This repository contains the code associated with the paper A global database of soil nematode abundance and functional group composition, doi: 10.1038/s41597-020-0437-3. When using these data please cite this publication.
All data are also available via figshare, doi: 10.6084/m9.figshare.c.4718003. Raw nematode abundance data (6,825 samples) are available as a csv file: “nematode_full_dataset_wBiome.csv”. Abundance data aggregated into 30 Arc-seconds pixels (1,933 unique locations), combined with environmental covariate data are available as a csv file: “nematode_abundance_aggregated_wCovar.csv”. Full metadata, including descriptions, units, and source information, of all global covariate layers are available as a csv file: “metadata.csv”.
Code to reproduce summaries, tables and most figures is available as an .Rmd document, knitted version available here.
In the folder data the following files can be found:
nematode_full_dataset_wBiome.csv
| Field | Description |
|---|---|
| Sample_ID | Sample identifier |
| Bacterivores | Number of bacterivorous nematodes per 100g dry soil |
| Fungivores | Number of fungivorous nematodes per 100g dry soil |
| Herbivores | Number of herbivorous nematodes per 100g dry soil |
| Omnivores | Number of omnivorous nematodes per 100g dry soil |
| Predators | Number of predatory nematodes per 100g dry soil |
| Unidentified | Number of unidentified nematodes per 100g dry soil |
| Total_Number | Total number of nematodes per 100g dry soil |
| Latitude | Latitude in WGS84 |
| Longitude | Longitude in WGS84 |
| Pixel_Lat | Pixel latitude in WGS84 |
| Pixel_Long | Pixel longitude in WGS84 |
| WWF_Biome | WWF Biome classification |
| sampling method | Sampling method |
| DOI/URL | Reference including doi where available |
| Data_provider | Original data provider |
nematode_abundance_aggregated_wCovar.csv:
| Band_Name | Description | Layer_Group | Units | Source |
|---|---|---|---|---|
| Aridity_Index | Global AI (Aridity Index) | Process | AI Value | http://www.cgiar-csi.org/data/global-aridity-and-pet-database |
| CliMond_Annual_Mean_Radiation | Annual_Mean_Radiation | Atmospheric/Topographic | W m-2d-1 | https://www.climond.org/BioclimRegistry.aspx#BioclimFAQ |
| CliMond_Highest_Weekly_Radiation | Highest_Weekly_Radiation | Atmospheric/Topographic | W m-2d-1 | https://www.climond.org/BioclimRegistry.aspx#BioclimFAQ |
| CliMond_Lowest_Weekly_Radiation | Lowest_Weekly_Radiation | Atmospheric/Topographic | W m-2d-1 | https://www.climond.org/BioclimRegistry.aspx#BioclimFAQ |
| CliMond_Radiation_Seasonality | Radiation_Seasonality | Atmospheric/Topographic | W m-2d-1 | https://www.climond.org/BioclimRegistry.aspx#BioclimFAQ |
| CliMond_Radiation_of_Coldest_Quarter | Radiation_of_Coldest_Quarter | Atmospheric/Topographic | W m-2d-1 | https://www.climond.org/BioclimRegistry.aspx#BioclimFAQ |
| CliMond_Radiation_of_Driest_Quarter | Radiation_of_Driest_Quarter | Atmospheric/Topographic | W m-2d-1 | https://www.climond.org/BioclimRegistry.aspx#BioclimFAQ |
| CliMond_Radiation_of_Warmest_Quarter | Radiation_of_Warmest_Quarter | Atmospheric/Topographic | W m-2d-1 | https://www.climond.org/BioclimRegistry.aspx#BioclimFAQ |
| CliMond_Radiation_of_Wettest_Quarter | Radiation_of_Wettest_Quarter | Atmospheric/Topographic | W m-2d-1 | https://www.climond.org/BioclimRegistry.aspx#BioclimFAQ |
| EVI | MYD13Q1.006 Vegetation Indices 16-Day Global 250m: NDVI and EVI | Vegetative | EVI Value | https://explorer.earthengine.google.com/#detail/MODIS%2F006%2FMYD13Q1 |
