NEWS

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SoilTaxonomy 0.2.4 (2023-11-16)

• taxonTree() default markup via special.chars argument emulates fs::dir_tree() output
• parse_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.

SoilTaxonomy 0.2.3 (2023-03-10)

• Fix unintended case-sensitivity of FormativeElements(); thanks to Shawn Salley (@swsalley)
• Fix for extractSMR() via fix for FormativeElements() applied at multiple levels (affects taxa above subgroup level)
• Add level_hierarchy() a helper function for creating ordered factors related to the levels: "order", "suborder", "greatgroup", "subgroup", "family".
• Taxon code lookup tables are now cached in the package environment (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 times
• getTaxonAtLevel() 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.
• Added 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.
  • This new class has a custom print method, and in the future there may be more dedicated functions for viewing and traversing the taxonomic hierarchy.
• Added 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).

SoilTaxonomy 0.2.2 (2022-10-17)

• The order of dataset 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.
• New function 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).
• New function 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.
• New function get_ST_formative_elements() a helper function for getting a data.frame containing descriptors of formative elements used at the specified level(s)
• New function extractSMR(): utilizes order to subgroup formative elements to identify Soil Moisture Regimes from taxon names

SoilTaxonomy 0.2.1

• New function newick_string(): used for creating parenthetical "Newick" (or "New Hampshire") format tree string inputs to functions such as ape::read.tree()

SoilTaxonomy 0.2.0 (2022-07-13)

• New vignette related to soil diagnostic features and characteristics get_ST_features()
• New function 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 modifier
• parse_family() now returns additional columns reflecting NASIS physical column names corresponding to components of the family-level taxonomy
  • This routine uses the NASIS metadata that ares cached in the {soilDB} package, which has been added to Suggests
  • 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.

SoilTaxonomy 0.1.5

• taxon_code_to_taxon and taxon_to_level now support family-level taxa with only one class e.g. "Thermic Typic Quartzipsamments"
• included data ST_unique_list is now sorted according to the order of appearance in the Keys to Soil Taxonomy (12th edition)

SoilTaxonomy 0.1.4 (2021-08-05)

• Update ST_formative_elements / explainST() with subgroup-level descriptions for missing taxa

SoilTaxonomy 0.1.3 (2021-05-03)

• Add code_to_level to abstract core from taxon_to_level for higher taxa with letter codes
• Add getChildTaxa counterpart to getParentTaxa; getParentTaxa can now be filtered with level argument
• Fixes for stringsAsFactors defaulting to TRUE on R <4.0

SoilTaxonomy 0.1.2 (2021-04-30)

• Extend explainST to work on Order, Suborder and Great Group taxonomic names
• Add methods level_to_taxon and taxon_to_level to determine where taxa occur in the hierarchy
• New data sets: ST_features, ST_family_classes for diagnostic horizons/features/properties and family-level class names and related content
  • Derived from 12th Edition Keys to Soil Taxonomy definitions and criteria until official release of 13th Edition
  • Data sourced from https://github.com/ncss-tech/SoilKnowledgeBase/ create_KST module JSON output
• Add parse_family method for separating family-level classes from higher taxonomic names
• Add get_ST_features wrapper method for filtering ST_features data set
• Add getLastChildTaxon method to determine last in Keys at specified level (Order, Suborder, or Great Group)

SoilTaxonomy 0.1.1

• Re-factored taxon_code_to_taxon & taxon_to_taxon_code to use LEFT JOIN
• Added a NEWS.md file to track changes to the package

SoilTaxonomy 0.1 (2021-02-25)

• Initial CRAN release