Package 'SoilTaxonomy' reference manual

Title:	A System of Soil Classification for Making and Interpreting Soil Surveys
Description:	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.
Authors:	Andrew Brown [aut, cre], Dylan Beaudette [aut]
Maintainer:	Andrew Brown <[email protected]>
License:	GPL (>= 3)
Version:	0.2.6
Built:	2024-10-31 05:36:24 UTC
Source:	https://github.com/ncss-tech/soiltaxonomy

Determine taxonomic level of a taxonomic letter code

Description

Determine taxonomic level of a taxonomic letter code

Usage

code_to_level(code)
code_to_level(code)

Arguments

code

A character vector of taxon codes (case sensitive)

Value

A character vector containing "order", "suborder", "greatgroup" or "subgroup"

Examples


# order level code (1 character)
code_to_level("B")

# subgroup level code (4 characters)
code_to_level("ABCD")

# subgroup level code (5 characters, 4 uppercase + 1 lowercase)
code_to_level("IFFZh")

# order level code (1 character)
code_to_level("B")

# subgroup level code (4 characters)
code_to_level("ABCD")

# subgroup level code (5 characters, 4 uppercase + 1 lowercase)
code_to_level("IFFZh")

Decompose taxon letter codes

Description

Find all codes that logically comprise the specified codes. For instance, code "ABC" ("Anhyturbels") returns "A" ("Gelisols"), "AB" ("Turbels"), "ABC" ("Anhyturbels"). Use in conjunction with a lookup table that maps Order, Suborder, Great Group and Subgroup taxa to their codes (see taxon_code_to_taxon and taxon_to_taxon_code).

Usage

decompose_taxon_code(codes)
decompose_taxon_code(codes)

Arguments

codes

A character vector of taxon codes to "decompose" – case sensitive

Details

Accounts for Keys that run out of capital letters (more than 26 subgroups) and use lowercase letters for a unique subdivision within the "fourth character position."

Value

A list with equal length to input vector; one character vector per element

Examples


decompose_taxon_code(c("ABC", "ABCDe", "BCDEf"))

decompose_taxon_code(c("ABC", "ABCDe", "BCDEf"))

Explain a taxon name using formative elements

Description

Explain a taxon name using formative elements

Usage

explainST(x, format = c("text", "html"), viewer = TRUE)
explainST(x, format = c("text", "html"), viewer = TRUE)

Arguments

`x`	a Subgroup, Great Group, Suborder or Order-level taxonomic name; matching is exact and case-insensitive
`format`	output format: 'text' \| 'html'
`viewer`	show `format = 'html'` output in browser? default: `TRUE`

Value

a block of text, suitable for display in fixed-width font

Examples


cat(explainST("ids"), "\n\n")              #  -ids (order suffix) 
cat(explainST("aridisols"), "\n\n")        # Aridisols (order name)
cat(explainST("argids"), "\n\n")           # Arg- (suborder) 
cat(explainST("haplargids"), "\n\n")       # Hap- (great group)
cat(explainST("typic haplargids"), "\n\n") # Typic (subgroup)

cat(explainST("ids"), "\n\n")              #  -ids (order suffix) 
cat(explainST("aridisols"), "\n\n")        # Aridisols (order name)
cat(explainST("argids"), "\n\n")           # Arg- (suborder) 
cat(explainST("haplargids"), "\n\n")       # Hap- (great group)
cat(explainST("typic haplargids"), "\n\n") # Typic (subgroup)

Extract Soil Moisture Regime from Subgroup or Higher Level Taxon

Description

Extract Soil Moisture Regime from Subgroup or Higher Level Taxon

Usage

extractSMR(taxon, as.is = FALSE, droplevels = FALSE, ordered = TRUE)
extractSMR(taxon, as.is = FALSE, droplevels = FALSE, ordered = TRUE)

Arguments

`taxon`	character. Vector of taxon names.
`as.is`	Return character labels rather than an (ordered) factor? Default: `FALSE`
`droplevels`	Drop unused levels? Default: `FALSE`
`ordered`	Create an ordinal factor? Default: `TRUE`

Value

an (ordered) factor of Soil Moisture Regimes, or character vector when as.is=TRUE

Examples

extractSMR(c("aquic haploxeralfs", "typic epiaqualfs", "humic inceptic eutroperox"))
extractSMR(c("aquic haploxeralfs", "typic epiaqualfs", "humic inceptic eutroperox"))

Identify formative elements in taxon names at Soil Order, Suborder, Great Group or Subgroup level

Description

Identify formative elements in taxon names at Soil Order, Suborder, Great Group or Subgroup level

Usage

FormativeElements(x, level = c("order", "suborder", "greatgroup", "subgroup"))

OrderFormativeElements(x)

SubOrderFormativeElements(x)

GreatGroupFormativeElements(x)

SubGroupFormativeElements(x)

get_ST_formative_elements(
  level = c("order", "suborder", "greatgroup", "subgroup")
)
FormativeElements(x, level = c("order", "suborder", "greatgroup", "subgroup"))

