Package 'geodata'

Title: Download Geographic Data
Description: Functions for downloading of geographic data for use in spatial analysis and mapping. The package facilitates access to climate, crops, elevation, land use, soil, species occurrence, accessibility, administrative boundaries and other data.
Authors: Robert J. Hijmans [cre, aut], Márcia Barbosa [ctb], Aniruddha Ghosh [ctb], Alex Mandel [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
License: GPL (>= 3)
Version: 0.5-9
Built: 2024-02-10 09:00:51 UTC
Source: CRAN

Help Index


Download Geographic Data

Description

Functions for downloading of geographic data for use in spatial analysis and mapping. The package facilitates access to climate, crops, elevation, land use, soil, species occurrence, accessibility, administrative boundaries and other data.

Function Description
bio_oracle Marine data from bio-oracle
cmip6_world Downscaled and calibrated CMIP6 projected future climate data
cmip6_tile Downscaled and calibrated CMIP6 data by tile
country_codes Country codes
crop_calendar_sacks Sachs crop calendar data
crop_monfreda Monfreda crop data (area, yield)
crop_spam SPAM crop data (area, yield, value)
cropland Cropland density for the world from three sources
elevation_3s Elevation data for tile (3 seconds resolution)
elevation_30s Elevation data for by country (30 seconds resolution)
elevation_global Global elevation data (various resolutions)
gadm Administrative boundaries for any country in the world
world Boundaries for the countries in the world
landcover Global landcover data
footprint Human footprint data
osm OpenStreetMap data by country
population Download population density data
soil_af Chemical and physical soil properties data for Africa for different soil depths
soil_af_water Physical soil properties for Africa for water balance computations
soil_af_elements Soil element concentration data for Africa
soil_af_isda Soil data for Africa derived from the iDSA data set
soil_world_vsi Virtually connect to the global soilgrids data
soil_world Global soils data
sp_occurrence Species occurrence data from the Global Biodiversity Information Facility
travel_time Travel time to cities and ports
worldclim_global Global climate data
worldclim_country Climate data by country
worldclim_tile Climate data by tile

Marine data

Description

Marine data from Bio-Oracle

Usage

bio_oracle(path, var, stat, benthic=FALSE, 
		depth="Mean", time="Present", rcp, ...)

Arguments

path

character. Path for storing the downloaded data. See geodata_path

var

character. Variable of interest. One of 'Calcite', 'Chlorophyll', 'Cloud.cover', 'Current.Velocity', 'Diffuse.attenuation', 'Dissolved.oxygen', 'Ice.cover', 'Ice.thickness', 'Iron', 'Light.bottom', 'Nitrate', 'Par', 'pH', 'Phosphate', 'Phytoplankton', 'Primary.productivity', 'Salinity', 'Silicate', 'Temperature'

stat

character. Statistic of interest. One of 'Lt.max', 'Lt.min', 'Max', 'Mean', 'Min', 'Range'. It should be "" if var is "pH"

benthic

logical. If FALSE surface data are returned

depth

character. Either "Min", "Mean", or "Max". Only relevant if benthic is TRUE

time

character. Either "Present", "2150" or "2100"

rcp

character. Either "26", "45", "60", or "85"

...

additional arguments passed to download.file

Value

SpatRaster

References

Assis, J., Tyberghein, L., Bosh, S., Verbruggen, H., Serrão, E.A., & De Clerck, O. (2017). Bio-ORACLE v2.0: Extending marine data layers for bioclimatic modelling. Global Ecology and Biogeography 27: 277-284.

See Also

https://bio-oracle.org/

Examples

x <- bio_oracle(path=tempdir(), "Salinity", "Max", 
		benthic=TRUE, depth="Mean", time="Present")

y <- bio_oracle(path=tempdir(), "Temperature", "Mean", 
		benthic=FALSE, time=2100, rcp=45)

CMIP6 climate model data

Description

Download downscaled and calibrated CMIP6 climate data for projected future climates. Either for the entire world or for a 30 degrees tile. For more information see https://www.worldclim.org/

Usage

cmip6_world(model, ssp, time, var, res, path, ...)

cmip6_tile(lon, lat, model, ssp, time, var, path, ...)

Arguments

model

character. Climate model abbrevation. One of "ACCESS-CM2", "ACCESS-ESM1-5", "AWI-CM-1-1-MR", "BCC-CSM2-MR", "CanESM5", "CanESM5-CanOE", "CMCC-ESM2", "CNRM-CM6-1", "CNRM-CM6-1-HR", "CNRM-ESM2-1", "EC-Earth3-Veg", "EC-Earth3-Veg-LR", "FIO-ESM-2-0", "GFDL-ESM4", "GISS-E2-1-G", "GISS-E2-1-H", "HadGEM3-GC31-LL", "INM-CM4-8", "INM-CM5-0", "IPSL-CM6A-LR", "MIROC-ES2L", "MIROC6", "MPI-ESM1-2-HR", "MPI-ESM1-2-LR", "MRI-ESM2-0", "UKESM1-0-LL"

ssp

character. A valid Shared Socio-economic Pathway code: "126", "245", "370" or "585".

time

character. A valid time period. One of "2021-2040", "2041-2060", or "2061-2080"

var

character. Valid variables names are "tmin", "tmax", "tavg", "prec" and "bioc"

res

numeric. Valid resolutions are 10, 5, 2.5 (minutes of a degree)

path

character. Path for storing the downloaded data. See geodata_path

...

additional arguments passed to download.file

lon

numeric. Longitude

lat

numeric. Latitude

Value

SpatRaster

See Also

vrt to combine tiles

Examples

bio10 <- cmip6_world("CNRM-CM6-1", "585", "2061-2080", 
					var="bioc", res=10, path=tempdir())

Get country codes

Description

Get country codes for all countries in the world.

