extractSMR: add support for SMR described only at subgroup level

Author: brownag

R/extractSMR.R

@@ -37,7 +37,7 @@ extractSMR <- function(taxon, as.is = FALSE, droplevels = FALSE, ordered = TRUE)
   co <- .get_SMR_element_connotation()
 
   # only consider SMR formative elements at or below taxon level
-  el$defs <- el$defs[el$defs$element %in% co$element & th <= el$defs$level,]
+  el$defs <- el$defs[el$defs$element %in% co$element & th <= el$defs$level, ]
 
   # THEN get highest level taxon SMR connotation
   co <- co[co$element %in% el$defs$element &
@@ -51,11 +51,18 @@ extractSMR <- function(taxon, as.is = FALSE, droplevels = FALSE, ordered = TRUE)
 }
 
 .get_SMR_element_connotation <- function() {
-  # x <- get_ST_formative_elements()
-  # x[grepl("SMR|wetness", x$connotation) & x$level != "subgroup",][c("element","level")]
   ## NB: currently there is no formative element connotation for "peraquic" soils
-  data.frame(element = c("per", "ids", "aqu", "torr", "ud", "ust", "xer", "torri", "ud", "ust", "xer", "aqu"),
-             level = c("suborder", "order", "suborder", "suborder", "suborder", "suborder", "suborder", "greatgroup", "greatgroup", "greatgroup", "greatgroup", "greatgroup"),
-             connotation = c("perudic", "aridic (torric)", "aquic", "aridic (torric)", "udic", "ustic", "xeric", "aridic (torric)", "udic", "ustic", "xeric", "aquic"),
+  data.frame(element = c("per", "ids", "aqu", "torr", "ud",
+                         "ust", "xer", "torri", "ud", "ust",
+                         "xer", "aqu", "udic", "ustic", "xeric",
+                         "aquic"),
+             level = c("suborder", "order", "suborder", "suborder", "suborder",
+                       "suborder", "suborder", "greatgroup", "greatgroup", "greatgroup",
+                       "greatgroup", "greatgroup", "subgroup", "subgroup", "subgroup",
+                       "subgroup"),
+             connotation = c("perudic", "aridic (torric)", "aquic", "aridic (torric)", "udic",
+                             "ustic", "xeric", "aridic (torric)", "udic", "ustic",
+                             "xeric", "aquic", "udic", "ustic", "xeric",
+                             "aquic"),
              stringsAsFactors = FALSE)
 }