| EarthEnvTexture_CoOfVar_EVI | Coefficient of variation (EVI Heterogeneity); Normalized dispersion of EVI | Process | >=0 | http://www.earthenv.org/texture |
| EarthEnvTexture_Contrast_EVI | Contrast (EVI Heterogeneity); Exponentially weighted difference in EVI between adjacent pixels | Process | >=0 | http://www.earthenv.org/texture |
| EarthEnvTexture_Correlation_EVI | Correlation (EVI Heterogeneity); Linear dependency of EVI on adjacent pixels | Process | >=-1; <=1 | http://www.earthenv.org/texture |
| EarthEnvTexture_Dissimilarity_EVI | Dissimilarity (EVI Heterogeneity); Difference in EVI between adjacent pixels | Process | >=0 | http://www.earthenv.org/texture |
| EarthEnvTexture_Entropy_EVI | Entropy (EVI Heterogeneity); Disorderliness of EVI | Process | >=0 | http://www.earthenv.org/texture |
| EarthEnvTexture_Evenness_EVI | Evenness (EVI Heterogeneity); Evenness of EVI | Process | >=0; <=1 | http://www.earthenv.org/texture |
| EarthEnvTexture_Homogeneity_EVI | Homogeneity (EVI Heterogeneity); Similarity of EVI between adjacent pixels | Process | >=0; <=1 | http://www.earthenv.org/texture |
| EarthEnvTexture_Maximum_EVI | Maximum (EVI Heterogeneity); Dominance of EVI combinations between adjacent pixels | Process | >=0; <=1 | http://www.earthenv.org/texture |
| EarthEnvTexture_Range_EVI | Range (EVI Heterogeneity); Range of EVI | Process | >=0 | http://www.earthenv.org/texture |
| EarthEnvTexture_Shannon_Index | Shannon (EVI Heterogeneity); Diversity of EVI | Process | >=0; <=ln(max # of different EVI) | http://www.earthenv.org/texture |
| EarthEnvTexture_Simpson_Index | Simpson (EVI Heterogeneity); Diversity of EVI | Process | >=0; <=1-1/(max # of different EVI) | http://www.earthenv.org/texture |
| EarthEnvTexture_Std_EVI | Standard deviation (EVI Heterogeneity); Dispersion of EVI | Process | >=0 | http://www.earthenv.org/texture |
| EarthEnvTexture_Uniformity_EVI | Uniformity (EVI Heterogeneity); Orderliness of EVI | Process | >=0; <=1 | http://www.earthenv.org/texture |
| EarthEnvTexture_Variance_EVI | Variance | Process | >=0 | http://www.earthenv.org/texture |
| EarthEnvTopoMed_Eastness | Eastness | Topography | eastness index (-1 to 1) | https://www.earthenv.org/topography |
| EarthEnvTopoMed_Elevation | Elevation (in meters) | Topography | meters | https://www.earthenv.org/topography |
| EarthEnvTopoMed_Hillshade | Hillshade | Topography | grayscale value (shade) | https://www.earthenv.org/topography |
| EarthEnvTopoMed_Northness | Northness | Topography | northness index (-1 to 1) | https://www.earthenv.org/topography |
| EarthEnvTopoMed_Slope | Slope | Topography | (see reference for more information on units) | https://www.earthenv.org/topography |
| Global_Biomass_IPCC | Global Biomass (IPCC Tier 1 Calculated Values) for 2000 | Vegetative | 0.01 tonnes of biomass carbon per hectare | http://cdiac.ess-dive.lbl.gov/epubs/ndp/global_carbon/carbon_documentation.html |
| Gpp | MOD17A3.055: Terra Net Primary Production Yearly Global 1km (including Gross PP) | Process | GPP & NPP Values | https://explorer.earthengine.google.com/#detail/MODIS%2F055%2FMOD17A3 |
| Human_Development_Percentage | Percentage of urban/built-up areas summed with cultivated/managed vegetation (summed via composite code) | Process | percentage (0-100) | https://www.earthenv.org/landcover |
| NDVI | MYD13Q1.006 Vegetation Indices 16-Day Global 250m: NDVI and EVI | Vegetative | EVI Value | https://explorer.earthengine.google.com/#detail/MODIS%2F006%2FMYD13Q1 |
| Nadir_Reflectance_Band1 | MCD43A4.005 BRDF-Adjusted Reflectance 16-Day Global 500m | Vegetative | 7 bands of reflectance (abbreviated "Nadir_Reflectance_Bandx") | https://explorer.earthengine.google.com/#detail/MODIS%2FMCD43A4 |
