From 224ea2698bd3bce87ff3043367a854a14f0b99d4 Mon Sep 17 00:00:00 2001
From: Andrew Gene Brown <andrew.g.brown@usda.gov>
Date: Fri, 7 May 2021 13:41:13 -0700
Subject: [PATCH] Add missing subgroup formative element descriptions (#32)

* Trying tokenizing for identifying similarities in criteria

* Fill in gaps in subgroup-level formative element explanations #5 #17
---
 DESCRIPTION                                   |   2 +-
 NEWS.md                                       |   3 +
 data/ST_formative_elements.rda                | Bin 4319 -> 5916 bytes
 .../dictionaries/subgroup.csv                 | 332 +++++++++---------
 misc/formative-elements/fill-missing-taxa.R   |  68 ++++
 .../formative-elements/formative-elements.rda | Bin 4273 -> 5870 bytes
 6 files changed, 238 insertions(+), 167 deletions(-)
 create mode 100644 misc/formative-elements/fill-missing-taxa.R

diff --git a/DESCRIPTION b/DESCRIPTION
index b5c6948..064bbca 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ 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.
-Version: 0.1.3
+Version: 0.1.3.9001
 Authors@R: c(person(given="Dylan", family="Beaudette", role = c("aut"), email = "dylan.beaudette@usda.gov"), person(given="Andrew", family="Brown", email="andrew.g.brown@usda.gov", role = c("aut", "cre")))
 Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
 Depends: R (>= 3.5)
diff --git a/NEWS.md b/NEWS.md
index a9da76d..3e0fa1b 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,6 @@
+# SoilTaxonomy 0.1.3.9001 (2021-05-03)
+ * Update `ST_formative_elements` / `explainST()` with subgroup-level descriptions for missing taxa
+
 # SoilTaxonomy 0.1.3 (2021-05-02)
  * 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
diff --git a/data/ST_formative_elements.rda b/data/ST_formative_elements.rda
index baaaafd6cfc11245278fc7d6d9448019a4ce6eb9..3fda4ed22164fb6ef20115ed206c2e760e513dd5 100644
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diff --git a/misc/formative-elements/dictionaries/subgroup.csv b/misc/formative-elements/dictionaries/subgroup.csv
index 41f4341..ccfbb36 100644
--- a/misc/formative-elements/dictionaries/subgroup.csv
+++ b/misc/formative-elements/dictionaries/subgroup.csv
@@ -1,166 +1,166 @@
-element,central,intergrade,extragrade,intragrade,derivation,connotation,simplified,link
-abruptic,FALSE,,,FALSE,torn off,abrupt textural change,,
-acric,FALSE,,,TRUE,at the end,low apparent CEC,,
-aeric,FALSE,,,TRUE,air,more aeration than typic subgroup,,
-albic,FALSE,,,FALSE,white,presence of albic minerals,,
-albaquic,FALSE,,,FALSE,white + water,"presence of albic minerals, wetter than typic subgroup",,
-alfic,FALSE,,,TRUE,alfisols,presence of an argillic or kandic horizon,,
-alic,FALSE,,,FALSE,alumina,high extractable Al content,,
-anionic,FALSE,,,FALSE,neutral,low CEC or positively charged,,
-anthraquic,FALSE,,,FALSE,human + water,human controlled flooding as in paddy rice culture,,
-anthropic,FALSE,,,FALSE,human,an anthropic epipedon,,
-aquic,FALSE,,,TRUE,water,wetter than typic subgroup,,
-arenic,FALSE,,,TRUE,sand,50-100cm sandy textured surface,,
-argic,FALSE,,,TRUE,clay,argillic horizon,,
-aridic,FALSE,,,TRUE,"hot, dry",more aridic than typic subgroup,,
