Simplify Great Group formative elements

misc/formative-elements/dictionaries/greatgroup.csv

@@ -1,86 +1,58 @@
-element,derivation,connotation,simplified,link
-acro,at the end,extreme weathering,,
-acr,at the end,extreme weathering,,
-al,aluminum,"high Al, low Fe",,
-alb,white,presence of an albic horizon,,
-anhy,dry,very dry,,
-anthra,human,presence of an anthropic epipedon,,
-aqui,water,wetness,,
-aqu,water,wetness,,
-argi,white clay,presence of an argillic horizon,,
-calci,lime,presence of a calcic horizon,,
-cryo,cold,cryic STR,,
-cry,cold,cryic STR,,
-duri,hard,presence of a duripan,,
-dur,hard,presence of a duripan,,
-dystro,infertile,low base saturation,,
-dystr,infertile,low base saturation,,
-endo,within,ground water table,,
-epi,above,perched water table,,
-eutro,fertile,high base saturation,,
-eutr,fertile,high base saturation,,
-ferr,iron,presence of Fe,,
-fibr,fiber,least decomposed stage,,
-fluv,river,flood plain,,
-fol,leaf,mass of leaves,,
-fragi,brittle,presence of a fragipan,,
-fragloss,brittle + tongue,presence of a fragipan and glossic horizon,,
-frasi,fresh,not salty,,
-fulvi,brownish yellow,dark brown with organic carbon,,
-fulv,brownish yellow,dark brown with organic carbon,,
-glac,icy,presence of ice lenses,,
-glosso,tongue,presence of a glossic horizon,,
-gloss,tongue,presence of a glossic horizon,,
-gypsi,gypsum,presence of a gypsic horizon,,
-hal,salt,salty,,
-haplo,simple,minimum horizon development,,
-hapl,simple,minimum horizon development,,
-hap,simple,minimum horizon development,,
-hemi,half,intermediate decomposition,,
-histo,tissue,organic soil material,,
-hist,tissue,organic soil material,,
-humi,earth,presence of organic carbon,,
-hum,earth,presence of organic carbon,,
-hydro,water,presence of water,,
-hydr,water,presence of water,,
-kandi,modified from kandite,presence of a kandic horizon,,
-kanhaplo,kandite + simple,thin kandic horizon,,
-kanhap,kandite + simple,thin kandic horizon,,
-luvi,to wash,illuvial organic material,,
-melano,black,presence of a melanic epipedon,,
-melan,black,presence of a melanic epipedon,,
-molli,soft,presence of a mollic epipedon,,
-moll,soft,presence of a mollic epipedon,,
-natri,sodium,presence of a natric horizon,,
-natr,sodium,presence of a natric horizon,,
-pale,old,excessive development,,
-petro,rock,petrocalcic horizon,,
-petr,rock,petrocalcic horizon,,
-plac,flat stone,presence of a thin pan,,
-plagg,sod,presence of a plaggen epipedon,,
-plinth,brick,presence of plinthite,,
-psammo,sand,sandy texture,,
-psamm,sand,sandy texture,,
-quartzi,quartz,high quartz content,,
-rhodo,rose,dark red colors,,
-rhod,rose,dark red colors,,
-sali,salt,presence of a salic horizon,,
-sal,salt,presence of a salic horizon,,
-sapr,rotten,most decomposed stage,,
-sombri,dark,presence of a sombric horizon,,
-sphagno,bog,presence of sphagnum moss,,
-sulfo,sulfur,presence of sulfides or their oxidation products,,
-sulfi,sulfur,presence of sulfides or their oxidation products,,
-sulf,sulfur,presence of sulfides or their oxidation products,,
-torri,hot and dry,torric/aridic SMR,,
-udi,humid,udic SMR,,
-ud,humid,udic SMR,,
-umbri,shade,presence of an umbric epipedon,,
-umbr,shade,presence of an umbric epipedon,,
-usti,burnt,ustic SMR,,
-ust,burnt,ustic SMR,,
-verm,worm,"wormy, or mixed by animals",,
-vitri,glass,presence of glass,,
-vitr,glass,presence of glass,,
-xero,dry,xeric SMR,,
-xer,dry,xeric SMR,,
+element,derivation,connotation,simplified,link
+acr,at the end,extreme weathering,,
+al,aluminum,"high Al, low Fe",,
+alb,white,presence of an albic horizon,,
+anhy,dry,very dry,,
+anthra,human,presence of an anthropic epipedon,,
+aqu,water,wetness,,
+argi,white clay,presence of an argillic horizon,,
+calci,lime,presence of a calcic horizon,,
+cry,cold,cryic STR,,
+dur,hard,presence of a duripan,,
+dystr,infertile,low base saturation,,
+endo,within,ground water table,,
+epi,above,perched water table,,
+eutr,fertile,high base saturation,,
+ferr,iron,presence of Fe,,
+fibr,fiber,least decomposed stage,,
+fluv,river,flood plain,,
+fol,leaf,mass of leaves,,
+fragi,brittle,presence of a fragipan,,
+fragloss,brittle + tongue,presence of a fragipan and glossic horizon,,
+frasi,fresh,not salty,,
+fulv,brownish yellow,dark brown with organic carbon,,
+glac,icy,presence of ice lenses,,
+gloss,tongue,presence of a glossic horizon,,
+gypsi,gypsum,presence of a gypsic horizon,,
+hal,salt,salty,,
+hap,simple,minimum horizon development,,
+hemi,half,intermediate decomposition,,
+hist,tissue,organic soil material,,
+hum,earth,presence of organic carbon,,
+hydr,water,presence of water,,
+kandi,modified from kandite,presence of a kandic horizon,,
+kanhap,kandite + simple,thin kandic horizon,,
+luvi,to wash,illuvial organic material,,
+melan,black,presence of a melanic epipedon,,
+moll,soft,presence of a mollic epipedon,,
+natr,sodium,presence of a natric horizon,,
+pale,old,excessive development,,
+petr,rock,petrocalcic horizon,,
+plac,flat stone,presence of a thin pan,,
+plagg,sod,presence of a plaggen epipedon,,
+plinth,brick,presence of plinthite,,
+psamm,sand,sandy texture,,
+quartzi,quartz,high quartz content,,
+rhod,rose,dark red colors,,
+sal,salt,presence of a salic horizon,,
+sapr,rotten,most decomposed stage,,
+sombri,dark,presence of a sombric horizon,,
+sphagno,bog,presence of sphagnum moss,,
+sulf,sulfur,presence of sulfides or their oxidation products,,
+torri,hot and dry,torric/aridic SMR,,
+ud,humid,udic SMR,,
+umbr,shade,presence of an umbric epipedon,,
+ust,burnt,ustic SMR,,
+verm,worm,"wormy, or mixed by animals",,
+vitr,glass,presence of glass,,
+xer,dry,xeric SMR,,