OrderFormativeElements(x)

SubOrderFormativeElements(x)

GreatGroupFormativeElements(x)

SubGroupFormativeElements(x)

get_ST_formative_elements(
  level = c("order", "suborder", "greatgroup", "subgroup")
)

Arguments

`x`	A character vector containing subgroup-level taxonomic names
`level`	one of `c("order","suborder","greatgroup","subgroup")`

Value

A list containing ⁠$defs⁠: a data.frame containing taxonomic elements, derivations, connotations and links. And ⁠$char.index⁠: a numeric denoting the position where the formative element occurs in the search text x

get_ST_formative_elements(): a data.frame containing descriptors of formative elements used at the specified level

Author(s)

D.E. Beaudette, A.G. Brown

Examples


FormativeElements("acrudoxic plinthic kandiudults", level = "subgroup")
SubGroupFormativeElements("acrudoxic plinthic kandiudults")

FormativeElements("acrudoxic plinthic kandiudults", level = "greatgroup")
GreatGroupFormativeElements("acrudoxic plinthic kandiudults")

FormativeElements("acrudoxic plinthic kandiudults", level = "suborder")
SubOrderFormativeElements("acrudoxic plinthic kandiudults")

FormativeElements("acrudoxic plinthic kandiudults", level = "order")
OrderFormativeElements("acrudoxic plinthic kandiudults")

FormativeElements("acrudoxic plinthic kandiudults", level = "subgroup")
SubGroupFormativeElements("acrudoxic plinthic kandiudults")

FormativeElements("acrudoxic plinthic kandiudults", level = "greatgroup")
GreatGroupFormativeElements("acrudoxic plinthic kandiudults")

FormativeElements("acrudoxic plinthic kandiudults", level = "suborder")
SubOrderFormativeElements("acrudoxic plinthic kandiudults")

FormativeElements("acrudoxic plinthic kandiudults", level = "order")
OrderFormativeElements("acrudoxic plinthic kandiudults")

Get soil family / series differentiae and class names

Description

All parameters to this function are optional (default NULL). If specified, they are used as filters.

Usage

get_ST_family_classes(
  classname = NULL,
  group = NULL,
  name = NULL,
  chapter = NULL,
  page = NULL,
  multiline_sep = "\n",
  multiline_col = "criteria"
)
get_ST_family_classes(
  classname = NULL,
  group = NULL,
  name = NULL,
  chapter = NULL,
  page = NULL,
  multiline_sep = "\n",
  multiline_col = "criteria"
)

Arguments

`classname`	optional filtering vector; levels of `ChoiceName` column from NASIS metadata
`group`	optional filtering vector; one or more of: `"Mineral Family"`, `"Organic Family"`, `"Mineral or Organic"`
`name`	optional filtering vector; one or more of: `"Mineralogy Classes"`, `"Mineralogy Classes Applied Only to Limnic Subgroups"`, `"Mineralogy Classes Applied Only to Terric Subgroups"`, `"Key to the Particle-Size and Substitute Classes of Mineral Soils"`, `"Calcareous and Reaction Classes of Mineral Soils"`, `"Reaction Classes for Organic Soils"`, `"Soil Moisture Subclasses"`, `"Other Family Classes"`, `"Soil Temperature Classes"`, `"Soil Moisture Regimes"`, `"Cation-Exchange Activity Classes"`, `"Use of Human-Altered and Human-Transported Material Classes"`
`chapter`	optional filtering vector for chapter number
`page`	optional filtering vector; page number (12th Edition Keys to Soil Taxonomy)
`multiline_sep`	default `"\n"` returns `multiline_col` column as a character vector concatenated with `"\n"`. Use `NULL` for list
`multiline_col`	character. vector of "multi-line" column names to concatenate. Default: `"criteria"`; use `NULL` for no concatenation.

Details

This is a wrapper method around the package data set ST_family_classes.

Value

a data.frame

a subset of ST_family_classes data.frame

Examples


# get classes in chapter 17
str(get_ST_family_classes(chapter = 17))

# get classes on page 323
get_ST_family_classes(page = 323)

# get the description for the mesic temperature class from list column
str(get_ST_family_classes(classname = "mesic")$description)

# get classes in chapter 17
str(get_ST_family_classes(chapter = 17))

# get classes on page 323
get_ST_family_classes(page = 323)

# get the description for the mesic temperature class from list column
str(get_ST_family_classes(classname = "mesic")$description)

Get soil diagnostic horizons, characteristics and features

Description

All parameters to this function are optional (default NULL). If specified, they are used as filters.