-calcic,FALSE,,,FALSE,lime,presence of a calcic horizon,,
-chromic,FALSE,,,TRUE,color,high chroma colors,,
-cumulic,FALSE,,,TRUE,heap,thickened epipedon,,
-duric,FALSE,,,FALSE,hard,presence of a duripan,,
-durinodic,FALSE,,,FALSE,hard + knot,presence of durinodes,,
-dystric,FALSE,,,TRUE,ill,lower base saturation percentage,,
-entic,FALSE,,,TRUE,entisols,minimal surface/subsurface development,,
-eutric,FALSE,,,TRUE,"good, fertile",higher base saturation percentage,,
-fibric,FALSE,,,FALSE,fiber,>25cm of fibric material,,
-fluvaquentic,FALSE,,,TRUE,flood plain + water + entisol,"wetter than typic subgroup, evidence of stratification",,
-fragic,FALSE,,,FALSE,brittle,presence of fragic properties,,
-fragiaquic,FALSE,,,FALSE,brittle + water,"presence of fragic properties, wetter than typic subgroup",,
-glacic,FALSE,,,FALSE,icy,presence of ice lenses or wedges,,
-glossic,FALSE,,,FALSE,tongue,interfingered horizon boundaries,,
-glossaquic,FALSE,,,FALSE,tongue + water,"interfingered horizon boundaries, wetter than typic subgroup",,
-grossarenic,FALSE,,,TRUE,thick + sand,>100cm sandy textured surface,,
-gypsic,FALSE,,,FALSE,gypsum,presence of gypsic horizon,,
-halic,FALSE,,,FALSE,salt,salty,,
-hemic,FALSE,,,FALSE,half,>25cm of hemic organic material,,
-humic,FALSE,,,TRUE,earth,higher organic matter content,,
-hydric,FALSE,,,FALSE,water,presence of water,,
-kandic,FALSE,,,FALSE,modified from kandite,low activity clay present,,
-lamellic,FALSE,,,FALSE,dim,presence of lamellae,,
-leptic,FALSE,,,TRUE,thin,thinner than typic subgroup,,
-limnic,FALSE,,,FALSE,lake,presence of a limnic layer,,
-lithic,FALSE,,,FALSE,stone,shallow lithic contact present,,
-natric,FALSE,,,FALSE,sodium,presence of sodium,,
-nitric,FALSE,,,FALSE,modified from nitron,presence of nitrate salts,,
-ombroaquic,FALSE,,,TRUE,rain + water,surface wetness,,
-oxyaquic,FALSE,,,TRUE,oxygen + water,water saturated but not reduced,,
-pachic,FALSE,,,TRUE,thick,epipedon thicker than typic subgroup,,
-petrocalcic,FALSE,,,FALSE,rock + lime,presence of a petrocalcic horizon,,
-petroferric,FALSE,,,FALSE,rock + iron,presence of petroferric contact,,
-petrogypsic,FALSE,,,FALSE,rock + gypsum,presence of a petrogypsic horizon,,
-petronodic,FALSE,,,FALSE,rock + knot,presence of concretions and/or nodules,,
-placic,FALSE,,,FALSE,flat stone,presence of a placic horizon,,
-plinthic,FALSE,,,FALSE,brick,presence of plinthite,,
-rhodic,FALSE,,,TRUE,rose,darker red colors than typic subgroup,,
-ruptic,FALSE,,,FALSE,broken,intermittent horizon,,
-salic,FALSE,,,FALSE,salt,presence of a salic horizon,,
-sapric,FALSE,,,FALSE,rotten,>25cm of sapric organic material,,
-sodic,FALSE,,,FALSE,sodium,high exchangeable Na content,,
-sombric,FALSE,,,FALSE,dark,presence of a sombric horizon,,
-sphagnic,FALSE,,,FALSE,moss,sphagnum organic material,,
-sulfic,FALSE,,,FALSE,sulfur,presence of sulfides,,
-terric,FALSE,,,TRUE,earth,mineral substratum within 1 meter,,
-thaptic,FALSE,,,FALSE,buried,presence of a buried soil horizon,,
-thapto,FALSE,,,FALSE,buried,presence of a buried soil horizon,,
-turbic,FALSE,,,TRUE,disturbed,evidence of cryoturbation,,
