SoilTaxonomy: 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.

Author(s)

Maintainer: Andrew Brown andrew.g.brown@usda.gov

Authors:

• Dylan Beaudette dylan.beaudette@usda.gov

See Also

Useful links:

• https://github.com/ncss-tech/SoilTaxonomy

• https://ncss-tech.github.io/SoilTaxonomy/

• Report bugs at https://github.com/ncss-tech/SoilTaxonomy/issues

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")
)

Arguments

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")

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)

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

Soil Moisture Regimes used in the Keys to Soil Taxonomy (13th Edition)

Description

A data.frame containing taxon codes and the Soil Moisture Regime associated with that taxon.

Usage

data(ST_SMR_13th)

Format

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

Details

Future revisions of this data set may additionally include the Soil Moisture Subclass.

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.

Keys to Soil Taxonomy Criteria (13th Edition)

Description

A lookup table relating taxon codes to specific criteria from the Keys to Soil Taxonomy (13th Edition)

Usage

data(ST_criteria_13th)

Format

An object of class list of length 3153.

Details

A list containing one element per taxon code at order to subgroup level. Each element contains a data.frame with 1 row per criterion, and 8 columns:

Each data.frame contains the following columns:

• content (text content of criterion)

• chapter (chapter number)

• page (page number)

• key (key name or level)

• taxon (taxon name)

• code (taxon code)

• clause (sequence number of criterion within taxon)

• logic (logical meaning of criterion)

  • One of:

    • FIRST (first)

    • OR (either this criterion OR the next criterion at same level)

    • END (end of hierarchical key)

    • NEW (go to new page/taxon specified)

    • AND (this criterion AND the next criterion at same level)

    • HAVE (criteria that must be met)

    • LAST (end of subgroup key)

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

Family-level Classes for Soil Taxonomy

Description

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

Usage

data(ST_family_classes)

Format

An object of class data.frame with 194 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)

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)

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)

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)

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

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)

Arguments

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")

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

Description

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

Usage

data(WRB_4th_2022)

Format

An object of class list of length 3.

Details

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

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.

Determine taxonomic level of a taxonomic letter code

Description

Determine taxonomic level of a taxonomic letter code

Usage

code_to_level(code)

Arguments

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")

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)

Arguments

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

See Also

preceding_taxon_codes, taxon_code_to_taxon, taxon_to_taxon_code

Examples

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)

Arguments

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)

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)

Arguments

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"))

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")
)

Arguments

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"))

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"))

Arguments

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 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")
)

Arguments

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)

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)

Arguments

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"))

Get Taxon Criteria from the Keys to Soil Taxonomy

Description

Get Taxon Criteria from the Keys to Soil Taxonomy

Usage

getTaxonCriteria(
  taxon = NULL,
  code = NULL,
  level = c("order", "suborder", "greatgroup", "subgroup")
)

Arguments

Value

A named list. Each list element is named based on the input value (either taxon or code) and contains a data.frame derived from dataset ST_criteria_13th.

See Also

taxon_to_taxon_code(), ST_criteria_13th

Examples

getTaxonCriteria(c("mollic haplocryalfs", "abruptic durixeralfs"))

getTaxonCriteria(code = "ABC", level = c("greatgroup"))

Lookup Pre-calculated Soil Moisture Regimes by Taxon

Description

Helper function for using latest version of the Keys to Soil Taxonomy standard lookup table for soil moisture information.

Usage

getTaxonSMR(
  taxon = NULL,
  code = NULL,
  as.is = FALSE,
  droplevels = FALSE,
  ordered = TRUE
)

Arguments

Value

character or factor (when as.is=FALSE) containing soil moisture regime labels extracted from 13th edition Keys to Soil Taxonomy taxa using extractSMR()

See Also

extractSMR() ST_SMR_13th

Examples

getTaxonSMR(c("aridisols", "haploxeralfs", NA, "abruptic durixeralfs", "ustic haplocryalfs"))

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"
)

Arguments

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

See Also

ST_family_classes ST_features get_ST_features()

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 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"
)

Arguments

Details

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

Value

a subset of ST_features data.frame

See Also

ST_features ST_family_classes get_ST_family_classes()

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)

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"))

Arguments

Value

logical vector, same length as needle

Examples

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
)

Arguments

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)

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"))

Arguments

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"))

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")
)

Arguments

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()
}

Parent/Child Hierarchy

Description

Parent/Child Hierarchy

Usage

parent_level(level, n = 1)

child_level(level, n = 1)

Arguments

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)

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)

Arguments

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))
}

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)

Arguments

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

See Also

decompose_taxon_code, taxon_code_to_taxon, taxon_to_taxon_code

Examples

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)

Arguments

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

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 = "",
  ...
)

Arguments

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"))

Convert taxon code to taxon name

Description

Convert taxon code to taxon name

Usage

taxon_code_to_taxon(code)

Arguments

Value

A character vector of matching Taxon Names

See Also

decompose_taxon_code, preceding_taxon_codes, taxon_to_taxon_code

Examples

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)

Arguments

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"))

Convert taxon name to taxon code

Description

Convert taxon name to taxon code

Usage

taxon_to_taxon_code(taxon)

Arguments

Value

A character vector of matching taxon codes

See Also

decompose_taxon_code, preceding_taxon_codes, taxon_code_to_taxon

Examples

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