Usage

get_ST_features(
  group = NULL,
  chapter = NULL,
  name = NULL,
  page = NULL,
  multiline_sep = "\n",
  multiline_col = "criteria"
)
get_ST_features(
  group = NULL,
  chapter = NULL,
  name = NULL,
  page = NULL,
  multiline_sep = "\n",
  multiline_col = "criteria"
)

Arguments

`group`	optional filtering vector; one of: `"Surface"`, `"Subsurface"`, `"Mineral"`, `"Organic"`, `"Mineral or Organic"`
`chapter`	optional filtering vector for chapter number
`name`	optional filtering vector; these are the "names" of features used in headers
`page`	optional filtering vector; page number (12th Edition Keys to Soil Taxonomy)
`multiline_sep`	default `"\n"` returns `multiline_col` column as a character vector concatenated with `"\n"`. Use `NULL` for list
`multiline_col`	character. vector of "multi-line" column names to concatenate. Default: `"criteria"`; use `NULL` for no concatenation.

Details

This is a wrapper method around the package data set ST_features.

Value

a subset of ST_features data.frame

Examples


# get all features
str(get_ST_features())

# get features in chapter 3
str(get_ST_features(chapter = 3))

# get features on pages 18, 19, 20
get_ST_features(page = 18:20)

# get the required characteristics for the mollic epipedon from list column
str(get_ST_features(name = "Mollic Epipedon")$criteria)

# get all features
str(get_ST_features())

# get features in chapter 3
str(get_ST_features(chapter = 3))

# get features on pages 18, 19, 20
get_ST_features(page = 18:20)

# get the required characteristics for the mollic epipedon from list column
str(get_ST_features(name = "Mollic Epipedon")$criteria)

Get the lower (child) taxa for a taxon name or code

Description

Get the lower (child) taxa for a taxon name or code

Usage

getChildTaxa(
  taxon = NULL,
  code = NULL,
  convert = TRUE,
  level = c("order", "suborder", "greatgroup", "subgroup")
)
getChildTaxa(
  taxon = NULL,
  code = NULL,
  convert = TRUE,
  level = c("order", "suborder", "greatgroup", "subgroup")
)

Arguments

`taxon`	A character vector of taxa (case-insensitive)
`code`	A character vector of taxon codes (case sensitive)
`convert`	Convert results from taxon codes to taxon names? Default: TRUE
`level`	Filter results to specific level? Default: `"order"`,`"suborder"`,`"greatgroup"`,`"subgroup"`

Value

A named list, where names are taxon codes and values are character vectors representing parent taxa

Examples


# suborder children of "Mollisols"
getChildTaxa("Mollisols", level = "suborder")

# get all children within a great group, given a subgroup
getChildTaxa(getTaxonAtLevel("Ultic Haploxeralfs", "greatgroup"))

# suborder children of "Mollisols"
getChildTaxa("Mollisols", level = "suborder")

# get all children within a great group, given a subgroup
getChildTaxa(getTaxonAtLevel("Ultic Haploxeralfs", "greatgroup"))

Get last child taxon in Keys at specified taxonomic level

Description

Get last child taxon in Keys at specified taxonomic level

Usage

getLastChildTaxon(level = c("order", "suborder", "greatgroup"))
getLastChildTaxon(level = c("order", "suborder", "greatgroup"))

Arguments

level

Get child taxa from keys at specified level. One of: "order", "suborder", "greatgroup"

Value

A data.frame containing key (parent key), taxon (last taxon name), code (letter code), position (relative taxon position)

Examples


# get last taxa in suborder-level keys
x <- getLastChildTaxon(level = "suborder")

# proportion of keys where last taxon has "Hap" formative element
prop.table(table(grepl("^Hap", x$taxon)))
# get last taxa in suborder-level keys
x <- getLastChildTaxon(level = "suborder")

# proportion of keys where last taxon has "Hap" formative element
prop.table(table(grepl("^Hap", x$taxon)))

Get the higher (parent) taxa for a taxon name or code

Description

Must specify either taxon or code. taxon is used if both are specified.

Usage

getParentTaxa(
  taxon = NULL,
  code = NULL,
  convert = TRUE,
  level = c("order", "suborder", "greatgroup", "subgroup")
)
getParentTaxa(
  taxon = NULL,
  code = NULL,
  convert = TRUE,
  level = c("order", "suborder", "greatgroup", "subgroup")
)

Arguments

`taxon`	A character vector of taxa (case-insensitive)
`code`	A character vector of taxon codes (case sensitive)
`convert`	Convert results from taxon codes to taxon names? Default: `TRUE`
`level`	level Filter results to specific level? Default: `"order"`,`"suborder"`,`"greatgroup"`,`"subgroup"`

Value

A named list, where names are taxon codes and values are character vectors representing parent taxa

Examples


getParentTaxa("ultic haploxeralfs")

getParentTaxa(code = c("ABCD", "DABC"))

getParentTaxa("folists", convert = FALSE)

getParentTaxa("ultic haploxeralfs")

getParentTaxa(code = c("ABCD", "DABC"))

getParentTaxa("folists", convert = FALSE)

Get the taxon name at the Soil Order, Suborder, Great Group or Subgroup level

Description

Get the taxon name at the Soil Order, Suborder, Great Group or Subgroup level

Usage

getTaxonAtLevel(x, level = "order", simplify = TRUE)
getTaxonAtLevel(x, level = "order", simplify = TRUE)

Arguments

`x`	A character vector containing subgroup-level taxonomic names
`level`	one of `c("order","suborder","greatgroup","subgroup")`
`simplify`	Return a vector when `level` has length `1`? Default: `TRUE`. Otherwise, a data.frame is returned.