Usage

country_codes(query=NULL)

Arguments

query

character. A single word that can be used to subset the returned data.frame

Value

data.frame

Examples

cc <- country_codes()
head(cc)

p <- country_codes(query="Per")
p

Sacks crop calendar data

Description

Download Sacks crop calendar data. The crops available are returned by sacksCrops

Usage

crop_calendar_sacks(crop="", path, ...)

sacksCrops()

Arguments

crop

character. Crop name. See sacksCrops for valid names

path

character. Path for storing the downloaded data. See geodata_path

...

additional arguments passed to download.file

Value

SpatRaster

References

Sacks, W.J., D. Deryng, J.A. Foley, and N. Ramankutty, 2010. Crop planting dates: an analysis of global patterns. Global Ecology and Biogeography 19: 607-620. doi:10.1111/j.1466-8238.2010.00551.x.

See Also

https://sage.nelson.wisc.edu/data-and-models/datasets/crop-calendar-dataset/

Examples

cas <- crop_calendar_sacks("cassava", path=tempdir())

Monfreda crop data

Description

Monfreda global crop data (area, yield) for 175 crops.

Data may be freely used for research, study, or teaching, but must be cited appropriately (see below). Re-release of the data, or incorporation of the data into a commercial product, is allowed only with explicit permission.

Usage

monfredaCrops()
crop_monfreda(crop="", var="area_ha", path, ...)

Arguments

crop

character. Crop name(s). See monfredaCrops for valid names

var

character. The variable(s) of interest. Choose from "area_ha" (crop area in ha per cell), "area_f" (crop area as a fraction of each cell), "area_q" (quality of the crop area data), "yield" (crop yield in Mg/ha), "yield_q" (quality of the yield data), "prod" (production per grid cell in Mg), or "all"

path

character. Path for storing the downloaded data. See geodata_path

...

additional arguments passed to download.file

Value

SpatRaster

References

Monfreda, C., N. Ramankutty, and J. A. Foley (2008), Farming the planet: 2. Geographic distribution of crop areas, yields, physiological types, and net primary production in the year 2000, Global Biogeochem. Cycles, 22, GB1022, doi:10.1029/2007GB002947.

See Also

http://www.earthstat.org/harvested-area-yield-175-crops/

Examples

mcas <- crop_monfreda("cassava", path=tempdir())
mcas
names(mcas)

SPAM crop data

Description

SPAM crop data. For each of 42 crops or crop groups get a 10-minute spatial resolution raster with the crop area, yield, production or value by cropping system (rainfed or irrigated, and subsistence, low-input or high-input).

The global data are for 2010. The Africa dataset is for 2017.

Usage

spamCrops()
crop_spam(crop="", var="area", path, africa=FALSE, ...)

Arguments

crop

character. See spamCrops for valid names

var

character. variable of interest. Must be one of "yield", "harv_area" (harvested area), "phys_area" (physical area), "prod" (production) or "val_prod" (value of production)

path

character. Path for storing the downloaded data. See geodata_path

africa

logical. retrieve the (more up to date) data for Africa instead of global data

...

additional arguments passed to download.file

Value

SpatRaster

References

International Food Policy Research Institute, 2019. Global Spatially-Disaggregated Crop Production Statistics Data for 2010 Version 2.0. https://doi.org/10.7910/DVN/PRFF8V, Harvard Dataverse, V4.

International Food Policy Research Institute, 2020. Spatially-Disaggregated Crop Production Statistics Data in Africa South of the Sahara for 2017. https://doi.org/10.7910/DVN/FSSKBW, Harvard Dataverse, V3.

See Also

https://www.mapspam.info/data/

Examples

cas <- crop_spam("cassava", "area", path=tempdir(), TRUE)

Cropland distribution data

Description

Cropland distribution data at a 30-seconds spatial resolution from three sources:

worldcover is derived from the ESA WorldCover data set at 0.3-seconds resolution. (License CC BY 4.0), see https://esa-worldcover.org/en. Values were aggregated and represent the fraction cropland in each cell.

glad is derived from the "Global cropland expansion in the 21st century" (Potatov et al) data available here. Values were aggregated and resampled. They represent the fraction cropland in each cell. There are five layers representing the following years: 2003, 2007, 2011, 2015, and 2019.

QED has cropland distribution data for Africa. The values are probabilities of cropland presence estimated with a neural network that was trained on an initial 1-million point Geosurvey conducted in 2015. License: CC-BY-SA 4.0; https://about.maps.qed.ai/

Usage

cropland(source, path, year, ...)