-udic,FALSE,,,TRUE,humid,more humid than typic subgroup,,
-umbric,FALSE,,,FALSE,shade,presence of an umbric epipedon,,
-ustic,FALSE,,,TRUE,burnt,more ustic than typic subgroup,,
-vermic,FALSE,,,FALSE,worms,animal mixed material,,
-vitric,FALSE,,,FALSE,glass,presence of glassy material,,
-xanthic,FALSE,,,TRUE,yellow,more yellow than typic subgroup,,
-xeric,FALSE,,,TRUE,dry,more xeric than typic subgroup,,
-typic,TRUE,FALSE,FALSE,FALSE,typical,central theme of subgroup concept,,
-haplic,TRUE,FALSE,FALSE,FALSE,simple,central theme of subgroup concept,,
-acraquoxic,,,,,low CEC + water + oxygen,very low ECEC and more aeration than central theme of subgroup concept,,
-acrudoxic,,,,,,,,
-acrustoxic,,,,,,,,
-albaquultic,,,,,,,,
-andic,,,,,,,,
-anhydritic,,,,,,,,
-anthraltic,,,,,,,,
-anthrodensic,,,,,,,,
-anthroportic,,,,,,,,
-aqualfic,,,,,,,,
-aquandic,,,,,,,,
-aquentic,,,,,,,,
-aqueptic,,,,,,,,
-aquertic,,,,,,,,
-aquicambidic,,,,,,,,
-aquodic,,,,,,,,
-aquollic,,,,,,,,
-aquultic,,,,,,,,
-argiaquic,,,,,,,,
-argidic,,,,,,,,
-argiduridic,,,,,,,,
-calciargidic,,,,,,,,
-calcidic,,,,,,,,
-cambidic,,,,,,,,
-duridic,,,,,,,,
-fluventic,,,,,,,,
-folistic,,,,,,,,
-grossic,,,,,,,,
-haplargidic,,,,,,,,
-haplocalcidic,,,,,,,,
-haploduridic,,,,,,,,
-haploplaggic,,,,,,,,
-haploxeralfic,,,,,,,,
-haploxerandic,,,,,,,,
-haploxerollic,,,,,,,,
-haplustandic,,,,,,,,
-histic,,,,,,,,
-humaqueptic,,,,,,,,
-hydraquentic,,,,,,,,
-inceptic,,,,,,,,
-kandiudalfic,,,,,,,,
-kandiustalfic,,,,,,,,
-kanhaplic,,,,,,,,
-lithic-ruptic-entic,,,,,,,,
-mollic,,,,,,,,
-natrargidic,,,,,,,,
-natrixeralfic,,,,,,,,
-oxic,,,,,,,,
-paleargidic,,,,,,,,
-palexerollic,,,,,,,,
-petrocalcidic,,,,,,,,
-plinthaquic,,,,,,,,
-psammentic,,,,,,,,
-rendollic,,,,,,,,
-ruptic-alfic,,,,,,,,
-ruptic-entic,,,,,,,,
-ruptic-histic,,,,,,,,
-ruptic-inceptic,,,,,,,,
-ruptic-lithic,,,,,,,,
-ruptic-ultic,,,,,,,,
-salidic,,,,,,,,
-spodic,,,,,,,,
-sulfaqueptic,,,,,,,,
-sulfuric,,,,,,,,
-thapto-histic,,,,,,,,
-torrertic,,,,,,,,
-torrifluventic,,,,,,,,
-torriorthentic,,,,,,,,
-torripsammentic,,,,,,,,
-torroxic,,,,,,,,
-udandic,,,,,,,,
-udertic,,,,,,,,
-udifluventic,,,,,,,,
-udollic,,,,,,,,
-udorthentic,,,,,,,,
-udoxic,,,,,,,,
-ultic,,,,,,,,
-ustalfic,,,,,,,,
-ustandic,,,,,,,,
-ustertic,,,,,,,,
-ustifluventic,,,,,,,,
-ustivitrandic,,,,,,,,
-ustollic,,,,,,,,
-ustoxic,,,,,,,,
-vertic,,,,,vertisols,,,
-vitrandic,,,,,,,,
-vitritorrandic,,,,,,,,
-vitrixerandic,,,,,glass + dry + andic,,,
-xeralfic,,,,,dry + alfisols,,,
-xereptic,,,,,dry + inceptisol,,,
-xerertic,,,,,dry + vertisols,,,
-xerofluventic,,,,,dry + fluventic,,,
-xerollic,,,,,dry + mollisols,,,
+element,central,intergrade,extragrade,intragrade,derivation,connotation,simplified,link
+abruptic,FALSE,,,FALSE,torn off,abrupt textural change,,
+acric,FALSE,,,TRUE,at the end,low apparent CEC,,
+aeric,FALSE,,,TRUE,air,more aeration than typic subgroup,,
+albic,FALSE,,,FALSE,white,presence of albic minerals,,
+albaquic,FALSE,,,FALSE,white + water,"presence of albic minerals, wetter than typic subgroup",,
+alfic,FALSE,,,TRUE,alfisols,presence of an argillic or kandic horizon,,
+alic,FALSE,,,FALSE,alumina,high extractable Al content,,
+anionic,FALSE,,,FALSE,neutral,low CEC or positively charged,,