| Nadir_Reflectance_Band2 | MCD43A4.005 BRDF-Adjusted Reflectance 16-Day Global 500m | Vegetative | 7 bands of reflectance (abbreviated "Nadir_Reflectance_Bandx") | https://explorer.earthengine.google.com/#detail/MODIS%2FMCD43A4 |
| Nadir_Reflectance_Band3 | MCD43A4.005 BRDF-Adjusted Reflectance 16-Day Global 500m | Vegetative | 7 bands of reflectance (abbreviated "Nadir_Reflectance_Bandx") | https://explorer.earthengine.google.com/#detail/MODIS%2FMCD43A4 |
| Nadir_Reflectance_Band4 | MCD43A4.005 BRDF-Adjusted Reflectance 16-Day Global 500m | Vegetative | 7 bands of reflectance (abbreviated "Nadir_Reflectance_Bandx") | https://explorer.earthengine.google.com/#detail/MODIS%2FMCD43A4 |
| Nadir_Reflectance_Band5 | MCD43A4.005 BRDF-Adjusted Reflectance 16-Day Global 500m | Vegetative | 7 bands of reflectance (abbreviated "Nadir_Reflectance_Bandx") | https://explorer.earthengine.google.com/#detail/MODIS%2FMCD43A4 |
| Nadir_Reflectance_Band6 | MCD43A4.005 BRDF-Adjusted Reflectance 16-Day Global 500m | Vegetative | 7 bands of reflectance (abbreviated "Nadir_Reflectance_Bandx") | https://explorer.earthengine.google.com/#detail/MODIS%2FMCD43A4 |
| Nadir_Reflectance_Band7 | MCD43A4.005 BRDF-Adjusted Reflectance 16-Day Global 500m | Vegetative | 7 bands of reflectance (abbreviated "Nadir_Reflectance_Bandx") | https://explorer.earthengine.google.com/#detail/MODIS%2FMCD43A4 |
| Npp | MOD17A3.055: Terra Net Primary Production Yearly Global 1km (including Gross PP) | Process | GPP & NPP Values | https://explorer.earthengine.google.com/#detail/MODIS%2F055%2FMOD17A3 |
| PET | Global PET (Potential Evapotranspiration) | Process | PET Value (mm) | http://www.cgiar-csi.org/data/global-aridity-and-pet-database |
| Pixel_Lat | The latitude value of the pixel's centroid | Process | Decimal degrees | (produced from a generator image with the composite); ee.Image.pixelLonLat() |
| Pixel_Long | The longitude value of the pixel's centroid | Process | Decimal degrees | (produced from a generator image with the composite); ee.Image.pixelLonLat() |
| Population_Density | Gridded Population of the World, Version 4 (GPWv4): UN-Adjusted Population Density | Anthropogenic | persons/km^2 | https://explorer.earthengine.google.com/#detail/CIESIN%2FGPWv4%2Funwpp-adjusted-population-density |
| SG_Bulk_density_015cm | BLDFIE_M_sl3_250m_ll = Bulk density (fine earth) at 0.15m | Soil | kg / cubic–meter | https://www.soilgrids.org ; https://www.isric.org/explore/wosis/accessing-wosis-derived-datasets |
| SG_CEC_015cm | CECSOL_M_sl3_250m_ll = Cation exchange capacity of soil at 0.15m | Soil | cmolc/kg | https://www.soilgrids.org ; https://www.isric.org/explore/wosis/accessing-wosis-derived-datasets |
| SG_Clay_Content_015cm | CLYPPT_M_sl3_250m_ll= Clay content (0–2 micro meter) at 0.15m | Soil | mass fraction in % | https://www.soilgrids.org ; https://www.isric.org/explore/wosis/accessing-wosis-derived-datasets |
| SG_Coarse_fragments_015cm | CRFVOL_M_sl3_250m_ll = Coarse fragments volumetric at 0.15m | Soil | % | https://www.soilgrids.org ; https://www.isric.org/explore/wosis/accessing-wosis-derived-datasets |
| SG_Depth_to_bedrock | BDRICM_M_250m_ll_b1 = Depth to Bedrock (up to 200cm) | Soil | cm (up to 200) | https://www.soilgrids.org ; https://www.isric.org/explore/wosis/accessing-wosis-derived-datasets |
| SG_Probability_of_occurrence_of_R_horizon | BDRLOG_M_250m_ll = Predicted Probability of Occurence (0-100%) in the R Horizon | Soil | (0-100)% | https://www.soilgrids.org ; https://www.isric.org/explore/wosis/accessing-wosis-derived-datasets |