Arguments

source

character. One of "WorldCover", "GLAD", or "QED"

path

character. Path for storing the downloaded data. See geodata_path

year

numeric. Optional for the GLAD dataset to get data for a single year. One of 2003, 2007, 2011, 2015, and 2019

...

additional arguments passed to download.file

Value

SpatRaster

References

WorldCover: Zanaga, D., Van De Kerchove, R., De Keersmaecker, W., Souverijns, N., Brockmann, C., Quast, R., Wevers, J., Grosu, A., Paccini, A., Vergnaud, S., Cartus, O., Santoro, M., Fritz, S., Georgieva, I., Lesiv, M., Carter, S., Herold, M., Li, Linlin, Tsendbazar, N.E., Ramoino, F., Arino, O., 2021. ESA WorldCover 10 m 2020 v100. doi:10.5281/zenodo.5571936.

GLAD: Potapov, P., S. Turubanova, M.C. Hansen, A. Tyukavina, V. Zalles, A. Khan, X.-P. Song, A. Pickens, Q. Shen, J. Cortez, 2021. Global maps of cropland extent and change show accelerated cropland expansion in the twenty-first century. Nature Food. doi:10.1038/s43016-021-00429-z

See Also

landcover

Examples

#x <- cropland("WorldCover", path=tempdir())

Elevation

Description

Elevation data for any country. The main data source is Shuttle Radar Topography Mission (SRTM) , specifically the hole-filled CGIAR-SRTM (90 m resolution) from https://srtm.csi.cgiar.org/. These data are only available for latitudes between -60 and 60.

The 1 km (30 arc seconds) data were aggregated from SRTM 90 m resolution data and supplemented with the GTOP30 data for high latitudes (>60 degrees).

Usage

elevation_3s(lon, lat, path, ...)
elevation_30s(country, path, mask=TRUE, subs="", ...)
elevation_global(res, path, ...)

Arguments

lon

numeric. Longitude

lat

numeric. Latitude

path

character. Path for storing the downloaded data. See geodata_path

country

character. Country name or code

mask

logical. set grid cells outside of the country boundaries to NA

subs

character

res

numeric. Valid resolutions are 10, 5, 2.5, and 0.5 (minutes of a degree)

...

additional arguments passed to download.file

Value

SpatRaster

Examples

## Not run: 
elevation_30s(country="FRA", path=tempdir() )

## End(Not run)

Human footprint

Description

The "human footprint" is an estimate of the direct and indirect human pressures on the environment. The human pressure is measured using eight variables including built-up environments, population density, electric power infrastructure, crop lands, pasture lands, roads, railways, and navigable waterways. It is expressed on a scale of 0 (low) to 50 (high footprint).

See https://www.nature.com/articles/sdata201667 for the details.

The original data are available here:

https://sedac.ciesin.columbia.edu/data/collection/wildareas-v3

Data are available for two years: 1993 and 2009, for all terrestrial areas except Antarctica. The footprint of seas and oceans was set to zero. The original data was in the Mollweide projection at a 1000 m spatial resolution. The data available through this function was transformed to a longitude/latitude grid at 30-seconds resolution.

Users are free to use, copy, distribute, transmit, and adapt the work for commercial and non-commercial purposes, without restriction, as long as clear attribution of the source is provided.

Usage

footprint(year=2009, path, ...)

Arguments

year

character. "1993" or "2009"

path

character. Path for storing the downloaded data. See geodata_path

...

additional arguments passed to download.file

Value

SpatRaster

References

Venter, O., E. W. Sanderson, A. Magrach, J. R. Allan, J. Beher, K. R. Jones, H. P. Possingham, W. F. Laurance, P. Wood, B. M. Fekete, M. A. Levy, and J. E. Watson. 2016. Sixteen Years of Change in the Global Terrestrial Human Footprint and Implications for Biodiversity Conservation. Nature Communications 7:12558. https://doi.org/10.1038/ncomms12558.

See Also

landcover


Administrative boundaries

Description

Get administrative boundaries for any country in the world. Data are read from files that are downloaded if necessary.

Usage

gadm(country, level=1, path, version="latest", resolution=1, ...)

Arguments

country

character. Three-letter ISO code or full country name. If you provide multiple names they are all downloaded and rbind-ed together

level

numeric. The level of administrative subdivision requested. (starting with 0 for country, then 1 for the first level of subdivision)

path

character. Path for storing the downloaded data. See geodata_path

version

character. Either "latest" or GADM version number (can be "3.6", "4.0" or "4.1")

resolution

integer indicating the level of detail. Only for version 4.1. It should be either 1 (high) or 2 (low)

...

additional arguments passed to download.file

Details

The data are from https://gadm.org

Value

SpatVector

See Also

world

Examples

fra <- gadm(country="FRA", level=1, path=tempdir())

Set the data path

Description

This function allows you set or get the default download path for the geodata package. By setting this path you can avoid downloading the same data many times over. This also guards against website service interruptions.

The default path is ignored if you use the path variable in a function.

To save the default path across sessions, you can add a line like this:

options( geodata_default_path = "c:/your/geodata/path")

to the file returned by

file.path( R.home(), "etc/Rprofile.site")

Alternatively, you can also set a system variable "GEODATA_PATH" to the desired path.

