fetchKSSL: Get Kellogg Soil Survey Laboratory Data from SoilWeb snapshot

In soilDB: Soil Database Interface

Get Kellogg Soil Survey Laboratory Data from SoilWeb snapshot

Description

Download soil characterization and morphologic data via BBOX, MLRA, or soil series name query, from the KSSL database.

Usage

fetchKSSL(
  series = NA,
  bbox = NA,
  mlra = NA,
  pedlabsampnum = NA,
  pedon_id = NA,
  pedon_key = NA,
  returnMorphologicData = FALSE,
  returnGeochemicalData = FALSE,
  simplifyColors = FALSE,
  progress = TRUE
)

Arguments

series	vector of soil series names, case insensitive
bbox	a single bounding box in WGS84 geographic coordinates e.g. c(-120, 37, -122, 38)
mlra	vector of MLRA IDs, e.g. "18" or "22A"
pedlabsampnum	vector of KSSL pedon lab sample number
pedon_id	vector of user pedon ID
pedon_key	vector of KSSL internal pedon ID
returnMorphologicData	logical, optionally request basic morphologic data, see details section
returnGeochemicalData	logical, optionally request geochemical, optical and XRD/thermal data, see details section
simplifyColors	logical, simplify colors (from morphologic data) and join with horizon data
progress	logical, optionally give progress when iterating over multiple requests

Details

This interface has largely been superseded by the Soil Data Access snapshot of the Laboratory Data Mart, available via fetchLDM().

Series-queries are case insensitive. Series name is based on the "correlated as" field (from KSSL snapshot) when present. The "sampled as" classification was promoted to "correlated as" if the "correlated as" classification was missing.

When returnMorphologicData is TRUE, the resulting object is a list. The standard output from fetchKSSL (SoilProfileCollection object) is stored in the named element "SPC". The additional elements are basic morphologic data: soil color, rock fragment volume, pores, structure, and redoximorphic features. There is a 1:many relationship between the horizon data in "SPC" and the additional dataframes in morph. See examples for ideas on how to "flatten" these tables.

When returnGeochemicalData is TRUE, the resulting object is a list. The standard output from fetchKSSL (SoilProfileCollection object) is stored in the named element "SPC". The additional elements are geochemical and mineralogy analysis tables, specifically: geochemical/elemental analyses "geochem", optical mineralogy "optical", and X-ray diffraction / thermal "xrd_thermal". returnGeochemicalData will include additional dataframes geochem, optical, and xrd_thermal in list result.

Setting simplifyColors=TRUE will automatically flatten the soil color data and join to horizon level attributes.

Function arguments (series, mlra, etc.) are fully vectorized except for bbox.

Value

a SoilProfileCollection object when returnMorphologicData is FALSE, otherwise a list.

Note

SoilWeb maintains a snapshot of these KSSL and NASIS data. The SoilWeb snapshot was developed using methods described here: https://github.com/dylanbeaudette/process-kssl-snapshot. Please use the link below for the live data.

Author(s)

D.E. Beaudette and A.G. Brown

References

http://ncsslabdatamart.sc.egov.usda.gov/

See Also

fetchOSD

Examples

    library(aqp)

    # search by series name
    s <- fetchKSSL(series='auburn')

    # search by bounding-box
    # s <- fetchKSSL(bbox=c(-120, 37, -122, 38))

    # how many pedons
    length(s)

    # plot
    plotSPC(s, name='hzn_desgn', max.depth=150)

    ##
    ## morphologic data
    ##

    # get lab and morphologic data
    s <- fetchKSSL(series='auburn', returnMorphologicData = TRUE)

    # extract SPC
    pedons <- s$SPC

   # if (requireNamespace("farver")) {
   #   ## automatically simplify color data (requires farver)
   #   s <- fetchKSSL(series='auburn', returnMorphologicData = TRUE, simplifyColors=TRUE)
   #   # check
   #   par(mar=c(0,0,0,0))
   #   plot(pedons, color='moist_soil_color', print.id=FALSE)
   # }

soilDB documentation built on Sept. 11, 2024, 8:28 p.m.