Value

A named character vector of taxa at specified level, where names are the internal Soil Taxonomy letter codes. When length(level) > 1? a data.frame is returned with column names for each level.

Examples


# default gets the soil order
getTaxonAtLevel(c("typic haplargids", "typic glacistels")) #, level = "order")

# specify alternate levels
getTaxonAtLevel("humic haploxerands", level = "greatgroup")

# can't get subgroup (child) from great group (parent)
getTaxonAtLevel("udifolists", level = "subgroup")

# but can do parents of children
getTaxonAtLevel("udifolists", level = "suborder")

# specify multiple levels (returns a list element for each level)
getTaxonAtLevel("hapludolls", c("order", "suborder", "greatgroup", "subgroup"))
# default gets the soil order
getTaxonAtLevel(c("typic haplargids", "typic glacistels")) #, level = "order")

# specify alternate levels
getTaxonAtLevel("humic haploxerands", level = "greatgroup")

# can't get subgroup (child) from great group (parent)
getTaxonAtLevel("udifolists", level = "subgroup")

# but can do parents of children
getTaxonAtLevel("udifolists", level = "suborder")

# specify multiple levels (returns a list element for each level)
getTaxonAtLevel("hapludolls", c("order", "suborder", "greatgroup", "subgroup"))

Check for valid taxonomic level (Order, Suborder, Great Group, Subgroup)

Description

Checks needle for matches against a single level of Soil Taxonomy hierarchy: order, suborder, greatgroup, subgroup. Matches are case-insensitive.

Usage

isValidST(needle, level = c("order", "suborder", "greatgroup", "subgroup"))
isValidST(needle, level = c("order", "suborder", "greatgroup", "subgroup"))

Arguments

`needle`	vector of taxa
`level`	single level of Soil Taxonomy hierarchy; one of: `"order"`, `"suborder"`, `"greatgroup"`, `"subgroup"`

Value

logical vector, same length as needle

Examples


isValidST('typic haploxeralfs', level = 'subgroup')

isValidST('typic haploxeralfs', level = 'subgroup')

Order of Hierarchical Levels in Soil Taxonomy

Description

Creates an ordered factor such that different levels (the values used in level arguments to various SoilTaxonomy package functions) in the Soil Taxonomy hierarchy can be distinguished or compared to one another.

Usage

level_hierarchy(
  x = c("order", "suborder", "greatgroup", "subgroup", "family"),
  family = TRUE,
  as.is = FALSE
)
level_hierarchy(
  x = c("order", "suborder", "greatgroup", "subgroup", "family"),
  family = TRUE,
  as.is = FALSE
)

Arguments

`x`	Passed as input to `factor()`; defaults to full set: `"order"`, `"suborder"`, `"greatgroup"`, `"subgroup"`, `"family"`,
`family`	Allow `"family"` as input in `x`? Used for validating inputs that must be a "taxon above family".
`as.is`	Return `x` "as is" (after validation)? Shorthand for `unclass(taxon_hierarchy())` to return simple character vector.

Details

The levels of Soil Taxonomy hierarchy include: "family", "subgroup", "greatgroup", "suborder", "order". The "order" is a level above "suborder". "subgroup" and above are "taxa above family". Note: "family" is always included as the "lowest" level when the result is an ordered factor, even when family-level input is disallowed by family=FALSE.

Value

An ordered factor with the values "order", "suborder", "greatgroup", "subgroup". or character when as.is=TRUE.

Examples


# is great group a taxon above family?

level_hierarchy("greatgroup") > "family"

# is order lower level than suborder?
level_hierarchy("order") < "suborder"

# what levels are above or equal to a particular taxon's level?
level_hierarchy(as.is = TRUE)[level_hierarchy() >= taxon_to_level("aquisalids")]

## this produces an error (used for checking for taxa above family)
# level_hierarchy("family", family = FALSE)
# is great group a taxon above family?

level_hierarchy("greatgroup") > "family"

# is order lower level than suborder?
level_hierarchy("order") < "suborder"

# what levels are above or equal to a particular taxon's level?
level_hierarchy(as.is = TRUE)[level_hierarchy() >= taxon_to_level("aquisalids")]

## this produces an error (used for checking for taxa above family)
# level_hierarchy("family", family = FALSE)

Get all taxa at specified level

Description

Convenience method for getting taxa from ST_unique_list

Usage

level_to_taxon(level = c("order", "suborder", "greatgroup", "subgroup"))
level_to_taxon(level = c("order", "suborder", "greatgroup", "subgroup"))

Arguments

level

character. One or more of "order", "suborder", "greatgroup", "subgroup"

Value

A character vector of taxa at the specified level

Examples


# get all order and suborder level taxa

level_to_taxon(level = c("order","suborder"))

# get all order and suborder level taxa

level_to_taxon(level = c("order","suborder"))

Generate Newick Tree Format Parenthetic Strings

Description

This function generates Newick tree format strings for a single tree. Taxa are assigned relative positions within their parent to indicate the order that they "key out."