Usage

geodata_path(path)

Arguments

path

character. Path name where the data should be downloaded to. If missing, the current default path is returned

Value

character

Examples

geodata_path()

Landcover data

Description

Landcover data at 30-seconds spatial resolution for (most of) the world. Values are the fraction of a landcover class in each cell. The values are derived from the ESA WorldCover data set at 0.3-seconds resolution. (License CC BY 4.0). See https://esa-worldcover.org/en for more information.

Usage

landcover(var, path, ...)

Arguments

var

character. One of "trees", "grassland", "shrubs", "cropland", "built", "bare", "snow", "water", "wetland", "mangroves", "moss"

path

character. Path for storing the downloaded data. See geodata_path

...

additional arguments passed to download.file

Value

SpatRaster

References

Zanaga, D., Van De Kerchove, R., De Keersmaecker, W., Souverijns, N., Brockmann, C., Quast, R., Wevers, J., Grosu, A., Paccini, A., Vergnaud, S., Cartus, O., Santoro, M., Fritz, S., Georgieva, I., Lesiv, M., Carter, S., Herold, M., Li, Linlin, Tsendbazar, N.E., Ramoino, F., Arino, O., 2021. ESA WorldCover 10 m 2020 v100. doi:10.5281/zenodo.5571936.

See Also

landcover


OpenStreetMap data

Description

Get OpenStreetMap (OSM) data

Usage

osm(country, var, path, proxy=FALSE, ...)

Arguments

country

character. Three-letter ISO code or full country name

var

character. Currently it can be one of "places", "highways", or "railway"

path

character. Path for storing the downloaded data. See geodata_path

proxy

logical. Return a SpatVectorProxy?

...

additional arguments passed to download.file

Details

License: Open Data Commons Open Database License (ODbL).

See https://www.openstreetmap.org/copyright

Value

SpatVector

Examples

aruba <- osm(country="Aruba", "places", path=tempdir())

population density

Description

Download population density data.

Source: Gridded Population of the World (GPW), v4. Documentation:

http://sedac.ciesin.columbia.edu/data/collection/gpw-v4/documentation

Usage

population(year, res, path, ...)

Arguments

year

numeric. One of 2000, 2005, 2010, 2015, 2020

res

numeric. Valid resolutions are 10, 5, 2.5, and 0.5 (minutes of a degree)

path

character. Path for storing the downloaded data. See geodata_path

...

additional arguments passed to download.file

Value

SpatRaster

References

Center for International Earth Science Information Network - CIESIN - Columbia University. 2018. Gridded Population of the World, Version 4 (GPWv4): Population Density, Revision 11. Palisades, NY: NASA Socioeconomic Data and Applications Center (SEDAC). doi:10.7927/H49C6VHW. Accessed 6 July 2021.

Examples

pop <- population(2020, 10, path=tempdir())

crop calendar for rice

Description

Get crop calendar and production data for rice

Usage

rice_calendar(path, ...)

Arguments

path

character. Path for storing the downloaded data. See geodata_path

...

additional arguments passed to download.file

Value

SpatVectorCollection

References

Laborte, A.G.; Gutierrez, M.A.; Balanza, J.G.; Saito, K.; Zwart, S.J.; Boschetti, M.; Murty, MVR; Villano, L.; Aunario, J.K.; Reinke, R.; Koo, J.; Hijmans, R.J.; Nelson, A., 2017. RiceAtlas, a spatial database of global rice calendars and production. Scientific Data 4: 170074 doi:10.1038/sdata.2017.74

Examples

rice <- rice_calendar(path=tempdir())
cal <- rice[1]

Soil data for Africa

Description

Download chemical soil properties data for Africa for different soil depths. The spatial resolution is 30 arc-seconds (about 1 km2), aggregated from the original 250m resolution.

There are more recent estimations for some of the properties available in other data sets. See soil_af_isda and soil_world.

For more info, see https://www.isric.org/projects/soil-property-maps-africa-250-m-resolution

The data have a CC-BY 4.0 NC license

Usage

soil_af(var, depth, path, ...)

Arguments

var

character. Variables name such as "pH" or "clay". See Details

depth

numeric. One of 5, 15, 30, 60, 100, 200. This is shorthand for the following depth ranges: 0-5, 5-15, 15-30, 30-60, 60-100, 100-200 cm. Or one of 20, 50 for 0-20 or 20-50 cm

path

character. Path for storing the downloaded data. See geodata_path

...

additional arguments passed to download.file

Details

var description unit
clay Soil texture fraction clay %
sand Soil texture fraction sand %
silt Soil texture fraction silt %
coarse Coarse fragments volumetric %
SOC Organic carbon g kg-1 (‰)
BLKD Bulk density (fine earth) kg m-3
poros Porosity (volum. fraction) based on PTF -
AWpF2.0 Avail. soil water capacity (vol. frac.) for FC = pF 2.0 -
AWpF2.3 Avail. soil water capacity (vol. frac.) for FC = pF 2.3 -
AWpF2.5 Avail. soil water capacity (vol. frac.) for FC = pF 2.4 -
AWpF4.2 Avail. soil wat. cap. (vol. frac.) at wilting point (pF 4.2) -
BDR Depth to bedrock cm
. . .
pH pH (H2O) -
ECN Electrical conductivity mS/m (?)
acid-exch Exchangeable acidity cmol(+) kg-1
bases-exch Sum of exchangeable bases cmol(+) kg-1
CEC Cation Exchange Capacity cmol(+) kg-1
Al-extr Extractable Aluminum (Mehlich 3) mg kg-1 (ppm)
Al-exch Exchangeable Aluminum cmol(+) kg-1
Ca-exch Exchangeable Calcium cmol(+) kg-1
K-exch Exchangeable Potassium cmol(+) kg-1
Mg-exch Exchangeable Magnesium cmol(+) kg-1
Na-exch Exchangeable Sodium cmol(+) kg-1
Ntot Total nitrogen g kg-1

