FedData – Getting assorted geospatial data into R

Kyle Bocinsky

5 years ago

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The package FedData has gone through software review and is now part of rOpenSci. FedData includes functions to automate downloading geospatial data available from several federated data sources (mainly sources maintained by the US Federal government).

Currently, the package enables extraction from six datasets:

The National Elevation Dataset (NED) digital elevation models (1 and 1/3 arc-second; USGS)
The National Hydrography Dataset (NHD) (USGS)
The Soil Survey Geographic (SSURGO) database from the National Cooperative Soil Survey (NCSS), which is led by the Natural Resources Conservation Service (NRCS) under the USDA,
The Global Historical Climatology Network (GHCN), coordinated by National Climatic Data Center at NOAA,
The Daymet gridded estimates of daily weather parameters for North America, version 3, available from the Oak Ridge National Laboratory's Distributed Active Archive Center (DAAC), and
The International Tree Ring Data Bank (ITRDB), coordinated by National Climatic Data Center at NOAA.

FedData is designed with the large-scale geographic information system (GIS) use-case in mind: cases where the use of dynamic web-services is impractical due to the scale (spatial and/or temporal) of analysis. It functions primarily as a means of downloading tiled or otherwise spatially-defined datasets; additionally, it can preprocess those datasets by extracting data within an area of interest (AoI), defined spatially. It relies heavily on the sp, raster, and rgdal packages.

Acknowledgements

FedData is a product of SKOPE (Synthesizing Knowledge of Past Environments) and the Village Ecodynamics Project.

FedData was reviewed for rOpenSci by @jooolia, with @sckott as onboarding editor, and was greatly improved as a result.

TODO

The current CRAN version of FedData, v2.4.6, will (hopefully) be the final CRAN release of FedData 2. FedData 3 will be released in the coming months, but some code built on FedData 2 will not be compatible with FedData 3.

FedData was initially developed prior to widespread use of modern web mapping services and RESTful APIs by many Federal data-holders. Future releases of FedData will limit data transfer by utilizing server-side geospatial and data queries. We will also implement dplyr verbs, tidy data structures, (magrittr) piping, functional programming using purrr, simple features for spatial data from sf, and local data storage in OGC-compliant data formats (probably GeoJSON and NetCDF). I am also aiming for 100% testing coverage.

All that being said, much of the functionality of the FedData package could be spun off into more domain-specific packages. For example, ITRDB download functions could be part of the dplR dendrochronology package; concepts/functions having to do with the GHCN data integrated into rnoaa; and Daymet concepts integrated into daymetr. I welcome any and all suggestions about how to improve the utility of FedData; please submit an issue.

Examples

Load `FedData` and define a study area

# FedData Tester
library(FedData)
library(magrittr)

# Extract data for the Village Ecodynamics Project "VEPIIN" study area:
# http://veparchaeology.org
vepPolygon <- polygon_from_extent(raster::extent(672800, 740000, 4102000, 4170000),
                                  proj4string = "+proj=utm +datum=NAD83 +zone=12")

Get and plot the National Elevation Dataset for the study area

# Get the NED (USA ONLY)
# Returns a raster
NED <- get_ned(template = vepPolygon,
               label = "VEPIIN")
# Plot with raster::plot
raster::plot(NED)

Get and plot the Daymet dataset for the study area

# Get the DAYMET (North America only)
# Returns a raster
DAYMET <- get_daymet(template = vepPolygon,
               label = "VEPIIN",
               elements = c("prcp","tmax"),
               years = 1980:1985)
# Plot with raster::plot
raster::plot(DAYMET$tmax$X1985.10.23)

Get and plot the daily GHCN precipitation data for the study area

# Get the daily GHCN data (GLOBAL)
# Returns a list: the first element is the spatial locations of stations,
# and the second is a list of the stations and their daily data
GHCN.prcp <- get_ghcn_daily(template = vepPolygon,
                            label = "VEPIIN",
                            elements = c('prcp'))
# Plot the NED again
raster::plot(NED)
# Plot the spatial locations
sp::plot(GHCN.prcp$spatial,
         pch = 1,
         add = TRUE)
legend('bottomleft',
       pch = 1,
       legend="GHCN Precipitation Records")

Get and plot the daily GHCN temperature data for the study area

# Elements for which you require the same data
# (i.e., minimum and maximum temperature for the same days)
# can be standardized using standardize==T
GHCN.temp <- get_ghcn_daily(template = vepPolygon,
                            label = "VEPIIN",
                            elements = c('tmin','tmax'),
                            years = 1980:1985,
                            standardize = TRUE)
# Plot the NED again
raster::plot(NED)
# Plot the spatial locations
sp::plot(GHCN.temp$spatial,
         add = TRUE,
         pch = 1)
legend('bottomleft',
       pch = 1,
       legend = "GHCN Temperature Records")

Get and plot the National Hydrography Dataset for the study area

# Get the NHD (USA ONLY)
NHD <- get_nhd(template = vepPolygon,
               label = "VEPIIN")
# Plot the NED again
raster::plot(NED)
# Plot the NHD data
NHD %>%
  lapply(sp::plot,
         col = 'black',
         add = TRUE)

Get and plot the NRCS SSURGO data for the study area

# Get the NRCS SSURGO data (USA ONLY)
SSURGO.VEPIIN <- get_ssurgo(template = vepPolygon,
                     label = "VEPIIN")
#> Warning: 1 parsing failure.
#> row # A tibble: 1 x 5 col     row     col               expected actual expected   <int>   <chr>                  <chr>  <chr> actual 1  1276 slope.r no trailing characters     .5 file # ... with 1 more variables: file <chr>
# Plot the NED again
raster::plot(NED)
# Plot the SSURGO mapunit polygons
plot(SSURGO.VEPIIN$spatial,
     lwd = 0.1,
     add = TRUE)

Get and plot the NRCS SSURGO data for particular soil survey areas

# Or, download by Soil Survey Area names
SSURGO.areas <- get_ssurgo(template = c("CO670","CO075"),
                           label = "CO_TEST")

# Let's just look at spatial data for CO675
SSURGO.areas.CO675 <- SSURGO.areas$spatial[SSURGO.areas$spatial$AREASYMBOL=="CO075",]

# And get the NED data under them for pretty plotting
NED.CO675 <- get_ned(template = SSURGO.areas.CO675,
                            label = "SSURGO_CO675")

# Plot the SSURGO mapunit polygons, but only for CO675
plot(NED.CO675)
plot(SSURGO.areas.CO675,
     lwd = 0.1,
     add = TRUE)

Get and plot the ITRDB chronology locations in the study area

# Get the ITRDB records
ITRDB <- get_itrdb(template = vepPolygon,
                        label = "VEPIIN",
                        makeSpatial = TRUE)
# Plot the NED again
raster::plot(NED)
# Map the locations of the tree ring chronologies
plot(ITRDB$metadata,
     pch = 1,
     add = TRUE)
legend('bottomleft',
       pch = 1,
       legend = "ITRDB chronologies")

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