+anthraquic,FALSE,,,FALSE,human + water,human controlled flooding as in paddy rice culture,,
+anthropic,FALSE,,,FALSE,human,an anthropic epipedon,,
+aquic,FALSE,,,TRUE,water,wetter than typic subgroup,,
+arenic,FALSE,,,TRUE,sand,50-100cm sandy textured surface,,
+argic,FALSE,,,TRUE,clay,argillic horizon,,
+aridic,FALSE,,,TRUE,"hot, dry",more aridic than typic subgroup,,
+calcic,FALSE,,,FALSE,lime,presence of a calcic horizon,,
+chromic,FALSE,,,TRUE,color,high chroma colors,,
+cumulic,FALSE,,,TRUE,heap,thickened epipedon,,
+duric,FALSE,,,FALSE,hard,presence of a duripan,,
+durinodic,FALSE,,,FALSE,hard + knot,presence of durinodes,,
+dystric,FALSE,,,TRUE,ill,lower base saturation percentage,,
+entic,FALSE,,,TRUE,entisols,minimal surface/subsurface development,,
+eutric,FALSE,,,TRUE,"good, fertile",higher base saturation percentage,,
+fibric,FALSE,,,FALSE,fiber,>25cm of fibric material,,
+fluvaquentic,FALSE,,,TRUE,flood plain + water + entisol,"wetter than typic subgroup, evidence of stratification",,
+fragic,FALSE,,,FALSE,brittle,presence of fragic properties,,
+fragiaquic,FALSE,,,FALSE,brittle + water,"presence of fragic properties, wetter than typic subgroup",,
+glacic,FALSE,,,FALSE,icy,presence of ice lenses or wedges,,
+glossic,FALSE,,,FALSE,tongue,interfingered horizon boundaries,,
+glossaquic,FALSE,,,FALSE,tongue + water,"interfingered horizon boundaries, wetter than typic subgroup",,
+grossarenic,FALSE,,,TRUE,thick + sand,>100cm sandy textured surface,,
+gypsic,FALSE,,,FALSE,gypsum,presence of gypsic horizon,,
+halic,FALSE,,,FALSE,salt,salty,,
+hemic,FALSE,,,FALSE,half,>25cm of hemic organic material,,
+humic,FALSE,,,TRUE,earth,higher organic matter content,,
+hydric,FALSE,,,FALSE,water,presence of water,,
+kandic,FALSE,,,FALSE,modified from kandite,low activity clay present,,
+lamellic,FALSE,,,FALSE,dim,presence of lamellae,,
+leptic,FALSE,,,TRUE,thin,thinner than typic subgroup,,
+limnic,FALSE,,,FALSE,lake,presence of a limnic layer,,
+lithic,FALSE,,,FALSE,stone,shallow lithic contact present,,
+natric,FALSE,,,FALSE,sodium,presence of sodium,,
+nitric,FALSE,,,FALSE,modified from nitron,presence of nitrate salts,,
+ombroaquic,FALSE,,,TRUE,rain + water,surface wetness,,
+oxyaquic,FALSE,,,TRUE,oxygen + water,water saturated but not reduced,,
+pachic,FALSE,,,TRUE,thick,epipedon thicker than typic subgroup,,
+petrocalcic,FALSE,,,FALSE,rock + lime,presence of a petrocalcic horizon,,
+petroferric,FALSE,,,FALSE,rock + iron,presence of petroferric contact,,
+petrogypsic,FALSE,,,FALSE,rock + gypsum,presence of a petrogypsic horizon,,
+petronodic,FALSE,,,FALSE,rock + knot,presence of concretions and/or nodules,,
+placic,FALSE,,,FALSE,flat stone,presence of a placic horizon,,
+plinthic,FALSE,,,FALSE,brick,presence of plinthite,,
+rhodic,FALSE,,,TRUE,rose,darker red colors than typic subgroup,,
+ruptic,FALSE,,,FALSE,broken,intermittent horizon,,
+salic,FALSE,,,FALSE,salt,presence of a salic horizon,,
+sapric,FALSE,,,FALSE,rotten,>25cm of sapric organic material,,
+sodic,FALSE,,,FALSE,sodium,high exchangeable Na content,,
+sombric,FALSE,,,FALSE,dark,presence of a sombric horizon,,