Value

SpatRaster

References

Hengl T, Heuvelink GBM, Kempen B, Leenaars JGB, Walsh MG, Shepherd KD, et al. (2015) Mapping Soil Properties of Africa at 250 m Resolution: Random Forests Significantly Improve Current Predictions. PLoS ONE 10(6): e0125814. doi:10.1371/journal.pone.0125814

See Also

soil_af_elements, soil_af_isda, soil_world_vsi

Examples

aph <- soil_af(var="ph", depth=5, path=tempdir())

Soil elements data for Africa

Description

Connect to or download chemical soil element concentration (for the 0-30 cm topsoil) data for Africa. The spatial resolution is 30 arc-seconds (about 1 km2), aggregated from the original 250 m spatial resolution.

The data have an Open Data Commons Open Database License (ODbL)

For more information, see https://www.isric.org/projects/soil-property-maps-africa-250-m-resolution

Usage

soil_af_elements(var, path, ...)

Arguments

var

character. Variables name. One of: "Al", "B", "Ca", "Cu", "Fe", "K", "Mg", "Mn", "N", "Na", "P", "Ptot", "Zn". See Details

path

character. Path for storing the downloaded data. See geodata_path

...

additional arguments passed to download.file

Details

var description unit
Al Extractable aluminum mg kg-1 (ppm)
B Extractable boron mg kg-1 (ppm)
Ca Extractable calcium mg kg-1 (ppm)
Cu Extractable copper mg kg-1 (ppm)
Fe Extractable iron mg kg-1 (ppm)
K Extractable potassium mg kg-1 (ppm)
Mg Extractable magnesium mg kg-1 (ppm)
Mn Extractable manganese mg kg-1 (ppm)
N Organic nitrogen mg kg-1 (ppm)
Na Extractable sodium mg kg-1 (ppm)
P Extractable phosphorus mg (100 kg-1)
Ptot Total phosphorus mg (100 kg-1)
Zn Extractable zinc mg kg-1 (ppm)

Value

SpatRaster

References

Hengl T, Heuvelink GBM, Kempen B, Leenaars JGB, Walsh MG, Shepherd KD, et al. (2015) Mapping Soil Properties of Africa at 250 m Resolution: Random Forests Significantly Improve Current Predictions. PLoS ONE 10(6): e0125814. doi:10.1371/journal.pone.0125814

See Also

soil_af, soil_af_isda, soil_world

Examples

fe <- soil_af_elements("Fe", path=tempdir(), quiet=TRUE)

iSDA soil data for Africa

Description

Download soil data for Africa derived from the iDSA data set. The original data were aligned and aggregated to 30 arc-seconds (about 1 km2). The original spatial resolution was 30m.

For more info see:

https://envirometrix.nl/isdasoil-open-soil-data-for-africa/

https://zenodo.org/search?page=1&size=20&q=iSDAsoil

Usage

soil_af_isda(var, depth=20, error=FALSE, path, virtual=FALSE, ...)

Arguments

var

character. The variables name, one of: "Al", "bdr", "clay", "C.tot", "Ca", "db.od", "eCEC.f", "Fe", "K", "Mg", "N.tot", "oc", "P", "pH.H2O", "sand", "silt", "S", "texture", "wpg2", "Zn".see Details

depth

numeric. One of 20 (for 0-20 cm) and 50 (for 20-50 cm). Ignored if var="bdr" for which the depth is always 0-200 cm

error

logical. If TRUE the error estimates are returned

path

character. Path for storing the downloaded data. See geodata_path

virtual

logical. If TRUE a virtual connection to the file is returned. This is useful if you want to extract a small area without downloading the entire raster

...

additional arguments passed to download.file

Details

var description unit
Al extractable aluminum mg kg-1
bdr bed rock depth cm
clay clay content %
C.tot total carbon kg-1
Ca extractable calcium mg kg-1
db.od bulk density kg m-3
eCEC.f effective cation exchange capacity cmol(+) kg-1
Fe extractable iron mg kg-1
K extractable potassium mg kg-1
Mg extractable magnesium mg kg-1
N.tot total organic nitrogen g kg-1
OC Organic Carbon g kg-1
P Phosphorus content mg kg-1
pH.H2O pH (H2O) -
sand Sand content %
silt Silt content %
S Extractable sulfer mg kg-1
texture texture class -
wpg2 stone content %
Zn Extractable zinc mg kg-1

Value

SpatRaster

References

Tomislav Hengl, Matthew A. E. Miller, Josip Križan, Keith D. Shepherd, Andrew Sila, Milan Kilibarda, Ognjen Antonijevic, Luka Glušica, Achim Dobermann, Stephan M. Haefele, Steve P. McGrath, Gifty E. Acquah, Jamie Collinson, Leandro Parente, Mohammadreza Sheykhmousa, Kazuki Saito, Jean-Martial Johnson, Jordan Chamberlin, Francis B. T. Silatsa, Martin Yemefack, John Wendt, Robert A. MacMillan, Ichsani Wheeler & Jonathan Crouch, 2021. African soil properties and nutrients mapped at 30 m spatial resolution using two-scale ensemble machine learning. Scientific Reports 11: 6130.

