soilDB: fetchOSD – R documentation

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fetchOSD

Fetch Official Series Descriptions and summaries from SoilWeb API

Description

This function fetches a variety of data associated with named soil series, extracted from the USDA-NRCS Official Series Description text files and detailed soil survey (SSURGO). These data are periodically updated and made available via SoilWeb.

Usage

fetchOSD(soils, colorState = "moist", extended = FALSE)

Arguments

`soils`	a character vector of named soil series; case-insensitive
`colorState`	color state for horizon soil color visualization: "moist" or "dry"
`extended`	if `TRUE` additional soil series summary data are returned, see details

Details

The standard set of "site" and "horizon" data are returned as a SoilProfileCollection object (extended=FALSE. The "extended" suite of summary data can be requested by setting extended=TRUE. The resulting object will be a list with the following elements:)

SPC: SoilProfileCollection containing standards "site" and "horizon" data
competing: competing soil series from the SC database snapshot
geog_assoc_soils: geographically associated soils, extracted from named section in the OSD
geomcomp: empirical probabilities for geomorphic component, derived from the current SSURGO snapshot
hillpos: empirical probabilities for hillslope position, derived from the current SSURGO snapshot
mtnpos: empirical probabilities for mountain slope position, derived from the current SSURGO snapshot
terrace: empirical probabilities for river terrace position, derived from the current SSURGO snapshot
flats: empirical probabilities for flat landscapes, derived from the current SSURGO snapshot
pmkind: empirical probabilities for parent material kind, derived from the current SSURGO snapshot
pmorigin: empirical probabilities for parent material origin, derived from the current SSURGO snapshot
mlra: empirical MLRA membership values, derived from the current SSURGO snapshot
climate: experimental climate summaries from PRISM stack
metadata: metadata associated with SoilWeb cached summaries

When using extended=TRUE, there are a couple of scenarios in which series morphology contained in SPC do not fully match records in the associated series summaries (e.g. competing).

1. A query for soil series that exist entirely outside of CONUS (e.g. PALAU).: - Climate summaries are empty data.frames because these summaries are currently generated from PRISM. We are working on a solution.
2. A query for data within CONUS, but OSD morphology missing due to parsing error (e.g. formatting, typos).: - Extended summaries are present but morphology missing from SPC. A warning is issued.
3. A query for multiple soil series, with one more more listed as "inactive" (e.g. BREADSPRINGS).: - Extended summaries are present but morphology missing from SPC. A warning is issued.

These last two cases are problematic for analysis that makes use of morphology and extended data, such as outlined in this tutorial on competing soil series.

Value

a SoilProfileCollection object containing basic soil morphology and taxonomic information.

Author(s)

D.E. Beaudette

References

USDA-NRCS OSD search tools: https://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/home/?cid=nrcs142p2_053587

Examples

if(requireNamespace("curl") &
   curl::has_internet()) {
  
  # soils of interest
  s.list <- c('musick', 'cecil', 'drummer', 'amador', 'pentz', 
              'reiff', 'san joaquin', 'montpellier', 'grangeville', 'pollasky', 'ramona')
  
  # fetch and convert data into an SPC
  s.moist <- fetchOSD(s.list, colorState='moist')
  s.dry <- fetchOSD(s.list, colorState='dry')
  
  # plot profiles
  # moist soil colors
  if(require("aqp")) {
    
    par(mar=c(0,0,0,0), mfrow=c(2,1))
    plot(s.moist, name='hzname', 
         cex.names=0.85, axis.line.offset=-4)
    plot(s.dry, name='hzname', 
         cex.names=0.85, axis.line.offset=-4)
    
    # extended mode: return a list with SPC + summary tables
    x <- fetchOSD(s.list, extended = TRUE, colorState = 'dry')
    
    par(mar=c(0,0,1,1))
    plot(x$SPC)
    str(x, 1)
  }
}

soilDB

Soil Database Interface

v2.6.1

GPL (>= 3)

Authors

Dylan Beaudette [aut], Jay Skovlin [aut], Stephen Roecker [aut], Andrew Brown [aut, cre]

Initial release

2021-04-7