NEWS.md
taxonTree() default markup via special.chars argument emulates fs::dir_tree() outputparse_family() now returns more complete information for taxa above family
taxminalogy column for taxa with strongly contrasting control sections now use " over " as the separator between class names.FormativeElements(); thanks to Shawn Salley (@swsalley)extractSMR() via fix for FormativeElements() applied at multiple levels (affects taxa above subgroup level)level_hierarchy() a helper function for creating ordered factors related to the levels: “order”, “suborder”, “greatgroup”, “subgroup”, “family”.SoilTaxonomy.env) after the first time they are used for a moderate boost in performance in scenarios calling taxon_code_to_taxon() or taxon_to_taxon_code() many timesgetTaxonAtLevel() now supports multiple level values. In this case, a data.frame with column for each level is returned. Thanks to Meyer Bohn (@MollicMeyer) in #42 for suggestion.taxonTree() a method for creating data.tree objects (added to Suggests). This function returns a custom SoilTaxonomy-specific subclass of data.tree Node called SoilTaxonNode.
ST_higher_taxa_codes_13th the 13th edition analog of ST_higher_taxa_codes_12th, which is the Keys to Soil Taxonomy taxon list and corresponding letter codes. This lookup table is used internally for many things related to the hierarchy of taxonomy. It has not been integrated into other datasets (pending next NASIS data model update in several months). Incorporating the edition of taxonomy will be a significant change when implemented (and may contain breaking changes to code-lookup tools).ST is now based on the full subgroup level code (https://github.com/ncss-tech/SoilTaxonomy/issues/35). Partial codes corresponding to each level of the hierarchy are also included in columns: order_code, suborder_code, greatgroup_code and subgroup_code.SoilTaxonomyLevels(): used for creating ordinal and nominal factors corresponding to taxonomic levels "order", "suborder", "greatgroup", and "subgroup" (https://github.com/ncss-tech/SoilTaxonomy/issues/39).SoilMoistureRegimeLevels() and SoilTemperatureRegimeLevels(): used for creating ordinal and nominal factors corresponding to Soil Moisture and Temperature Regimes (https://github.com/ncss-tech/SoilTaxonomy/issues/34).FormativeElements() can now take multiple level values, returning the formative elements found at each level combined in a single data.frame.get_ST_formative_elements() a helper function for getting a data.frame containing descriptors of formative elements used at the specified level(s)extractSMR(): utilizes order to subgroup formative elements to identify Soil Moisture Regimes from taxon namesnewick_string(): used for creating parenthetical “Newick” (or “New Hampshire”) format tree string inputs to functions such as ape::read.tree()
get_ST_features()
get_ST_family_classes() (the ST_family_classes analogue of ST_features/get_ST_features())ST_family_classes gains information on the "aniso" particle-size class modifierparse_family() now returns additional columns reflecting NASIS physical column names corresponding to components of the family-level taxonomy
parse_family() gains flat argument (default TRUE) to toggle returning list columns for “child” table taxonomic family data such as mineralogy class and “other” taxonomic family class.taxon_code_to_taxon and taxon_to_level now support family-level taxa with only one class e.g. “Thermic Typic Quartzipsamments”ST_unique_list is now sorted according to the order of appearance in the Keys to Soil Taxonomy (12th edition)ST_formative_elements / explainST() with subgroup-level descriptions for missing taxacode_to_level to abstract core from taxon_to_level for higher taxa with letter codesgetChildTaxa counterpart to getParentTaxa; getParentTaxa can now be filtered with level argumentstringsAsFactors defaulting to TRUE on R <4.0explainST to work on Order, Suborder and Great Group taxonomic nameslevel_to_taxon and taxon_to_level to determine where taxa occur in the hierarchyST_features, ST_family_classes for diagnostic horizons/features/properties and family-level class names and related content
create_KST module JSON outputparse_family method for separating family-level classes from higher taxonomic namesget_ST_features wrapper method for filtering ST_features data setgetLastChildTaxon method to determine last in Keys at specified level (Order, Suborder, or Great Group)