See Also

soil_af_elements, soil_af, soil_world

Examples

afph <- soil_af_isda("ph.h2o", path=tempdir(), quiet=TRUE)

Soil data for water balance computation (Africa only)

Description

Download physical soil properties data for Africa that can be used in water balance computation. The values are for a soil depth of 0 to 30 cm. The spatial resolution is 30 arc-seconds (about 1 km2), aggregated from the original 250m resolution.

For other properties see soil_af, soil_af_elements, soil_af_isda.

For more info, see https://www.isric.org/projects/soil-property-maps-africa-250-m-resolution

The data have a CC-BY 4.0 NC license

Usage

soil_af_water(var, depth = "30cm", path, ...)

Arguments

var

character. Variables name such as "awcpf23" or "pwp". See Details

depth

character. Either "30cm" or "erzd" (the effective rooting zone depth of maize)

path

character. Path for storing the downloaded data. See geodata_path

...

additional arguments passed to download.file

Details

var description unit
awcpf23 Available water capacity of the fine earth at field capacity (pF 2.3) volumetric %
pwp Moisture content of the fine earth at permanent wilting point (pF 4.2) volumetric %
tetas Moisture content of the fine earth at saturation volumetric %
tawcpf23 Absolute total available water capacity cm?
tawcpf23mm Absolute total available water capacity in mm mm
erzd Effective root zone depth (for maize) cm

Value

SpatRaster

See Also

soil_af_elements, soil_af_isda, soil_world

Examples

tetaS <- soil_af_water(var="tetas", depth="erzd", path=tempdir())

Global soil data

Description

Download global soils data. The data are derived from the SoilGRIDS database. The data were aggregated and transformed to a longitude/latitude coordinate reference system with 30-second spatial resolution.

See https://www.isric.org/explore/soilgrids for more info.

data license: CC-BY 4.0

Usage

soil_world(var, depth, stat="mean", name="", path, ...)

Arguments

var

character. Variables name. One of: "bdod", "cfvo", "clay", "nitrogen", "ocd", "ocs", "phh2o", "sand", "silt", "soc", "wrb". See Details

depth

numeric. One of 5, 15, 30, 60, 100, 200. This is shorthand for the following depth ranges: 0-5, 5-15, 15-30, 30-60, 60-100, 100-200 cm. Ignored if var="wrb"

stat

character. One of "mean", "uncertainty", "Q0.05", "Q0.5", "Q0.95". Ignored if var="wrb"

name

character. One of "Acrisols", "Albeluvisols", "Alisols", "Andosols", "Arenosols", "Calcisols", "Cambisols", "Chernozems", "Cryosols", "Durisols", "Ferralsols", "Fluvisols", "Gleysols", "Gypsisols", "Histosols", "Kastanozems", "Leptosols", "Lixisols", "Luvisols", "Nitisols", "Phaeozems", "Planosols", "Plinthosols", "Podzols", "Regosols", "Solonchaks", "Solonetz", "Stagnosols", "Umbrisols", "Vertisols". Only used when var="wrb"

path

character. Path for storing the downloaded data. See geodata_path

...

additional arguments passed to download.file

Details

var description unit
bdod Bulk density of the fine earth fraction kg dm-3
cec Cation Exchange Capacity of the soil cmol(+) kg-1
cfvo Vol. fraction of coarse fragments (> 2 mm) %
nitrogen Total nitrogen (N) g kg-1
phh2o pH (H2O) -
sand Sand (> 0.05 mm) in fine earth %
silt Silt (0.002-0.05 mm) in fine earth %
clay Clay (< 0.002 mm) in fine earth %
soc Soil organic carbon in fine earth g kg-1
ocd Organic carbon density kg m-3
ocs Organic carbon stocks kg m-2

Value

SpatRaster

References

Poggio L., de Sousa L.M., Batjes N.H., Heuvelink G.B.M., Kempen B., Ribeiro E., Rossiter D., 2021. SoilGrids 2.0: producing soil information for the globe with quantified spatial uncertainty. Soil 7:217-240, 2021. doi:10.5194/soil-7-217-2021

See Also

For virtual access to the original data: soil_world_vsi For Africa: soil_af_isda, soil_af, soil_af_elements

Examples

gph <- soil_world(var="phh2o", depth=5, path=tempdir())

soil grids_vsi

Description

Virtually connect to the global soilgrids data. See https://www.isric.org/explore/soilgrids for more info.

data license: CC-BY 4.0

Usage

soil_world_vsi(var, depth, stat="mean", name="")

