Taxonomic dictionaries, formative element lists, and functions related to the maintenance, development and application of U.S. Soil Taxonomy.
Data and functionality are based on official U.S. Department of Agriculture sources including the latest edition of the Keys to Soil Taxonomy. Descriptions and metadata are obtained from the National Soil Information System or Soil Survey Geographic databases. Other sources are referenced in the data documentation.
Provides tools for understanding and interacting with concepts in the U.S. Soil Taxonomic System. Most of the current utilities are for working with taxonomic concepts at the “higher” taxonomic levels: Order, Suborder, Great Group, and Subgroup.
Get the stable version from CRAN.
install.packages("SoilTaxonomy")Get the development version from GitHub.
remotes::install_github("ncss-tech/SoilTaxonomy")library(SoilTaxonomy)# hierarchy: order to subgroup
data('ST', package = 'SoilTaxonomy')
# unique taxa: just the taxon names (in order that they "key out" in the keys)
data('ST_unique_list', package = 'SoilTaxonomy')
# formative element dictionary
data('ST_formative_elements', package = 'SoilTaxonomy')
# codes denoting higher taxonomic parent-child relationships (12th Edition Keys to Soil Taxonomy)
data('ST_higher_taxa_codes_12th', package = 'SoilTaxonomy')
# definitions of diagnostic features and characteristics (12th Edition Keys to Soil Taxonomy)
data('ST_features', package = 'SoilTaxonomy')
# definitions of family-level classes and differentiae (12th Edition Keys to Soil Taxonomy)
data('ST_family_classes', package = 'SoilTaxonomy')Several vignettes are included with the package to demonstrate basic functionality:
Two helpful functions that make use of the internal lookup tables are
getTaxonAtLevel() and explainST()
getTaxonAtLevel:
Get taxonomic levels within higher taxonomic groupsgetTaxonAtLevel('acrudoxic plinthic kandiudults') # level = "order" # default
#> acrudoxic plinthic kandiudults
#> "ultisols"
getTaxonAtLevel('acrudoxic plinthic kandiudults', level = "suborder")
#> acrudoxic plinthic kandiudults
#> "udults"
getTaxonAtLevel('acrudoxic plinthic kandiudults', level = "greatgroup")
#> acrudoxic plinthic kandiudults
#> "kandiudults"
getTaxonAtLevel('acrudoxic plinthic kandiudults', level = "subgroup")
#> acrudoxic plinthic kandiudults
#> "acrudoxic plinthic kandiudults"getTaxonAtLevel('folists')
#> folists
#> "histosols"
getTaxonAtLevel('folists', level = "suborder")
#> folists
#> "folists"
getTaxonAtLevel('folists', level = "greatgroup")
#> folists
#> NA
getTaxonAtLevel('folists', level = "subgroup")
#> folists
#> NAexplainST:
Label formative elements with brief explanationsexplainST provides simple narrative explanations of the
formative elements of taxa at the Order, Suborder, Great Group or
Subgroup levels.
cat(explainST('folistels'))
#> folistels
#> | | |
#> mass of leaves
#> | |
#> presence of organic soil materials
#> |
#> soils with permafrost or gelic material within 100cm
cat(explainST('typic endoaqualfs'))
#> typic endoaqualfs
#> | | | |
#> central theme of subgroup concept
#> | | |
#> ground water table
#> | |
#> characteristics associated with wetness
#> |
#> soils with an argillic, kandic, or natric horizon
cat(explainST('abruptic haplic durixeralfs'))
#> abruptic haplic durixeralfs
#> | | | | |
#> abrupt textural change
#> | | | |
#> central theme of subgroup concept
#> | | |
#> presence of a duripan
#> | |
#> xeric SMR
#> |
#> soils with an argillic, kandic, or natric horizon
# convert "taxon code" to taxon name (subgroup)
cat(explainST(taxon_code_to_taxon("ABCD"))) # ABCD = gypsic anhyturbels
#> gypsic anhyturbels
#> | | | |
#> presence of gypsic horizon
#> | | |
#> very dry
#> | |
#> presence of cryoturbation
#> |
#> soils with permafrost or gelic material within 100cm
# all soil orders (LETTERS[1:12]; taxon codes A through L)
res <- lapply(LETTERS[1:12], function(l) cat(explainST(taxon_code_to_taxon(l)), "\n\n"))
#> gelisols
#> |
#> soils with permafrost or gelic material within 100cm
#>
#> histosols
#> |
#> soils with more than 30% organic matter content to a depth of 40cm or more
#>
#> spodosols
#> |
#> soils with a spodic horizon within a depth of 200cm
#>
#> andisols
#> |
#> soils with andic soils properties in 1/2 or more of the upper 60cm
#>
#> oxisols
#> |
#> soils with an oxic horizon, or >40% clay in the surface 18cm and a kandic horizon with < 10% weatherable minerals
#>
#> vertisols
#> |
#> soils containing >30% clay in all horizons and cracks that open and close periodically
#>
#> aridisols
#> |
#> soils with some diagnostic horizons and an aridic SMR
#>
#> ultisols
#> |
#> soils with an argillic or kandic horizon and a base saturation at pH 8.2 <35% at a depth of 180cm
#>
#> mollisols
#> |
#> soils with a mollic epipedon and base saturation at pH 7 >=50% in all depths above 180cm
#>
#> alfisols
#> |
#> soils with an argillic, kandic, or natric horizon
#>
#> inceptisols
#> |
#> soils with an umbric, mollic, or plaggen epipedon, or cambic horizon
#>
#> entisols
#> |
#> other soilsThe ./inst/extdata folder (formerly
./databases) of the GitHub repository formerly contained
data tables related to taxonomic and map unit concepts within the U.S.
Soil Survey Geographic Database (SSURGO).
These databases included:
Statistics on taxonomic subgroups, family-level components, and soil series.
MLRA Overlap tables for series, national map unit symbols and map unit keys.
Summaries of KSSL records per series as well as geomorphic position, parent material origin and kind.
These tables have been moved to a dedicated repository called SoilWeb-data.