+sphagnic,FALSE,,,FALSE,moss,sphagnum organic material,,
+sulfic,FALSE,,,FALSE,sulfur,presence of sulfides,,
+terric,FALSE,,,TRUE,earth,mineral substratum within 1 meter,,
+thaptic,FALSE,,,FALSE,buried,presence of a buried soil horizon,,
+thapto,FALSE,,,FALSE,buried,presence of a buried soil horizon,,
+turbic,FALSE,,,TRUE,disturbed,evidence of cryoturbation,,
+udic,FALSE,,,TRUE,humid,more humid than typic subgroup,,
+umbric,FALSE,,,FALSE,shade,presence of an umbric epipedon,,
+ustic,FALSE,,,TRUE,burnt,more ustic than typic subgroup,,
+vermic,FALSE,,,FALSE,worms,animal mixed material,,
+vitric,FALSE,,,FALSE,glass,presence of glassy material,,
+xanthic,FALSE,,,TRUE,yellow,more yellow than typic subgroup,,
+xeric,FALSE,,,TRUE,dry,more xeric than typic subgroup,,
+typic,TRUE,FALSE,FALSE,FALSE,typical,central theme of subgroup concept,,
+haplic,TRUE,FALSE,FALSE,FALSE,simple,central theme of subgroup concept,,
+acraquoxic,FALSE,,,TRUE,acraquox,low apparent CEC (like acraquox),,
+acrudoxic,FALSE,,,TRUE,acrudox,low apparent CEC (like acrudox),,
+acrustoxic,FALSE,,,TRUE,acrudox,low apparent CEC (like acrustox),,
+albaquultic,FALSE,,,TRUE,albaqults,like albaquults,,
+andic,FALSE,,,TRUE,andisols,low bulk density and short range order minerals,,
+anhydritic,FALSE,,,FALSE,anhydrite,presence of an anhydritic horizon,,
+anthraltic,FALSE,,,FALSE,anthro + altered,presence of 50 cm or more of human-altered material,,
+anthrodensic,FALSE,,,FALSE,anthro + dense,presence of densic contact due to mechanical compaction,,
+anthroportic,FALSE,,,FALSE,anthro + transported,presence of 50 cm or more of human-transported material,,
+aqualfic,FALSE,,,TRUE,aqualfs,like aqualfs,,
+aquandic,FALSE,,,TRUE,aquands,"wetter than typic subgroup, low bulk density and short range order minerals",,
+aquentic,FALSE,,,TRUE,aquents,like aquents,,
+aqueptic,FALSE,,,TRUE,aquepts,like aquepts,,
+aquertic,FALSE,,,TRUE,aquerts,redox depletions with cracks and/or high linear extensibility,,
+aquicambidic,FALSE,,,TRUE,aquicambids,like aquicambids,,
+aquodic,FALSE,,,TRUE,aquods,like aquods,,
+aquollic,FALSE,,,TRUE,aquiolls,like aquolls,,
+aquultic,FALSE,,,TRUE,aquults,redox depletions and base saturation by sum of cations 75% or less,,
+argiaquic,FALSE,,,FALSE,,no abrupt textural change between albic and argillic horizon,,
+argidic,FALSE,,,TRUE,argids,duripan that is strongly cemented or less cemented,,
+argiduridic,FALSE,,,TRUE,argidurids,"aridic SMR with argillic horizon plus duripan, durinodes or brittle manner of failure",,
+calciargidic,FALSE,,,TRUE,calciargids,like calciargids,,
+calcidic,FALSE,,,TRUE,calcids,presence of calcic horizon and low available moisture during growing season,,
+cambidic,FALSE,,,TRUE,cambids,aridic SMR with duripan that is strongly cemented or less cemented,,
+duridic,FALSE,,,TRUE,durids,like durids,,
+fluventic,FALSE,,,TRUE,fluvents,low slope and irregular decrease in geologically-recent organic-carbon content,,
+folistic,FALSE,,,TRUE,folists,presence of folistic epipedon,,
+grossic,FALSE,,,FALSE,thick,fluid materials (high n value) in all horizons from 20 to 100 cm,,
+haplargidic,FALSE,,,TRUE,haplargids,like haplargids,,
+haplocalcidic,FALSE,,,TRUE,haplocalcids,like haplocalcids,,
