Skip to content

Data sets

Finding a comprehensive dataset on biodiversity that covers population data, population viability analysis (PVA), and species interactions across regions can be challenging but is possible through several established biodiversity and ecological data repositories. Here are some valuable resources you can explore:

PVA features in biodiversity database:

Categorization of PVA List

Category PVA Data
General Settings st, nruns, nyears, yrdays, npops, popbase, vmacrofile, rfile, animlistflag, fullanimlist, censusruns, outhflag, outgsvars, outpsvars, psinclude, excludelastpop, delaymort0
Environmental and Evolutionary Effects sp_inbrdepr, sp_lethalequiv, sp_percentlethals, sp_evldcorrelation, sp_evcorrelation, Inbreeding_depression, Population_supplementation, other population estimates
Population Density Dependence pop_densitydependence_ddrepro, pop_densitydependence_ddp0, pop_densitydependence_ddpk, pop_densitydependence_ddallee, pop_densitydependence_ddslope
Reproductive Rates pop_reproductiverates_evbreed, pop_reproductiverates_broodmean, pop_reproductiverates_broodsd, pop_reproductiverates_percentbreed, pop_reproductiverates_brood, pop_reproductiverates_broodsize, Percentage_of_females_breeding, Percentage_of_females_at birth
Mortality Rates pop_mortalityrates_evfemalemort, pop_mortalityrates_evmalemort, pop_mortalityrates_femalemort, pop_mortalityrates_malemort, Mortality_ages_0to1, Mortality_after_age_2, Mortality_ages_1to2
Carrying Capacity pop_carryingcapacity_k, pop_carryingcapacity_evk, pop_carryingcapacity_ktrend, pop_carryingcapacity_kchange, pop_carryingcapacity_kcriteria, pop_carryingcapacity_ktest, pop_carryingcapacity_kpriority, pop_carryingcapacity_allowk, pop_carryingcapacity_kallow, pop_carryingcapacity_kyears
Output and File Management extdef1sex, extdeffunc, ext threshold, extdefn, gdinclude
Catastrophe Data pop__catastrophe.label, pop__catastrophe.globallocal, pop__catastrophe.frequency, pop__catastrophe.severityrepro, pop__catastrophe.severitymort, pop_catastrophe1_globallocal, pop_catastrophe1_frequency, pop_catastrophe1_severityrepro, pop_catastrophe1_severitymort, pop_severe_el_nino_globallocal, pop_severe_el_nino_frequency, pop_severe_el_nino_severityrepro, pop_severe_el_nino_severitymort, pop_harsh_winter_globallocal, pop_harsh_winter_frequency, pop_harsh_winter_severityrepro, pop_harsh_winter_severitymort, pop_drought_globallocal, pop_drought_frequency, pop_drought_severityrepro, pop_drought_severitymort, pop_fire_globallocal, pop_fire_frequency, pop_fire_severityrepro, pop_fire_severitymort, pop_hurricane_globallocal, pop_hurricane_frequency, pop_hurricane_severityrepro, pop_hurricane_severitymort, pop_hurricanes_globallocal, pop_hurricanes_frequency, pop_hurricanes_severityrepro, pop_hurricanes_severitymort, pop_disease_globallocal, pop_disease_frequency, pop_disease_severityrepro, pop_disease_severitymort, pop_hunting_globallocal, pop_hunting_frequency, pop_hunting_severityrepro, pop_hunting_severitymort, pop_rodent_crash_globallocal, pop_rodent_crash_frequency, pop_rodent_crash_severityrepro, pop_rodent_crash_severitymort, pop_war_globallocal, pop_war_frequency, pop_war_severityrepro, pop_war_severitymort
Harvest Data pop_harvest_harvest, pop_harvest_startyear, pop_harvest_endyear, pop_harvest_interval, pop_harvest_harvcriteria, pop_harvest_iharvcriteria, pop_harvest_femalesage, pop_harvest_malesage
Supplementation Data pop_supplementation_supplement, pop_supplementation_startyear, pop_supplementation_interval, pop_supplementation_criteria, pop_supplementation_femalesage, pop_supplementation_malesage, pop_supplementation_endyear
Genetic Management Data pop_geneticmanagement_breedmaintaink, pop_geneticmanagement_avoidinbr, pop_geneticmanagement_avoidinbrf, pop_geneticmanagement_pairmkdynamic, pop_geneticmanagement_pairmkstatic, pop_geneticmanagement_setkin, pop_geneticmanagement_maxnmates, pop_geneticmanagement_numtriesfindmate
Other Data pop_monopolization, sex_monogamy, sex_ltmonogamy, sex_femalebreedingage, sex_femalelastbreedingage, sex_maxbroods, sex_usenormal, pop_initialpopulationsize_initialn, Age_of_maturity (months), pop_initialpopulationsize_femalesage, pop_initialpopulationsize_malesage, Reproductive_system, Maximum_age_reproduction, Broods_per_year, Offspring_per_brood, Percentage_of_females_at.birth, scenario, project, reps, runs, r, geomean, geomean bad, sd r, lambda, geomean good, sex_polygamy, sex_ltpolygamy, sex_hermaphroditic, sex_malebreedingage, sex_malelastbreedingage, sex_maximumage, sex_maxbroodsize, sex_sexratio, sex_usefulldistr

