memoll/2020_global_nematode_dataset

Global Nematode Dataset

Global database of soil nematodes

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.

Data

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

Code to reproduce summaries, tables and most figures is available as an .Rmd document, knitted version available here.

Metadata

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