Usage

newick_string(
  x = NULL,
  level = c("suborder", "greatgroup", "subgroup"),
  what = c("taxon", "code")
)
newick_string(
  x = NULL,
  level = c("suborder", "greatgroup", "subgroup"),
  what = c("taxon", "code")
)

Arguments

`x`	Optional: a taxon name to get children of.
`level`	Level to build the tree at. One of `"suborder"`, `"greatgroup"`, `"subgroup"`. Defaults to `"suborder"` when `x` is not specified. When `x` is specified but `level` is not specified, `level` is calculated from `taxon_to_level(x)`.
`what`	Either `"taxon"` (default; for taxon names (quoted for subgroups)) or `"code"`

Details

The output from this function is a character string with parenthetical format encoding a single tree suitable for input into functions such as ape::read.tree(). Multiple trees can be combined together in the file or text string supplied to your tree-parsing function of choice.

Value

character. A single tree in parenthetical Newick or New Hampshire format.

Examples

if (requireNamespace("ape")) {
  par(mar = c(0, 0, 0, 0))

  # "fan"
  mytr <- ape::read.tree(text = newick_string(level = "suborder"))
  plot(mytr, "f", rotate.tree = 180, cex = 0.75)

  # "cladogram"
  mytr <- ape::read.tree(text = newick_string("durixeralfs", level = "subgroup"))
  plot(mytr, "c")

  # "cladogram" (using taxon codes instead of subgroups)
  mytr <- ape::read.tree(text = newick_string("xeralfs", level = "subgroup", what = "code"))
  plot(mytr, "c")

  dev.off()
}
if (requireNamespace("ape")) {
  par(mar = c(0, 0, 0, 0))

  # "fan"
  mytr <- ape::read.tree(text = newick_string(level = "suborder"))
  plot(mytr, "f", rotate.tree = 180, cex = 0.75)

  # "cladogram"
  mytr <- ape::read.tree(text = newick_string("durixeralfs", level = "subgroup"))
  plot(mytr, "c")

  # "cladogram" (using taxon codes instead of subgroups)
  mytr <- ape::read.tree(text = newick_string("xeralfs", level = "subgroup", what = "code"))
  plot(mytr, "c")

  dev.off()
}

Parent/Child Hierarchy

Description

Parent/Child Hierarchy

Usage

parent_level(level, n = 1)

child_level(level, n = 1)
parent_level(level, n = 1)

child_level(level, n = 1)

Arguments

`level`	character. Initial level name of a taxon. Vectors include values that are one of: `"order"`, `"suborder"`, `"greatgroup"`, `"subgroup"`, `"family"`
`n`	Number of levels above/below (parent/child). Default: `1`

Value

character. Level name of parent or child at specified level above input level.

Examples

parent_level('subgroup')

child_level('greatgroup')

parent_level('family', 3)

# no level above order
parent_level('family', 5)
parent_level('subgroup')

child_level('greatgroup')

parent_level('family', 3)

# no level above order
parent_level('family', 5)

Parse components of a "family-level" taxon name

Description

Parse components of a "family-level" taxon name

Usage

parse_family(family, column_metadata = TRUE, flat = TRUE)
parse_family(family, column_metadata = TRUE, flat = TRUE)

Arguments

`family`	character. vector of taxonomic families, e.g. `"fine-loamy, mixed, semiactive, mesic ultic haploxeralfs"`
`column_metadata`	logical. include parsed NASIS physical column names and values from family taxon components? Default: `TRUE` requires soilDB package.
`flat`	logical Default: `TRUE` to return concatenated family-level classes for `"taxminalogy"` and `"taxfamother"`? Alternately, if `FALSE`, list columns are returned.

Value

a data.frame containing column names: "family" (input), "subgroup" (parsed taxonomic subgroup), "subgroup_code" (letter code for subgroup), "class_string" (comma-separated family classes), "classes_split" (split class_string vector stored as list column).