API

  1. Global Biodiversity Information Facility (GBIF) • Content: Provides access to global biodiversity occurrence data, including species distribution and abundance data. • Use for PVA: While GBIF focuses on occurrences, the data can be used in conjunction with PVA tools. • Interaction data: Limited, but ecological metadata may provide interaction insights.

  2. IUCN Red List and Spatial Data • Content: Population data, conservation status, and species range maps for many taxa. • Use for PVA: Offers population trends and threats, useful for viability modeling. • Interaction data: Limited but includes information on threats and ecosystem roles.

    1. For example, Bald Eagle-Haliaeetus Leucocephalus**

      1. Search: https://www.iucnredlist.org/species/22695144/264598530
      2. API access: https://api.iucnredlist.org/

    2. Copy Right The IUCN Red List Terms and Conditions specify the following key points related to data usage, including its application in machine learning:

      • Commercial Use Prohibited Without Permission: You cannot use IUCN Red List Data for commercial purposes, which includes using it in projects or activities conducted by a for-profit entity or for revenue generation, without obtaining prior written consent from IUCN. If your machine learning work aligns with these definitions, you will need explicit permission .
      • Derivative Works: Creating derivative works, such as training machine learning models using the data, requires these works to be “transformative” and “include originality.” However, even transformative works that qualify as derivatives require a permission waiver if intended for redistribution or commercial purposes .
      • Permitted Uses: The data may be used for: • Conservation purposes. • Scientific analyses. • Educational activities. Machine learning projects that are non-commercial and aimed at conservation or research could align with these terms if they meet other conditions .
      • Redistribution Restrictions: Redistribution or reposting of data, including through APIs or machine learning models that expose the underlying data, is strictly prohibited unless expressly authorized .
      • Acknowledgement and Citation: Any publications or outputs (even machine learning-based) derived from the data must provide proper attribution to the IUCN Red List .

    3. Implications for Machine Learning

      • Is purely academic or for conservation research,
      • Does not redistribute the data or derivatives without authorization, and
      • Properly acknowledges the IUCN Red List, you are likely within permitted uses. However, commercial projects or those involving public redistribution of models (e.g., via APIs or published tools) would require explicit permission.

  3. BioTIME Database • Content: Temporal biodiversity data, focusing on species abundance and richness over time. • Use for PVA: Excellent for understanding population dynamics and trends. • Interaction data: Focuses on species diversity but lacks detailed interaction networks.

    1. For example, BioTIME Database
      1. DB Download: https://biotime.st-andrews.ac.uk/getFullDownload.php

  4. The Web of Life Database • Content: Contains ecological networks, focusing on species interactions such as pollination, food webs, and mutualisms. • Use for PVA: Provides interaction matrices useful for ecological modeling. • Interaction data: Comprehensive species interaction networks for various ecosystems.

  5. Data Dryad • Content: A repository of ecological datasets, including biodiversity studies, population data, and sometimes interaction data. • Use for PVA: Often includes raw datasets that can be adapted for PVA. • Interaction data: Availability depends on the dataset.

  6. Species Interaction Database (SID) • Content: Global database of species interactions, focusing on plant-animal interactions. • Use for PVA: Use interaction data to model community dynamics. • Interaction data: Detailed interaction data on mutualism and herbivory.

  7. Ecoinformatics Data Portal • Content: Datasets related to species interactions, population studies, and ecological research. • Use for PVA: Offers access to high-quality population and environmental data. • Interaction data: Includes datasets that explicitly detail ecological interactions.

Recommendations for Specific Analysis:

•   Population Viability Analysis (PVA):

Tools like VORTEX or RAMAS can be used alongside raw population data. • Interaction Studies: Explore The Web of Life or integrate network datasets from SID and GBIF with graph-based analysis tools (e.g., R packages like igraph).

Would you like help with extracting or working with these datasets?