read merging (default parameter maxMismatch = 0 of function mergePairs). ASVs were then classified with BLAST against the PR2 v5.01 reference database, integrated with 1,293 sequences from GoN protist strains and fungi environmental sequences. Highest bit score matching with the best taxonomic resolution were then selected among the returned results.
DOI: 10.5281/zenodo.12801941
title: 18S Amplicon sequence variants (ASVs) data of NEREA Augmented Observatory

description: Illumina paired-end V9-18S raw reads (FASTQ format, 2 X 150 PE) were pre-processed with cutadapt and vsearch to remove primer sequences, trim low quality bases and unify mixed orientation reads produced in the ligation-based library preparation; the procedure was implemented in a custom bash script. Processed reads were then used to generate amplicon sequence variants (ASVs) using the DADA2 R library; the pipeline was adapted from the one described on the program website (https://benjjneb.github.io/dada2/tutorial.html); no further quality filtering was implemented at this stage, except for discarding all reads with ambiguities (parameter maxN = 0 of function filterAndTrim). Filtered forward (F) and reverse (R) reads were used to train the error model and then denoised by applying the trained error model to generate ASVs. Finally, F and R reads were merged and checked for chimeras; allowing no mismatches in read merging (default parameter maxMismatch = 0 of function mergePairs). ASVs were then classified with BLAST against the PR2 v5.01 reference database, integrated with 1,293 sequences from GoN protist strains and fungi environmental sequences. Highest bit score matching with the best taxonomic resolution were then selected among the returned results.
DOI: 10.13020/b8v2-0j33
title: Data and R-code for: “Integrating DNA fingerprinting of invasive watermilfoil strains into aquatic vegetation monitoring and assessment”

description: Invasive Eurasian watermilfoil (Myriophyllum spicatum L.) hybridizes with native northern watermilfoil (Myriophyllum sibiricum Komarov). Previous genetic studies have identified numerous distinct Eurasian and hybrid strains that can differ in their invasiveness (e.g., growth and potential for spread) and response to herbicides. To identify problematic or invasive strains of watermilfoil we assessed the response of different watermilfoil strains to aquatic vegetation management in eight Minnesota lakes over the course of 3 yr. Specifically, we looked for changes in strain composition of watermilfoil populations over time to identify strains of specific interest for further characterization of growth and herbicide response. Eurasian watermilfoil was collected from point intercept surveys (125 to 230 points at each waterbody) before and after herbicide treatments and generally twice per year over 3 years. Plants were idented to genotype using microsatellite markers and changes in genotype occurrence and frequency were assess for changes over time and in response to treatment. Additional details and methods are presented in Gannon et al. 2022.
description: The raw data (All_Lakes_KAG_020322.csv) are read into DRUM_All_Lakes_KAG_072324.rmd where statistical summaries are printed and saved, data is analyzed and visualizations are produced. All code was written in R, analysis code was subsequently converted to .Rmd file then to the .html file in this repository.
DOI: 10.15468/dl.gqceqq
title: Occurrence Download

description: A dataset containing 745191 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Xeno-canto - Bird sounds from around the world"
 ]
}

 The dataset includes 745191 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033958-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x5nvk5
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tigridia chrysantha Cruden & S.J.Walker"
 ]
}

 The dataset includes 13 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033960-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ueyqt3
title: Occurrence Download

description: A dataset containing 19932 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "TaxonKey is Pteropodidae"
 ]
}

 The dataset includes 19932 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033961-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.affes7
title: Occurrence Download

description: A dataset containing 19932 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "TaxonKey is Pteropodidae"
 ]
}

 The dataset includes 19932 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033962-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u5nktc
title: Occurrence Download

description: A dataset containing 367 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Fundulopanchax gardneri (Boulenger, 1911)"
 ]
}

 The dataset includes 367 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033963-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10553808
title: Dataset and code for "Methods to evaluate subcolumn profiles based on two-point diagnostics"

description: Description of included files

 

WRF code base (wrf_clubb_silhs.tar.gz)

This WRF repo (using the stephens_et_al_2024_lidar_paper branch) can be used to generate both the high-resolution reproductions of LASSO runs with 60-second snapshot output (note that the resulting files will be quite large, it may be convenient to eliminate variables from the history stream), and the coarse-grained, essentially single-column model LASSO reproductions using CLUBB-SILHS.  The code base was compiled with gfortran for the CLUBB-SILHS runs, and with ifort for the LES runs.  The appropriate test case to compile is "em_crm", and within the wrf_clubb_silhs/WRF/test/em_crm directory there are two bash scripts that will automate the setup of the cases (and in the coarse-grained case, run the model as well).  The bash scripts are named runlasso_silhs.bash and runlasso_les.bash, for the coarse-grained and LES versions respectively.  For the coarse-grained CLUBB-SILHS cases, the user will need to modify the value of the vertical decorrelation coefficient (vert_decorr_coef) manually.  This parameter can be modified in wrf_clubb_silhs/WRF/test/clubb_input/tunable_parameters/silhs_parameters.in.