Arguments

var

character. Variables name. One of: "bdod", "cfvo", "clay", "nitrogen", "ocd", "ocs", "phh2o", "sand", "silt", "soc", "wrb". See Details

depth

numeric. One of 5, 15, 30, 60, 100, 200. This is shorthand for the following depth ranges: 0-5, 5-15, 15-30, 30-60, 60-100, 100-200 cm. Ignored if var="wrb"

stat

character. One of "mean", "uncertainty", "Q0.05", "Q0.5", "Q0.95". Ignored if var="wrb"

name

character. One of 'Acrisols', 'Albeluvisols', 'Alisols', 'Andosols', 'Arenosols', 'Calcisols', 'Cambisols', 'Chernozems', 'Cryosols', 'Durisols', 'Ferralsols', 'Fluvisols', 'Gleysols', 'Gypsisols', 'Histosols', 'Kastanozems', 'Leptosols', 'Lixisols', 'Luvisols', 'Nitisols', 'Phaeozems', 'Planosols', 'Plinthosols', 'Podzols', 'Regosols', 'Solonchaks', 'Solonetz', 'Stagnosols', 'Umbrisols', 'Vertisols'. Only used when var="wrb"

Details

The below table lists the variable names, a description, and the units of the variables. Note that these units are not standard units, and are different from the data for other soil data available through this package.

var description unit
bdod Bulk density of the fine earth fraction cg cm-3
cec Cation Exchange Capacity of the soil mmol(+) kg-1
cfvo Vol. fraction of coarse fragments (> 2 mm)
nitrogen Total nitrogen (N) cg kg-1
phh2o pH (H2O) -
sand Sand (> 0.05 mm) in fine earth
silt Silt (0.002-0.05 mm) in fine earth
clay Clay (< 0.002 mm) in fine earth
soc Soil organic carbon in fine earth dg kg-1
ocd Organic carbon density hg m-3
ocs Organic carbon stocks hg m-2

Value

SpatRaster

References

Poggio, L., de Sousa, L.M., Batjes, N.H., Heuvelink, G.B.M., Kempen, B., Ribeiro, E., and Rossiter, D., 2021. SoilGrids 2.0: producing soil information for the globe with quantified spatial uncertainty. Soil 7:217-240, 2021. doi:10.5194/soil-7-217-2021

See Also

soil_world to download these data at 30-seconds spatial resolution.

For Africa: soil_af_isda, soil_af, soil_af_elements

Examples

ph <- soil_world_vsi(var="phh2o", depth=5)
# perhaps this does not work anymore
#plot(ph, maxcell=10000)

Download species occurrence data from GBIF

Description

Download data from the Global Biodiversity Information Facility (GBIF) data portal.

sp_genus returns a data.frame with all the species names associated with a genus.

sp_occurrence downloads species occurrence records. You can download data for a single species or for an entire genus by using species="". Note that the maximum number of records that can be downloaded for a single search is 100,000.

You can check the number of records returned by using the option download=FALSE.

To avoid getting more than 100,000 records, you can do separate queries for different geographic areas. This has been automated in sp_occurrence_split. This function recursively splits the area of interest into smaller areas until the number of records in an area is less than 50,000. It then downloads these records and saves them in a folder called "gbif". After all areas have been evaluated, the data are combined into a single file and returned as a data.frame). If the function is interrupted, it can be run again, and it will resume where it left off.

If you want to download data for an entire genus, first run sp_genus and then download data for the returned species names one by one.

Before using this function, please first check the GBIF data use agreement and see the note below about how to cite these data.

Usage

sp_genus(genus, simple=TRUE, ...)

sp_occurrence(genus, species="", ext=NULL, args=NULL, geo=TRUE, 
	removeZeros=FALSE, download=TRUE, ntries=5, nrecs=300, 
	start=1, end=Inf, fixnames=TRUE, ...)

sp_occurrence_split(genus, species="", path=".", ext=c(-180,180,-90,90),
	args=NULL, geo=TRUE, removeZeros=FALSE, ntries=5, nrecs=300,
	fixnames=TRUE, prefix=NULL, ...)

Arguments

genus

character. genus name

species

character. species name. Can be left blank to get the entire genus

ext

SpatExtent object to limit the geographic extent of the records. A SpatExtent can be created using functions like ext and draw

args

character. Additional arguments to refine the query. See query parameters in http://www.gbif.org/developer/occurrence for more details

geo

logical. If TRUE, only records that have a georeference (longitude and latitude values) will be downloaded

removeZeros

logical. If TRUE, all records that have a latitude OR longitude of zero will be removed if geo==TRUE, or set to NA if geo==FALSE. If FALSE, only records that have a latitude AND longitude that are zero will be removed or set to NA

download

logical. If TRUE, records will be downloaded, else only the number of records will be shown

ntries

integer. How many times should the function attempt to download the data, if an invalid response is returned (perhaps because the GBIF server is very busy)

nrecs

integer. How many records to download in a single request (max is 300)?

start

integer. Record number from which to start requesting data

end

integer. Last record to request

fixnames

If TRUE a few unwieldy and poorly chosen variable names are changed as follows. "decimalLatitude" to "lat", "decimalLongitude" to "lon", "stateProvince" to "adm1", "county" to "adm2", "countryCode" to "ISO2". The names in "country" are replaced with the common (short form) country name, the original values are stored as "fullCountry"

path

character. Where should the data be downloaded to (they will be put in a subdirectory "gbif")?

prefix

character. prefix of the downloaded filenames (best left NULL, the function will then use "genus_species"

simple

logical. If TRUE, a vector the accepted species names are returned. Otherwise a data.frame with much more information is returned

...

additional arguments passed to download.file

Value

data.frame

Note

Under the terms of the GBIF data user agreement, users who download data agree to cite a DOI. Citation rewards data-publishing institutions and individuals and provides support for sharing open data [1][2]. You can get a DOI for the data you downloaded by creating a "derived" dataset. For this to work, you need to keep the "datasetKey" variable in your dataset.