+haploduridic,FALSE,,,TRUE,haplodurids,aridic SMR with duripan that is less than very strongly cemented ,,
+haploplaggic,FALSE,,,FALSE,,surface horizon >25cm thick meets all of the requirements for a plaggen epipedon,,
+haploxeralfic,FALSE,,,TRUE,haploxeralfs,aridic SMR borders on xeric with duripan that is less than very strongly cemented,,
+haploxerandic,FALSE,,,TRUE,haploxerands,xeric SMR with low bulk density and short range order minerals,,
+haploxerollic,FALSE,,,TRUE,haploxerolls,no argillic horizon above duripan,,
+haplustandic,FALSE,,,TRUE,haplustands,like haploxerolls,,
+histic,FALSE,,,TRUE,histosols,have a histic epipedon or buried layer of organic soil materials,,
+humaqueptic,FALSE,,,TRUE,humaquepts,color and base saturation of umbric epipedon in upper 15 cm,,
+hydraquentic,FALSE,,,TRUE,hydraquents,fluid materials (high n value) near surface,,
+inceptic,FALSE,,,TRUE,inceptisols,"discontinuous, thin or minimally developed illuvial horizons",,
+kandiudalfic,FALSE,,,TRUE,kandiudalfs,presence of a kandic horizon within 150 cm of the soil surface,,
+kandiustalfic,FALSE,,,TRUE,kandiustalfs,like kandiustalfs,,
+kanhaplic,FALSE,,,FALSE,kandite + simple,low CEC (at pH 7) in 50 percent or more of the upper 100 cm of argillic horizon,,
+lithic-ruptic-entic,FALSE,,,FALSE,rock + interrupted + entisols,presence of a discontinuous argillic horizon and lithic contact within 50 cm of soil surface,,
+mollic,FALSE,,,TRUE,mollisols,color and base saturation of mollic epipedon in upper 15 cm,,
+natrargidic,FALSE,,,TRUE,natriargids,duripan that is less than very strongly cemented ,,
+natrixeralfic,FALSE,,,TRUE,natrixeralfs,like natrixeralfs,,
+oxic,FALSE,,,TRUE,oxisols,low CEC with high water retention compared to measured clay content,,
+paleargidic,FALSE,,,TRUE,paleargids,like paleargids,,
+palexerollic,FALSE,,,TRUE,palexerolls,abrupt textural change or abrupt increase in clay content,,
+petrocalcidic,FALSE,,,TRUE,petrocalcids,like petrocalcids,,
+plinthaquic,FALSE,,,FALSE,,plinthite and redox depletions,,
+psammentic,FALSE,,,TRUE,psamments,sandy particle-size class upper 75 cm of the argillic horizon ,,
+rendollic,FALSE,,,TRUE,rendolls,like rendolls,,
+ruptic-alfic,FALSE,,,FALSE,interrupted + alfisols,"presence of cambic horizon with less than half by volume illuvial parts meeting requirements for argillic, kandic, or natric horizon",,
+ruptic-entic,FALSE,,,FALSE,interrupted + entisols,presence of a discontinuous argillic horizon or lithic contact,,
+ruptic-histic,FALSE,,,FALSE,interrupted + histosols,organic soil materials that are discontinuous at the surface or change in thickness fourfold or more within a pedon,,
+ruptic-inceptic,FALSE,,,FALSE,interrupted + inceptisols,presence of a discontinuous argillic horizon and lithic contact within 50 cm of soil surface,,
+ruptic-lithic,FALSE,,,FALSE,interrupted + rock,presence of a discontinuous lithic contact within 50 cm of soil surface,,
+ruptic-ultic,FALSE,,,FALSE,intrerupted + ultisols,"presence of cambic horizon with less than half by volume illuvial parts meeting requirements for argillic, kandic, or natric horizon",,