misc/formative-elements/extract-and-prepare-dictionaries.R

@@ -1,34 +1,34 @@
-
-library(jsonlite)
-
-# order
-soilorder <- read.csv('dictionaries/order.csv', stringsAsFactors=FALSE)
-str(soilorder)
-
-# suborder
-suborder <- read.csv('dictionaries/suborder.csv', stringsAsFactors=FALSE)
-str(suborder)
-
-# greatgroup
-greatgroup <- read.csv('dictionaries/greatgroup.csv', stringsAsFactors=FALSE)
-str(greatgroup)
-
-# subgroup
-subgroup <- read.csv('dictionaries/subgroup.csv', stringsAsFactors=FALSE)
-str(subgroup)
-
-
-# pack into a list
-ST.formative_elements <- list(
-  soilorder=soilorder,
-  suborder=suborder,
-  greatgroup=greatgroup,
-  subgroup=subgroup
-)
-
-# try saving as JSON
-ST.json <- toJSON(ST.formative_elements, auto_unbox = TRUE, pretty = TRUE, na='string')
-cat(ST.json, file = 'formative-elements.json')
-
-# save in compressed format for packaging
-save(ST.formative_elements, file='formative-elements.rda')
+
+library(jsonlite)
+
+# order
+soilorder <- read.csv('misc/formative-elements/dictionaries/order.csv', stringsAsFactors=FALSE)
+str(soilorder)
+
+# suborder
+suborder <- read.csv('misc/formative-elements/dictionaries/suborder.csv', stringsAsFactors=FALSE)
+str(suborder)
+
+# greatgroup
+greatgroup <- read.csv('misc/formative-elements/dictionaries/greatgroup.csv', stringsAsFactors=FALSE)
+str(greatgroup)
+
+# subgroup
+subgroup <- read.csv('misc/formative-elements/dictionaries/subgroup.csv', stringsAsFactors=FALSE)
+str(subgroup)
+
+
+# pack into a list
+ST.formative_elements <- list(
+  soilorder=soilorder,
+  suborder=suborder,
+  greatgroup=greatgroup,
+  subgroup=subgroup
+)
+
+# try saving as JSON
+ST.json <- toJSON(ST.formative_elements, auto_unbox = TRUE, pretty = TRUE, na='string')
+cat(ST.json, file = 'misc/formative-elements/formative-elements.json')
+
+# save in compressed format for packaging
+save(ST.formative_elements, file='misc/formative-elements/formative-elements.rda')

tests/testthat/test-formative-element-parsing.R

@@ -101,7 +101,7 @@ test_that("greatgroup formative elements", {
 
   # full subgroup
   x <- GreatGroupFormativeElements('typic haploxerolls')
-  expect_equal(x$defs$element, 'haplo')
+  expect_equal(x$defs$element, 'hap')
   expect_equal(x$char.index, 7L)
 
   # more complex example
@@ -110,7 +110,7 @@ test_that("greatgroup formative elements", {
   expect_equal(x$char.index, 15)
 
   x <- GreatGroupFormativeElements('alfic humic vitrixerands')
-  expect_equal(x$defs$element, 'vitri')
+  expect_equal(x$defs$element, 'vitr')
   expect_equal(x$char.index, 13)
 
   x <- GreatGroupFormativeElements('acrustoxic kanhaplustults')