 

WRF-CLUBB-SILHS files

These are output files from coarse-grained versions of the LASSO LES runs, on a 4x4 grid, with CLUBB-SILHS active.  Two cases are included:



vdc_10.tar.gz.  This test uses the standard SILHS sampling algorithm, with a vertical decorrelation coefficient (VDC, or vert_decorr_coef in the SILHS source code) equal to 10.

vdc_10_cdf.tar.gz.  Uses new CDF sampling method described in the paper, with VDC=10.

vdc_30.tar.gz.  Uses standard sampling method, with VDC=30.

vdc_30_cdf.tar.gz.  Uses new CDF sampling method, with VDC=30.


 

Python script:

The included python script will generate the figures and table shown in the paper, as long as the user has the WRF-CLUBB-SILHS files (included here) and the necessary LASSO and lidar files (not included).  Note that the sampling technique in the paper incorporates some randomness so the table values will not be the same as in the paper but should be statistically identical.  The script can also be found in the wrf_clubb_silhs.tar.gz code base, at wrf_clubb_silhs/WRF/scripts/stephens_et_al_2024_lidar_paper_figures.py.



As mentioned above, the WRF-CLUBB-SILHS runs can also be reproduced using the included WRF code base and the wrf_clubb_silhs/WRF/test/em_crm/runlasso_silhs.bash script.  

The raw lidar and value-added product with lidar statistics can be obtained from the ARM Data Discovery site (Data Discovery (arm.gov)).

The original LASSO files can be obtained through ARM's LASSO Bundle Browser (LASSO Bundle Browser (arm.gov)).

The LASSO reproductions with 60-second snapshot output would have to be generated by the user with the WRF code base included here and the wrf_clubb_silhs/WRF/test/em_crm/runlasso_les.bash script.
DOI: 10.15468/dl.cwnnqk
title: Occurrence Download

description: A dataset containing 11996 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rhamdia Bleeker, 1858"
 ]
}

 The dataset includes 11996 records from 215 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033964-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10719207
title: Electrochemical Sensor Data (Cavallaro et al)

description: Raw EIS data for electrochemical aptasensors developed by Cavallaro et al.
DOI: 10.5281/zenodo.10719208
title: Electrochemical Sensor Data (Cavallaro et al)

description: Raw EIS data for electrochemical aptasensors developed by Cavallaro et al.
DOI: 10.5281/zenodo.12796743
title: GenerativeGI - GPTP 2024 Dataset

description: Generated images, image collages, and log data from GenerativeGI GPTP 2024 experiments.  Supports "Crafting Generative Art through Genetic Improvement: Managing Creative Outputs in Diverse Fitness Landscapes" by Fredericks, Bobeldyk and Moore.
DOI: 10.5281/zenodo.12796744
title: GenerativeGI - GPTP 2024 Dataset

description: Generated images, image collages, and log data from GenerativeGI GPTP 2024 experiments.  Supports "Crafting Generative Art through Genetic Improvement: Managing Creative Outputs in Diverse Fitness Landscapes" by Fredericks, Bobeldyk and Moore.
DOI: 10.15468/dl.xuzf3a
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Togo",
 "OccurrenceStatus is Present",
 "TaxonKey is Cajanus cajan (L.) Huth"
 ]
}

 The dataset includes 62 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033965-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q3fpxy
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bursera brunea (Urb.) Urb. & Ekman"
 ]
}

 The dataset includes 28 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033966-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9rr85b
title: Occurrence Download

description: A dataset containing 29332 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Corytophanidae",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 }
 ]
}

 The dataset includes 29332 records from 265 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033967-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dwtpab
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Venezuela (Bolivarian Republic of)",
 "OccurrenceStatus is Present",
 "StateProvince is one of (Yaracuy, Yaracuy State, Yaracuy, Estado)",
 "TaxonKey is Phoenicopterus ruber Linnaeus, 1758"
 ]
}