In addition, the following column names are identified and returned based on NASIS (National Soil Information System) metadata (via soilDB package):

"taxpartsize", "taxpartsizemod", "taxminalogy", "taxceactcl", "taxreaction", "taxtempcl", "taxfamhahatmatcl", "taxfamother", "taxsubgrp", "taxgreatgroup", "taxsuborder", "taxorder"

Examples

if (requireNamespace('soilDB')) {
  families <- c("fine, kaolinitic, thermic typic kanhapludults",
                "fine-loamy, mixed, semiactive, mesic ultic haploxeralfs",
                "euic, thermic typic haplosaprists",
                "coarse-loamy, mixed, active, mesic aquic dystrudepts")

  # inspect parsed list result
  str(parse_family(families))
}
if (requireNamespace('soilDB')) {
  families <- c("fine, kaolinitic, thermic typic kanhapludults",
                "fine-loamy, mixed, semiactive, mesic ultic haploxeralfs",
                "euic, thermic typic haplosaprists",
                "coarse-loamy, mixed, active, mesic aquic dystrudepts")

  # inspect parsed list result
  str(parse_family(families))
}

Get taxon codes of preceding taxa

Description

Find all codes that logically precede the specified codes. For instance, code "ABC" ("Anhyturbels") returns "AA" ("Histels") "ABA" ("Histoturbels") and "ABB" ("Aquiturbels"). Use in conjunction with a lookup table that maps Order, Suborder, Great Group and Subgroup taxa to their codes (see taxon_code_to_taxon and taxon_to_taxon_code).

Usage

preceding_taxon_codes(codes)
preceding_taxon_codes(codes)

Arguments

codes

A character vector of codes to calculate preceding codes for

Details

Accounts for Keys that run out of capital letters (more than 26 subgroups) and use lowercase letters for a unique subdivision within the "fourth character position."

Value

A list with equal length to input vector; one character vector per element

Examples


preceding_taxon_codes(c("ABCDe", "BCDEf"))

preceding_taxon_codes(c("ABCDe", "BCDEf"))

Determine relative position of taxon within Keys to Soil Taxonomy (Order to Subgroup)

Description

The relative position of a taxon is ⁠[number of preceding Key steps] + 1⁠, or NA if it does not exist in the lookup table.

Usage

relative_taxon_code_position(code)
relative_taxon_code_position(code)

Arguments

code

A character vector of taxon codes to determine the relative position of.

Value

A numeric vector with the relative position of each code with respect to their individual Keys.

Examples


# "ABCD" -> "Gypsic Anhyturbels", relative position 7
# "WXYZa" does not exist, theoretical position is 97
# "BAD" -> "Udifolists", relative position is 5

relative_taxon_code_position(c("ABCD", "WXYZa", "BAD"))

# [1]  7 NA  5

# "ABCD" -> "Gypsic Anhyturbels", relative position 7
# "WXYZa" does not exist, theoretical position is 97
# "BAD" -> "Udifolists", relative position is 5

relative_taxon_code_position(c("ABCD", "WXYZa", "BAD"))

# [1]  7 NA  5

Get (Ordered) Factors based on Soil Taxonomy Key position

Description

Get (Ordered) Factors based on Soil Taxonomy Key position

Usage

SoilTaxonomyLevels(
  level = c("order", "suborder", "greatgroup", "subgroup"),
  as.is = FALSE,
  ordered = TRUE
)

SoilMoistureRegimeLevels(as.is = FALSE, ordered = TRUE)

SoilTemperatureRegimeLevels(as.is = FALSE, ordered = TRUE)
SoilTaxonomyLevels(
  level = c("order", "suborder", "greatgroup", "subgroup"),
  as.is = FALSE,
  ordered = TRUE
)

SoilMoistureRegimeLevels(as.is = FALSE, ordered = TRUE)

SoilTemperatureRegimeLevels(as.is = FALSE, ordered = TRUE)

Arguments

`level`	One of: `"order"`, `"suborder"`, `"greatgroup"`, `"subgroup"`
`as.is`	Return character labels rather than an (ordered) factor? Default: `FALSE`
`ordered`	Create an ordinal factor? Default: `TRUE`

Value

an (ordered) factor or character vector (when as.is=TRUE)

Examples


SoilTaxonomyLevels("order")

SoilTaxonomyLevels("order", ordered = FALSE)

SoilTaxonomyLevels("order", as.is = TRUE)

SoilTaxonomyLevels("suborder")

SoilTaxonomyLevels("order")

SoilTaxonomyLevels("order", ordered = FALSE)

SoilTaxonomyLevels("order", as.is = TRUE)

SoilTaxonomyLevels("suborder")

Soil Taxonomy Hierarchy

Description

The first 4 levels of the US Soil Taxonomy hierarchy (soil order, suborder, greatgroup, subgroup), presented as a data.frame (denormalized) and a list of unique taxa.

Usage

data(ST)
data(ST)

Format

An object of class data.frame with 2665 rows and 9 columns.

Details

Ordered based on the unique letter codes denoting taxa from the 13th edition of the Keys to Soil Taxonomy.

References

Soil Survey Staff. 1999. Soil taxonomy: A basic system of soil classification for making and interpreting soil surveys. 2nd edition. Natural Resources Conservation Service. U.S. Department of Agriculture Handbook 436. https://www.nrcs.usda.gov/resources/guides-and-instructions/soil-taxonomy

Soil Survey Staff. 2014. Keys to Soil Taxonomy, 12th ed. USDA-Natural Resources Conservation Service, Washington, DC. https://www.nrcs.usda.gov/resources/guides-and-instructions/keys-to-soil-taxonomy

Family-level Classes for Soil Taxonomy

Description

A database of family-level class names for Soil Taxonomy.