| SG_SOC_Content_015cm | ORCDRC_M_sl3_250m_ll = Soil organic carbon content (fine earth fraction) at 0.15m | Soil | g per kg | https://www.soilgrids.org ; https://www.isric.org/explore/wosis/accessing-wosis-derived-datasets |
| SG_SOC_Stock_005cm_to_015cm | OCSTHA_M_sd2_250m_ll = Soil Organic Carbon Stock from 0.05m-0.15m | Soil | tonnes per ha | https://www.soilgrids.org ; https://www.isric.org/explore/wosis/accessing-wosis-derived-datasets |
| SG_Sand_Content_015cm | SNDPPT_M_sl3_250m_ll = Sand content (50–2000 micro meter) at 0.15m | Soil | mass fraction in % | https://www.soilgrids.org ; https://www.isric.org/explore/wosis/accessing-wosis-derived-datasets |
| SG_Silt_Content_015cm | SLTPPT_M_sl3_250m_ll = Silt content (2–50 micro meter) at 0.15m | Soil | mass fraction in % | https://www.soilgrids.org ; https://www.isric.org/explore/wosis/accessing-wosis-derived-datasets |
| SG_Soil_pH_H2O_015cm | PHIHOX_M_sl3_250m_ll = Soil pH x 10 in H2O at 0.15m | Soil | pH x 10 | https://www.soilgrids.org ; https://www.isric.org/explore/wosis/accessing-wosis-derived-datasets |
| WorldClim2_Annual_Mean_Temperature | WC01 / BIO01 = Annual Mean Temperature | Climatic | ºC | WorldClim2 |
| WorldClim2_Annual_Precipitation | WC12 / BIO12 = Annual Precipitation | Climatic | mm | WorldClim2 |
| WorldClim2_Isothermality | WC03 / BIO03 = Isothermality (BIO2/BIO7) (* 100) | Climatic | Unitless | WorldClim2 |
| WorldClim2_Max_Temperature_of_Warmest_Month | WC05 / BIO05 = Max Temperature of Warmest Month | Climatic | ºC | WorldClim2 |
| WorldClim2_Mean_Diurnal_Range | WC02 / BIO02 = Mean Diurnal Range (Mean of monthly (max temp - min temp)) | Climatic | ºC | WorldClim2 |
| WorldClim2_Mean_Temperature_of_Coldest_Quarter | WC11 / BIO11 = Mean Temperature of Coldest Quarter | Climatic | mm | WorldClim2 |
| WorldClim2_Mean_Temperature_of_Driest_Quarter | WC09 / BIO09 = Mean Temperature of Driest Quarter | Climatic | ºC | WorldClim2 |
| WorldClim2_Mean_Temperature_of_Warmest_Quarter | WC10 / BIO10 = Mean Temperature of Warmest Quarter | Climatic | ºC | WorldClim2 |
| WorldClim2_Mean_Temperature_of_Wettest_Quarter | WC08 / BIO08 = Mean Temperature of Wettest Quarter | Climatic | ºC | WorldClim2 |
| WorldClim2_Min_Temperature_of_Coldest_Month | WC06 / BIO06 = Min Temperature of Coldest Month | Climatic | ºC | WorldClim2 |
| WorldClim2_Precipitation_Seasonality | WC15 / BIO15 = Precipitation Seasonality (Coefficient of Variation) | Climatic | mm | WorldClim2 |
| WorldClim2_Precipitation_of_Coldest_Quarter | WC19 / BIO19 = Precipitation of Coldest Quarter | Climatic | mm | WorldClim2 |
| WorldClim2_Precipitation_of_Driest_Month | WC14 / BIO14 = Precipitation of Driest Month | Climatic | mm | WorldClim2 |
| WorldClim2_Precipitation_of_Driest_Quarter | WC17 / BIO17 = Precipitation of Driest Quarter | Climatic | mm | WorldClim2 |
| WorldClim2_Precipitation_of_Warmest_Quarter | WC18 / BIO18 = Precipitation of Warmest Quarter | Climatic | mm | WorldClim2 |
| WorldClim2_Precipitation_of_Wettest_Month | WC13 / BIO13 = Precipitation of Wettest Month | Climatic | mm | WorldClim2 |
| WorldClim2_Precipitation_of_Wettest_Quarter | WC16 / BIO16 = Precipitation of Wettest Quarter | Climatic | mm | WorldClim2 |
| WorldClim2_Temperature_Annual_Range | WC07 / BIO07 = Temperature Annual Range (BIO5-BIO6) | Climatic | ºC | WorldClim2 |
| WorldClim2_Temperature_Seasonality | WC04 / BIO04 = Temperature Seasonality (standard deviation *100) | Climatic | ºC | WorldClim2 |