 The dataset includes 17 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033968-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w3zjpr
title: Occurrence Download

description: A dataset containing 47827 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Chile",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 47827 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033969-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4evuxv
title: Occurrence Download

description: A dataset containing 8174 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-123.75386 42.94112,-121.57728 42.94112,-121.57728 44.90534,-123.75386 44.90534,-123.75386 42.94112))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Aquilegia formosa Fisch., Asclepias speciosa Torr., Lupinus latifolius Lindl. ex J.Agardh, Polystichum munitum (Kaulf.) C.Presl, Anaphalis margaritacea (L.) Benth., Eucephalus ledophyllus (A.Gray) Greene, Solidago elongata Nutt., Achillea millefolium L., Ceanothus velutinus Douglas, Ceanothus integerrimus Hook. & Arn., Polypodium glycyrrhiza D.C.Eaton, Rhododendron macrophyllum D.Don, Delphinium menziesii DC., Chamaenerion angustifolium (L.) Scop., Sambucus racemosa L., Rubus parviflorus Kük., Sambucus cerulea Raf., Lupinus polyphyllus Lindl.)"
 ]
}

 The dataset includes 8174 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033970-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v3mw4c
title: Occurrence Download

description: A dataset containing 103 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-95.88684 20.67088,-95.88684 5.37953,-71.45992 1.45259,-72.67783 13.17684,-95.88684 20.67088))",
 "OccurrenceStatus is Present",
 "TaxonKey is Herotilapia multispinosa (Günther, 1867)"
 ]
}

 The dataset includes 103 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033971-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pru48u
title: Occurrence Download

description: A dataset containing 83 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bursera exequielii León de la Luz"
 ]
}

 The dataset includes 83 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033972-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.24082128
title: Population weighted average Travel Time to nearest 24-hr ED by CSD (csv)

description: Contains the CSD identifier (CSDUID) and the spaces population weighted average travel time to closest 24-hr Emergency department
DOI: 10.6084/m9.figshare.24082128.v3
title: Population weighted average Travel Time to nearest 24-hr ED by CSD (csv)

description: Contains the CSD identifier (CSDUID) and the spaces population weighted average travel time to closest 24-hr Emergency department
DOI: 10.3535/aj8-nvj-k0a
title: Eleocharis quinqueflora (Hartmann) O.Schwarz

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aj8-psf-854
title: Trifolium arvense L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aj9-1zs-1a8
title: Stuckenia pectinata (L.) Börner

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aj9-2qg-ajj
title: Trisetum flavescens (L.) P.Beauv.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aj9-4jd-vke
title: Botrychium lunaria (L.) Sw.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aj9-56r-sey
title: Carex elata All.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aj9-6mp-eq0
title: Potentilla L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aj9-l26-r4k
title: Zannichellia palustris subsp. palustris

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aj9-lzy-dsd
title: Tofieldia pusilla (Michx.) Pers.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aj9-mgr-zbs
title: Dryopteris expansa (C. Presl) Fraser-Jenk. & Jermy

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aja-1p0-1nd
title: Rabelera holostea (L.) M. T. Sharples & E. A. Tripp

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aja-3ym-6g2
title: Neottia ovata (L.) Hartm.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aja-4s6-a70
title: Butomus umbellatus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aja-8px-96t
title: Plantae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aja-bzm-ctb
title: Anthoxanthum nitens (Weber) Y.Schouten & Veldkamp

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aja-jgf-2z1
title: Botrychium lunaria (L.) Sw.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aja-knj-k2s
title: Rumex acetosella var. tenuifolius Wallr.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aja-nn5-fkz
title: Lathyrus sylvestris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aja-p8y-pzj
title: Spergula morisonii Boreau

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aja-pcx-akz
title: Chenopodium suecicum Murr

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aja-rsm-sng
title: Lolium temulentum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aja-trv-6l4
title: Persicaria maculosa Gray

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aja-vfd-7fz
title: Glyceria maxima (Hartm.) Holmb.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ajb-c4b-yky
title: Rorippa palustris (L.) Besser

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ajb-cjh-r05
title: Luzula multiflora (Ehrh.) Lej.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ajb-jdh-csp
title: Hordeum vulgare L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ajb-k38-nbs
title: Carex rostrata Stokes

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aja-gk2-2gp
title: Chenopodium berlandieri var. zschackei (Murr) Murr

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ajb-fb1-nmx
title: Papaver somniferum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ajb-q0v-1sd
title: Carex muricata L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ajb-xkq-vv1
title: Cerastium semidecandrum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ajc-af0-7yg
title: Dactylorhiza maculata (L.) Soó

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ajc-f9z-vdm
title: Neottia cordata (L.) Rich.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ajc-lk9-whv
title: Noccaea Moench

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ajc-rpf-jn5
title: Spergula morisonii Boreau

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ajc-wrk-elk
title: Plantae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ajc-xg6-ezc
title: Juncus gerardi Loisel.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ajc-xpa-acd
title: Sorbus aucuparia subsp. glabrata (Wimm. & Grab.) Hedl.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ajd-06b-wv4
title: Dryopteris cristata (L.) A. Gray

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.