Usage

data(ST_family_classes)
data(ST_family_classes)

Format

An object of class data.frame with 193 rows and 8 columns.

References

Soil Survey Staff. 2014. Keys to Soil Taxonomy, 12th ed. USDA-Natural Resources Conservation Service, Washington, DC. https://www.nrcs.usda.gov/resources/guides-and-instructions/keys-to-soil-taxonomy

Epipedons, Diagnostic Horizons, Characteristics and Features in Soil Taxonomy

Description

A data.frame with columns "group", "name", "chapter", "page", "description", "criteria". Currently page numbers and contents are referenced to 12th Edition Keys to Soil Taxonomy and derived from products in the ncss-tech SoilKnowledgeBase repository (https://github.com/ncss-tech/SoilKnowledgeBase).

Usage

data(ST_features)
data(ST_features)

Format

An object of class data.frame with 84 rows and 6 columns.

References

Soil Survey Staff. 2014. Keys to Soil Taxonomy, 12th ed. USDA-Natural Resources Conservation Service, Washington, DC. https://www.nrcs.usda.gov/resources/guides-and-instructions/keys-to-soil-taxonomy

Formative Elements used by Soil Taxonomy

Description

A database of formative elements used by the first 4 levels of US Soil Taxonomy hierarchy (soil order, suborder, greatgroup, subgroup).

Usage

data(ST_formative_elements)
data(ST_formative_elements)

Format

An object of class list of length 4.

References

S. W. Buol and R. C. Graham and P. A. McDaniel and R. J. Southard. Soil Genesis and Classification, 5th edition. Iowa State Press, 2003.

Letter Code Lookup Table for Position of Taxa within the Keys to Soil Taxonomy (12th Edition)

Description

A lookup table mapping unique taxonomic Order, Suborder, Great Group and Subgroups to letter codes that denote their logical position within the Keys.

Usage

data(ST_higher_taxa_codes_12th)
data(ST_higher_taxa_codes_12th)

Format

An object of class data.frame with 3082 rows and 2 columns.

Details

The lookup table has been corrected to reflect errata that were posted after the print publication of the 12th Edition Keys, as well as typos in the Spanish language edition.

References

Soil Survey Staff. 2014. Keys to Soil Taxonomy, 12th ed. USDA-Natural Resources Conservation Service, Washington, DC. https://www.nrcs.usda.gov/resources/guides-and-instructions/keys-to-soil-taxonomy

Soil Survey Staff. 2014. Claves para la Taxonomía de Suelos, 12th ed. USDA-Natural Resources Conservation Service, Washington, DC. https://www.nrcs.usda.gov/resources/guides-and-instructions/keys-to-soil-taxonomy

Letter Code Lookup Table for Position of Taxa within the Keys to Soil Taxonomy (13th Edition)

Description

A lookup table mapping unique taxonomic Order, Suborder, Great Group and Subgroups to letter codes that denote their logical position within the Keys.

Usage

data(ST_higher_taxa_codes_13th)
data(ST_higher_taxa_codes_13th)

Format

An object of class data.frame with 3153 rows and 2 columns.

References

Soil Survey Staff. 2022. Keys to Soil Taxonomy, 13th ed. USDA-Natural Resources Conservation Service. https://www.nrcs.usda.gov/resources/guides-and-instructions/keys-to-soil-taxonomy

Convert taxon code to taxon name

Description

Convert taxon code to taxon name

Usage

taxon_code_to_taxon(code)
taxon_code_to_taxon(code)

Arguments

code

A character vector of Taxon Codes

Value

A character vector of matching Taxon Names

Examples


taxon_code_to_taxon(c("ABC", "XYZ", "DAB", NA))

taxon_code_to_taxon(c("ABC", "XYZ", "DAB", NA))

Determine taxonomic level of specified taxa

Description

Taxa that resolve to a subgroup level taxon and contain a comma "," are assumed to be "family"-level.

Usage

taxon_to_level(taxon)
taxon_to_level(taxon)

Arguments

taxon

character vector of taxon names at Order, Suborder, Great Group or Subgroup level.

Value

character of taxonomic hierarchy levels (such as "order", "suborder", "greatgroup", "subgroup", "family") for each element of input vector.

Examples


# get the taxonomic levels for various taxa

taxon_to_level(c("gelisols", NA, "foo", "typic folistels", "folistels"))

# get the taxonomic levels for various taxa

taxon_to_level(c("gelisols", NA, "foo", "typic folistels", "folistels"))

Convert taxon name to taxon code

Description

Convert taxon name to taxon code

Usage

taxon_to_taxon_code(taxon)
taxon_to_taxon_code(taxon)

Arguments

taxon

A character vector of taxon names, case insensitive

Value

A character vector of matching taxon codes

Examples


taxon_to_taxon_code(c("Anhyturbels", "foo", "Cryaquands", NA))

taxon_to_taxon_code(c("Anhyturbels", "foo", "Cryaquands", NA))

Create a `data.tree` Object from Taxon Names

Description

This function takes one or more taxon names and taxonomic levels as input.