References

https://www.gbif.org/occurrence https://www.gbif.org/derived-dataset/about

Examples

## Not run: 

sp_occurrence("solanum", download=FALSE)
sp_occurrence("solanum", "acaule", download=FALSE)

sp_occurrence("Batrachoseps", "" , down=FALSE)
sp_occurrence("Batrachoseps", "luciae", down=FALSE)
g <- sp_occurrence("Batrachoseps", "luciae", geo=TRUE, end=25)
plot(g[, c("lon", "lat")])


## args
a1 <- sp_occurrence("Elgaria", "multicarinata", 
			args="recordNumber=Robert J. Hijmans RH-2")
a2 <- sp_occurrence("Batrachoseps", "luciae",
			args=c("year=2023", "identifiedBy=Anthony Ye"))

## year supports "range queries"
a3 <- sp_occurrence("Batrachoseps", "luciae", 
			args=c("year=2020,2023", "identifiedBy=Kuoni W"))
table(a3[,c("year")])

## End(Not run)

Travel time to a city or port

Description

Download travel time to a city or port data on rasters at a 30 arc-seconds (about 1 km2) resolution.

Usage

travel_time(to="city", size=1, up=FALSE, path, ...)

Arguments

to

character. "city" or "port"

size

positive integer indicating the size of the city or port. Can be between 1 and 9 if to="city" or between 1 and 5 if to="port". See Details

up

logical. If TRUE the travel time to a city of the size chosen or larger is returned

path

character. Path for storing the downloaded data. See geodata_path

...

additional arguments passed to download.file

Details

Description of the the size argument.

to="city"

size Inhabitants
1 5,000,000 to 50,000,000
2 1,000,000 to 5,000,000
3 500,000 to 1,000,000
4 200,000 to 500,000
5 100,000 to 200,000
6 50,000 to 100,000
7 20,000 to 50,000
8 10,000 to 20,000
9 5,000 to 10,000

to="port"

size Description Number of ports
1 Large 160
2 Medium 361
3 Small 990
4 Very small 2,153
5 Any 3,778

Value

SpatRaster

References

Nelson, A., D.J. Weiss, J. van Etten, A. Cattaneo, T.S. McMenomy & J. Koo, 2019. A suite of global accessibility indicators. Scientific Data 6: 266. doi:10.1038/s41597-019-0265-5

Version 3 (2019-05-15) from https://figshare.com/articles/dataset/Travel_time_to_cities_and_ports_in_the_year_2015/7638134/3

Examples

ttime <- travel_time("city", 2, path=tempdir(), quiet=TRUE)

Administrative boundaries

Description

Get the borders for all the countries in the world. Data are read from files that are downloaded if necessary.

Usage

world(resolution=5, level=0, path, version="latest", ...)

Arguments

resolution

integer between 1 and 5 indicating the level of detail. 1 is high 5 is low

level

numeric. The level of administrative subdivision requested. (starting with 0 for country, then 1 for the first level of subdivision). Only level 0 is currently available

path

character. Path for storing the downloaded data. See geodata_path

version

character. Only "3.6" is currently supported

...

additional arguments passed to download.file

Details

The data are from https://gadm.org

Value

SpatVector

See Also

gadm

Examples

w <- world(path=tempdir())

WorldClim climate data

Description

Download climate data from WorldClim version 2.1. See Details for variables and units.

Usage

worldclim_global(var, res, path, version="2.1", ...)
worldclim_country(country, var, path, version="2.1", ...)
worldclim_tile(var, lon, lat, path, version="2.1", ...)

Arguments

var

character. Valid variables names are "tmin", "tmax", "tavg", "prec", "wind", "vapr", and "bio"

res

numeric. Valid resolutions are 10, 5, 2.5, and 0.5 (minutes of a degree)

path

character. Path for storing the downloaded data. See geodata_path

country

character. Country name or code

lon

numeric. Longitude

lat

numeric. Latitude

version

character or numeric. WorldClim version number. Only "2.1" supported at the moment

...

additional arguments passed to download.file

Details

These are the WorldClim monthly average climate data.

Variable Description Unit
tmin minimum temperature °C
tmax maximum temperature °C
tavg average temperature °C
prec total precipitation mm
srad incident solar radiation kJ m-2 day-1
wind wind speed (2 m above the ground) m s-1
vapr vapor pressure kPa

Value

SpatRaster

See Also

https://www.worldclim.org/

Examples

lux <- worldclim_country("Luxembourg", var="tmin", path=tempdir())