+salidic,FALSE,,,TRUE,salids,presence of a salic horizon within 75 cm of the mineral soil surface,,
+spodic,FALSE,,,TRUE,spodosols,accumulation of Fe and Al complexed with organic matter,,
+sulfaqueptic,FALSE,,,TRUE,sulfaquepts,like sulfaquepts,,
+sulfuric,FALSE,,,FALSE,sulfur,presence of a sulfuric horizon or sulfidic materials within 100 cm,,
+thapto-histic,FALSE,,,FALSE,buried + histosols,"have a buried layer of organic soil materials, 20 cm or more thick, within 100 cm of the mineral soil surface",,
+torrertic,FALSE,,,TRUE,torrerts,aridic SMR with cracks and/or high linear extensibility,,
+torrifluventic,FALSE,,,TRUE,torrifluvents,"low slope, irregular decrease in organic-carbon content, and very low available moisture during growing season",,
+torriorthentic,FALSE,,,TRUE,torriorthents,no cambic horizon or free carbonates throughout the cambic horizon/lower mollic epipedon,,
+torripsammentic,FALSE,,,TRUE,torripsamments,like torripsamments,,
+torroxic,FALSE,,,TRUE,torrox,like torrox,,
+udandic,FALSE,,,TRUE,udands,"low bulk density and short range order minerals, and relatively high available moisture during growing season",,
+udertic,FALSE,,,TRUE,uderts,"cracks and/or high linear extensibility, and relatively high available moisture during growing season",,
+udifluventic,FALSE,,,TRUE,udifluvents,"low slope, irregular decrease in organic-carbon content, and relatively high available moisture during growing season",,
+udollic,FALSE,,,TRUE,udolls,upper 18 cm of the mineral soil meets requirements for a mollic epipedon with chroma 2 or higher in most of upper 75 cm,,
+udorthentic,FALSE,,,TRUE,udorthents,like udorthents,,
+udoxic,FALSE,,,TRUE,udox,like udox,,
+ultic,FALSE,,,TRUE,ultisols,base saturation (by sum of cations) lower than typic subgroup,,
+ustalfic,FALSE,,,TRUE,ustalfs,like ustalfs,,
+ustandic,FALSE,,,TRUE,ustands,ustic SMR with low bulk density and short range order minerals,,
+ustertic,FALSE,,,TRUE,usterts,ustic SMR with cracks and/or high linear extensibility,,
+ustifluventic,FALSE,,,TRUE,ustifluvents,like ustifluvents,,
+ustivitrandic,FALSE,,,TRUE,ustivitrands,like ustivitrands,,
+ustollic,FALSE,,,TRUE,ustolls,near ustic SMR with color of mollic epipedon and base saturation of mollisols,,
+ustoxic,FALSE,,,TRUE,ustox,like ustox,,
+vertic,FALSE,,,TRUE,vertisols,cracks and/or high linear extensibility,,
+vitrandic,FALSE,,,TRUE,vitrands,"high volcanic glass, cinders and/or pumice content",,
+vitritorrandic,FALSE,,,TRUE,vitritorrands,"high volcanic glass, cinders and/or pumice content and very low available moisture during growing season",,
+vitrixerandic,FALSE,,,TRUE,vitrixerands,"high volcanic glass, cinders and/or pumice content and low available moisture during growing season",,
+xeralfic,FALSE,,,TRUE,xeralfs,like xeralfs,,
+xereptic,FALSE,,,TRUE,xerepts,near xeric SMR, duripan that is less than very strongly cemented ,
+xerertic,FALSE,,,TRUE,xererts,near xeric SMR, cracks and/or high linear extensibility,
+xerofluventic,FALSE,,,TRUE,xerofluvents,like xerofluvents,,
+xerollic,FALSE,,,TRUE,xerolls,xeric SMR with color of mollic epipedon and base saturation of mollisols,,
