SoilTaxonomy

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.

The R package is still in early stages of development, but is entering an "active testing" phase as the scope and application of these tools has become refined over time.

The ./inst/extdata folder (formerly ./databases) of this repository contains a variety of assets related to taxonomic and map unit concepts within the U.S. Soil Survey Geographic Database (SSURGO). See "Static Databases" below for more.

Installation

Get the development version from Github.

remotes::install_github("ncss-tech/SoilTaxonomy")

library(SoilTaxonomy)

Soil Taxonomy "Data Dictionaries"

# hierarchy: order to subgroup
data('ST', package = 'SoilTaxonomy')

# unique taxa: just the names
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')

Functions

getTaxonAtLevel: Get taxonomic levels within higher taxonomic groups

HHCH = Acrudoxic Plinthic Kandiudults

getTaxonAtLevel('acrudoxic plinthic kandiudults') # level = "order" # default
#>       HCCH 
#> "ultisols"

getTaxonAtLevel('acrudoxic plinthic kandiudults', level = "suborder")
#>     HCCH 
#> "udults"

getTaxonAtLevel('acrudoxic plinthic kandiudults', level = "greatgroup")
#>          HCCH 
#> "kandiudults"

getTaxonAtLevel('acrudoxic plinthic kandiudults', level = "subgroup")
#>                             HCCH 
#> "acrudoxic plinthic kandiudults"

BA = Folists

getTaxonAtLevel('folists')
#>          BA 
#> "histosols"

getTaxonAtLevel('folists', level = "suborder")
#>        BA 
#> "folists"

getTaxonAtLevel('folists', level = "greatgroup")
#> BA 
#> NA 

getTaxonAtLevel('folists', level = "subgroup")
#> BA 
#> NA 

explainST: Label formative elements with brief explanations

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

Static Databases

The static data products in this repository include:

• 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.

NOTICE: In the near future, these products may (depending on their data requirements) be:

1. Converted to internal (R package) data sets in SoilTaxonomy, or possibly a new "data" package
2. Routinely generated and provided via SoilKnowledgeBase
3. Provided via a new API (from SoilWeb or ?)

They will after that point be removed from this repository.

Visualize and Extend with data.tree

Static data sets in this R package can be readily visualized with the data.tree package.

Example: show "parent" taxa (Subgroup -> Great Group -> Suborder -> Order)

library(SoilTaxonomy)
library(data.tree)

# load the full hierarchy at the subgroup level
data("ST", package = 'SoilTaxonomy')

# pick 10 taxa
x <- ST[sample(1:nrow(ST), size = 10),]

# construct path
# note: must include a top-level ("ST") in the hierarchy
path <- with(x, paste('ST', subgroup,
                      greatgroup,
                      suborder,
                      order,
                      sep = '/'
))

# convert to data.tree object
n <- as.Node(data.frame(pathString = path), pathDelimiter = '/')

# print
print(n, limit = NULL)
#>                       levelName
#> 1  ST                          
#> 2   ¦--dystric haplustands     
#> 3   ¦   °--haplustands         
#> 4   ¦       °--ustands         
#> 5   ¦           °--andisols    
#> 6   ¦--sodic haplogypsids      
#> 7   ¦   °--haplogypsids        
#> 8   ¦       °--gypsids         
#> 9   ¦           °--aridisols   
#> 10  ¦--lithic calcicryids      
#> 11  ¦   °--calcicryids         
#> 12  ¦       °--cryids          
#> 13  ¦           °--aridisols   
#> 14  ¦--xeric kandihumults      
#> 15  ¦   °--kandihumults        
#> 16  ¦       °--humults         
#> 17  ¦           °--ultisols    
#> 18  ¦--typic acraquox          
#> 19  ¦   °--acraquox            
#> 20  ¦       °--aquox           
#> 21  ¦           °--oxisols     
#> 22  ¦--petroferric haplustults 
#> 23  ¦   °--haplustults         
#> 24  ¦       °--ustults         
#> 25  ¦           °--ultisols    
#> 26  ¦--cumulic haploxerolls    
#> 27  ¦   °--haploxerolls        
#> 28  ¦       °--xerolls         
#> 29  ¦           °--mollisols   
#> 30  ¦--glossic ustic natrargids
#> 31  ¦   °--natrargids          
#> 32  ¦       °--argids          
#> 33  ¦           °--aridisols   
#> 34  ¦--xeric torriorthents     
#> 35  ¦   °--torriorthents       
#> 36  ¦       °--orthents        
#> 37  ¦           °--entisols    
#> 38  °--glacic haploturbels     
#> 39      °--haploturbels        
#> 40          °--turbels         
#> 41              °--gelisols