Family-level Taxonomic Classes"

In SoilTaxonomy: A System of Soil Classification for Making and Interpreting Soil Surveys

knitr::opts_chunk$set(
  eval = SoilTaxonomy:::.soilDB_metadata_available(min_version = "2.0.0"),
  collapse = TRUE,
  comment = "#>"
)

library(SoilTaxonomy)

parse_family()

The function parse_family() provides a way to separate lower taxonomic levels ("family-level classes") from the higher taxonomic levels (Order, Suborder, Great Group, and Subgroup) in a soil taxon name.

The user provides a vector of family names, and the result is a data.frame containing:

• family (input)
• subgroup (taxonomic subgroup)
• subgroup_code (four or five letter code for subgroup)
• class_string (comma-separated family-level class string in taxon name)
• classes_split (list column containing class_string; split using "," as delimiter)

parse_family("fine-loamy, mixed, semiactive, mesic ultic haploxeralfs")

ST_family_classes

The ST_family_classes data set provides information on the lower taxonomic class names and the Keys used to determine what, if any, class to use for a particular soil.

This data set is a data.frame with the following columns:

• classname (class name used in Soil Taxonomy family name)
• group (simplified grouping of related classes/keys/criteria)
• name (name of relevant section from Keys to Soil Taxonomy)
• chapter (chapter number from Keys to Soil Taxonomy)
• page ([first] page number from Keys to Soil Taxonomy)
• description (narrative description of section; may not be present)
• criteria (criteria listed under "Required Characteristics"; may not be present)

data("ST_family_classes")
head(ST_family_classes)

Here we determine the family-level classes for a single taxonomic family and match them to the class descriptions stored in ST_family_classes using get_ST_family_classes(). We set parse_family(..., column_metadata=FALSE) to not parse family components into corresponding NASIS domains (requires soilDB).

f <- "fine-loamy, mixed, semiactive, mesic ultic haploxeralfs"
family_classes <- parse_family(f, column_metadata = FALSE)$classes_split[[1]]

get_ST_family_classes(classname = family_classes)

SoilTaxonomy documentation built on Nov. 17, 2023, 1:07 a.m.