diff --git a/misc/formative-elements/fill-missing-taxa.R b/misc/formative-elements/fill-missing-taxa.R
new file mode 100644
index 0000000..e725aa2
--- /dev/null
+++ b/misc/formative-elements/fill-missing-taxa.R
@@ -0,0 +1,68 @@
+library(dplyr, warn=FALSE)
+library(tokenizers)
+
+scu <- read.csv("~/workspace/SoilTaxonomy/misc/formative-elements/subgroup_criteria_unexplained.csv", stringsAsFactors = FALSE)
+
+scut <- scu %>% 
+  group_by(element, taxon) %>% 
+  summarize(element = unique(element), 
+            content = paste0(content, collapse = "\n"))
+
+scut$content_tokens <- tokenizers::tokenize_words(scut$content)
+
+fmt_colormatch <- lapply(split(scut, f = scut$element), function(scusub) {
+  
+  nidx <- 1:nrow(scusub)
+  
+  # create token comparison sets; n taxa in a element group get compared to n - 1 non-self criteria
+  res1 <- lapply(nidx, function(i)
+    lapply(nidx[nidx != i], function(j) {
+      tokens <- scusub[i, 'content_tokens'][[1]][[1]]
+      nonselftokens <- do.call('c', scusub[j, 'content_tokens'][[1]])
+      tokens[tokens %in% nonselftokens]
+    }))
+  
+  # take the shortest (most restrictive) set of matches
+  res2 <- lapply(res1, function(x) x[[which.min(sapply(x, length))[1]]])
+  
+  res3 <- lapply(nidx, function(i) {
+    foo <- gsub("\xbd|1 /2","1/2", gsub("&nbsp;"," ",scusub$content[i]))
+    foo2 <- NULL
+    try(foo2 <- tolower(foo[1]), silent = TRUE)
+    if (!is.null(foo2)) {
+      foo2 <- foo
+    } else {
+      cat("### ",unique(scusub$element),"\n\n")
+    }
+    if(is.null(res2[[i]])) return(NULL)
+    res <- as.list(apply(stringr::str_locate(foo2[1], res2[[i]]), 1,
+                  function(x)
+                   if (!is.na(x[1]))# && x[2] - x[1] > 0)
+                    list(
+                      old = substr(foo, x[1], x[2]),
+                      new = substr(foo, x[1], x[2]))#crayon::red(substr(foo, x[1], x[2])))
+                    ))
+    if(length(res))
+      for(j in 1:length(res)) {
+        re <- res[[j]]
+        if(!is.null(re))
+          foo <- gsub(paste0("\\b",re$old,"\\b"), re$new, foo)
+      }
+    cat(foo)
+    cat("\n\n")
+    foo
+  })
+})
+
+foo <- lapply(seq_along(fmt_colormatch)[[6]], function(i) {cat("## ", names(fmt_colormatch)[i], "\n\n")#, 
+                                                          # file = "foo.txt", append = TRUE)
+                                                         sapply(fmt_colormatch[[i]], cat, "\n\n"#,
+                                                                # file = "foo.txt", append = TRUE)
+                                                         )})
+
+a_list <- as.list(rep("",93))
+names(a_list) <- names(fmt_colormatch)
+a_list[["vitrixerandic"]] <- "xeric SMR with significant amount of volcanic glass particles"
+a_list[["xereptic"]] <- "duripan strongly or less cemented, SMR borders on xeric"
+a_list[["xerertic"]] <- "xeric SMR with cracks 5mm or more wide and slickensides or wedge-shaped peds"
+a_list[["xerollic"]] <- "xeric SMR with color and base saturation of mollic epipedon"
diff --git a/misc/formative-elements/formative-elements.rda b/misc/formative-elements/formative-elements.rda
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