Usage

taxonTree(
  taxon,
  level = c("order", "suborder", "greatgroup", "subgroup"),
  root = "Soil Taxonomy",
  verbose = TRUE,
  special.chars = c("|--", "|", "|", "-"),
  file = "",
  ...
)
taxonTree(
  taxon,
  level = c("order", "suborder", "greatgroup", "subgroup"),
  root = "Soil Taxonomy",
  verbose = TRUE,
  special.chars = c("|--", "|", "|", "-"),
  file = "",
  ...
)

Arguments

`taxon`	A vector of taxon names
`level`	One or more of: `"order"`, `"suborder"`, `"greatgroup"`, `"subgroup"`. The lowest level is passed to `getChildLevel()` to generate the leaf nodes.
`root`	Label for root node. Default: `"Soil Taxonomy"`; `NULL` for "unrooted" tree.
`verbose`	Print tree output? Default: `TRUE`
`special.chars`	Characters used to print the tree to console. Default: `c("\|--", "\|", "\|", "-")`. For fancy markup try: `c("\u251c","\u2502", "\u2514", "\u2500 ")`
`file`	Optional: path to output file. Default: `""` prints to standard output connection (unless redirected by `sink()`)
`...`	Additional arguments to `data.tree::as.Node.data.frame()`

Details

A subclass of data.tree Node object is returned. This object has a custom print() method

Value

A SoilTaxonNode (subclass of data.tree Node) object (invisibly). A text representation of the tree is printed to stdout when verbose=TRUE.

Examples




# hapludults and hapludalfs (to subgroup level)
taxonTree(c("hapludults", "hapludalfs"))

# alfisols suborders and great groups
taxonTree("alfisols", root = "Alfisols", level = c("suborder", "greatgroup"))
# hapludults and hapludalfs (to subgroup level)
taxonTree(c("hapludults", "hapludalfs"))

# alfisols suborders and great groups
taxonTree("alfisols", root = "Alfisols", level = c("suborder", "greatgroup"))

World Reference Base for Soil Resources (4th Edition, 2022)

Description

A list containing three data.frame elements "rsg", "pq", and "sq" providing information on the 'Representative Soil Groups', 'Principal Qualifiers,' and 'Supplementary Qualifiers,' respectively.

Usage

data(WRB_4th_2022)
data(WRB_4th_2022)

Format

An object of class list of length 3.

Details

Each element has the column "code" which is a number (1-32) referring to the position in the Reference Soil Groups, and the column "reference_soil_group" which is the corresponding group name. The "pq" and "sq" qualifier name columns (primary_qualifier and supplementary_qualifier) contain individual qualifier terms. Related qualifiers are identified using qualifier_group column derived from qualifier names separated with a forward slash " / "

The data.frame "rsg" has column "criteria", describing the logical criteria for each Reference Soil Group.
The data.frame "pq" has qualifier names in column "principal_qualifier"
The data.frame "sq" has column "supplementary_qualifier".

References

IUSS Working Group WRB. 2022. World Reference Base for Soil Resources. International soil classification system for naming soils and creating legends for soil maps. 4th edition. International Union of Soil Sciences (IUSS), Vienna, Austria.

Package 'SoilTaxonomy'

Help Index

Determine taxonomic level of a taxonomic letter code

Description

Usage

Arguments

Value

Examples

Decompose taxon letter codes

Description

Usage

Arguments

Details

Value

See Also

Examples

Explain a taxon name using formative elements

Description

Usage

Arguments

Value

Examples

Extract Soil Moisture Regime from Subgroup or Higher Level Taxon

Description

Usage

Arguments

Value

Examples

Identify formative elements in taxon names at Soil Order, Suborder, Great Group or Subgroup level

Description

Usage

Arguments

Value

Author(s)

Examples

Get soil family / series differentiae and class names

Description

Usage

Arguments

Details

Value

See Also

Examples

Get soil diagnostic horizons, characteristics and features

Description

Usage

Arguments

Details

Value

See Also

Examples

Get the lower (child) taxa for a taxon name or code

Description

Usage

Arguments

Value

Examples

Get last child taxon in Keys at specified taxonomic level

Description

Usage

Arguments

Value

Examples

Get the higher (parent) taxa for a taxon name or code

Description

Usage

Arguments

Value

Examples

Get the taxon name at the Soil Order, Suborder, Great Group or Subgroup level

Description

Usage

Arguments

Value

Examples

Check for valid taxonomic level (Order, Suborder, Great Group, Subgroup)

Description

Usage

Arguments

Value